The need for next-generation, broadly protective coronavirus vaccines is underscored by the accelerated pace at which human coronaviruses have been emerging, the evolution of the current pandemic and the long-term threat of a continual rise of novel coronavirus variants, strains and species. In an effort to take a forward-looking approach toward coronavirus vaccine development, we designed and developed an adjuvanted SARS-CoV-2 Spike ferritin nanoparticle (SpFN) vaccine that confers a wide breadth of protective immunity against multiple sarbecovirus lineages. We found that SpFN elicits potent, broadly neutralizing antibody responses against wild-type SARS-CoV-2, variants of concern as well as SARS-CoV-1 that exceed levels elicited by other major vaccines. The robust immunity elicited by this vaccine translates into rapid protection against virus challenge across multiple animal models. With its current evaluation in a first-in-human clinical trial nearing completion and plans for further development, SpFN’s may extend beyond sarbecoviruses to serve as a promising platform as a broadly protective coronavirus vaccine.

Learning Objectives:

1. Describe the basic design and nanoparticle approach of a vaccine that confers broadly protective immunity against sarbecoviruses.

2. Summarize the development pathway of an adjuvanted SARS-CoV-2 Spike ferritin nanoparticle vaccine through preclinical assessements and translation to clinical evaluation.

3. Introduce the key considerations for the clinical development for a broadly protective sarbecovirus and betacoronavirus vaccine in the context of a immunologically primed population. 
 

The Sarbecoviruses encodes a large panel of highly heterogeneous, but related zoonotic, epidemic and pandemic coronaviruses that include SARS-CoV and SARS-CoV2, which have been associated with significant human disease in 2003 and 2020-21, respectively. These viruses exist in zoonotic reservoirs and many are poised to move easily between species. SARS-CoV2 has caused over hundreds of millions of cases and over 6 million deaths, globally. The presentation will discuss SARS-CoV2 host range, cross species transmission strategies, viral genetics, replication, evolution, pathogenic mechanisms and immunity, framed in the context of the development of novel countermeasures to control COVID19 disease severity in human populations.

The IHME COVID-19 Projection Model has been two years in the making, and this talk will share details on how it works and what it says about our current point in the COVID pandemic as well as what we might expect in the future.  We will review how the model brings together all available data, including case counts, hospitalizations, and COVID-19 deaths, and this can help us understand the impact of the waning of vaccine effectiveness at preventing infection and severe disease over time, the true excess mortality due to COVID over the last two years, and how the omicron variant has changed the course of the pandemic.  As we look to the future, a comprehensive model of where we are and how we have arrived here can also help us prepare for what is to come if and when a new variant emerges.

With over 500 million COVID-19 cases and more than 6 million deaths, the COVID-19 pandemic remains a global health threat maintained by the impact of a changing virus. Emerging SARS-CoV-2 variants have changed the endgame of the COVID-19 pandemic. As new variants and/or subvariants emerge by virtue of mutations in the virus, there is a risk of new surges of infection. To date, the three globally dominant SARS-CoV-2 variants have been D614G, Delta and Omicron. Omicron subvariants BA.1 and BA.2 were the causes of majority of COVID-19 infections over the last few months around the world but are currently being overtaken by BA.4 and BA.5 in South Africa. The impact of new variants varies in individuals in relation to age, vaccination status and time since last vaccine dose; nevertheless, COVID-19 vaccines still offer individual and community benefits. The various vaccines have had varying effectiveness in preventing asymptomatic and clinical infection but have proven to be highly effective in preventing severe disease, hospitalization and death over time for all past variants. Vaccines also lower secondary attack rates, ie. they reduce SARS-CoV-2 transmission to contacts such as household and workplace contacts. Secondary attack rates are lower because vaccinated individuals who get infected are less infectious due to a lower viral load and a shorter duration of infectiousness. Waves of infection can continue to be expected if past trends continue. In South Africa, a new surge of infections driven by BA.4 and BA.5 may lead to a fifth wave of COVID-19 infections.

Learning Objectives:

1. Describe the global epidemiology of SARS-CoV-2 infection.

2. Describe the impact of SARS-CoV-2 variants on the trends of the ongoing pandemic.

3. Discuss the individual and community benefits of Covid-19 vaccines.

The coronavirus SARS-CoV-2 has led to a worldwide pandemic. Beside respiratory symptoms, infected people may develop neurologic dysfunctions such as loss of smell and taste, also seizures, and stroke. Even after recovery, patients frequently suffer from neurologic manifestations including dizziness, headache, impaired consciousness, cerebrovascular disease, ataxia, seizure, vision impairment, and nerve pain. The molecular events leading to the sometimes severe neurologic complications seen in COVID-19 patients are currently not well understood. However, involvement of the immune system and/or the vasculature have been proposed. We and others could show that SARS-CoV-2 may enter the brain and the central nervous system (CNS); however, several entry routes into the CNS have been discussed. Using an advanced Blood Brain Barrier (BBB) model based on human induced pluripotent stem cell (hiPSC)-derived brain capillary endothelial-like cells (BCECs), we showed that endothelial cells of the BBB can be infected by SARS-CoV-2. Moreover, we determined a significant upregulation of interferon-gamma signaling in infected BCECs. The latter was also detected in the neurovascular unit (NVU) in post mortem COVID-19 brain by spatial transcriptomics using the NanoString GeoMx Digital Spatial Profiler, which was confirmed on a protein level in tissue, in particular for Interferon Induced Transmembrane Proteins 1 and 2 (IFITM1/IFITM2), hinting at a molecular response to SARS-CoV-2 infection. Together, our data provide strong probability for SARS-CoV-2 brain entry across the BBB resulting in an increase in interferon signaling. Elucidating such mechanisms may finally lead to development of therapeutic approaches to ameliorate disease severity and improve survival of those affected with COVID-19.

Learning Objectives:

1. Explain which cells of the blood brain barrier are infected by SARS-CoV-2.

2. Discuss the significance of interferon-gamma signaling in human induced pluripotent stem cell (hiPSC)-derived brain capillary endothelial-like cells (BCECs) infected with SARS-CoV-2.

3. Describe how spatial transcriptomics can be used to study gene expression in FFPE tissue sections.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). Little is known about the host tissue and cellular responses associated with infection, symptoms and disease severity. As the consequences of the illness unfolds, it is clear that survival is accompanied by complex and damaging respiratory sequelae due to hyperactivated inflammatory immune cells linked to destructive lung damage, even in mild cases. A better definition of the pulmonary host response to SARS-CoV-2 infection is required to understand viral pathogenesis and to validate putative COVID-19 biomarkers that have been proposed in clinical studies. Here, we’ve used innovative, cutting-edge spatial transcriptomics approaches to delineate tissue signatures unique to COVID-19 and common across acute respiratory distress syndrome.

Learning Objectives:

1. Describe the differences seen in gene expression between COVID-19 and ARDS lung tissue.

2. Explain how hyperactivated inflammatory immune cells can lead to lung damage in COVID-19.

3. Discuss how spatial transcriptomics can be used to study gene expression in FFPE tissue sections from COVID-19 autopsies.

This presentation will focus on the near- and medium-term future of COVID. COVID will become endemic, but what does this really mean?  How will COVID affect longevity in the United States?  What is the future of COVID vaccinations and boosters?  Will COVID become "like the flu", and in what ways?

Learning Objectives:

1. Discuss some major similarities and differences between covid and the 1918 flu pandemic.

2. Explain what is infectious disease endemicity and how it applies to covid.

3. Discuss how 500,000 covid deaths in the USA translate into declines in life expectancy.

Diagnostics have never been more important or visible on the world stage as they are today in the midst of the COVID-19 global pandemic. Mara will speak about how COVID diagnostics have been developed, and how they are and should be used to fight the virus through timely diagnosis and monitoring – as well as introduce you to the largest database of COVID tests worldwide, TestingCommons.com, which she created with the team at Arizona State University and The Rockefeller Foundation.

Learning Objectives:

1.  Discuss the role of diagnostics in controlling the COVID-19 pandemic.

2.  Discuss the different types of COVID tests and how testing has changed during the pandemics.

3. Discuss the role of COVID mutations on testing.

4. Explain how COVID compares to the Flu and other epidemics and pandemics.

During the first year of the SARS-CoV-2 pandemic, international monitoring of SARS-CoV-2 genomic RNA revealed that the virus accumulated roughly 2 mutations per month. Nonetheless, one nonsynonymous mutation in the viral S gene, D614G, was first detected at the end of January 2020, and already by June this mutation had gone to fixation. We showed that D614G increased virion infectivity, and that this was associated with increased stability of S1 on virions and with a change in Spike trimer conformation such that the receptor binding domain was dramatically more open and available for interaction with the ACE2 receptor (Cell 183:739). Towards the end of 2020, with the first waves of infection by Variants of Concern, a sudden and unexplained jump in the frequency of mutations was observed. Here we will discuss several hypotheses about the origin of these highly mutated variants and present data that support each of them. 

Learning Objectives:

1. Discuss how coronaviruses have the largest genomes of any RNA viruses and this is made possible by the fact that they encode a proof-reading enzyme.

2. Discuss the large numbers of mutations that suddenly appeared in Variants of Concern that were likely generated in people with persistent infection.

3. Explain how the SARS-CoV-2 nonsynonymous Spike mutation D614G is required to maintain the functional integrity of the highly mutated Spike proteins found in the Variants of Concern.

Neurological manifestations, including headache, altered mental status, and stroke, are a major complication of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and coronavirus disease-19 (COVID-19). In addition, continued neurological difficulties, such as impaired memory and attention or difficulty finding or understanding words, are often reported by individuals suffering from post-acute sequalae of COVID-19 (PASC) or “long COVID”. Understanding how SARS-CoV-2 effects the brain of infected patients is critical for appropriate treatment of infected patients, as well as initiating relevant follow-up care after recovery. Through our investigation of brain from SARS-CoV-2 infected non-human primates (NHPs), we found significant neuropathology that is consistent with that reported among human patients. Similar to humans, pathology was variable but included wide-spread neuroinflammation, nodular lesions, neuronal death, and microhemorrhages. Importantly, this was seen among infected animals that did not develop severe respiratory disease. Sparse virus was detected in brain endothelial cells but did not associate with the severity of CNS injury. These findings reveal SARS-CoV-2-associated neuropathology that has advanced our current understanding of how SARS-CoV-2 infection effects the brain. Furthermore, this work demonstrates SARS-CoV-2 infected NHPs are a highly relevant animal model for investigating COVID-19 neuropathogenesis among human subjects.

Learning Objectives:

1. Describe the variable neurological manifestations of SARS-CoV-2 infection.

2. Describe the neuropathology in brain of relevant non-human primate models of SARS-CoV-2 infection.

3. List important risk factors predisposing patients to neurological injury in the context of SARS-CoV-2 infection.

During COVID-19, he has been one of the leaders of institutional and community education around the disease. He has been part of numerous University initiatives including outreach to the Asian American community, and the Association of Black Cardiologists national webinars on the impact of COVID-19 on minority populations. He helped create and disseminate a petition validating protest as a response to structural racism in COVID times. For the impact of tear gas, he has worked on a declaration with the public defenders in the city of Portland advocating for limiting its use on the public. He worked on the declaration in the Von Staich case which was upheld by the California Court of Appeals who agreed that the indifference at CDCR met the standard of ‘cruel and unusual punishment’ prohibited by the Eighth Amendment of the Constitution. He has also worked with attorneys from Disability Rights California highlighting the unsafe practices at Patton State Hospital for the mentally ill, resulting in the immediate and rapid vaccinations against COVID in that facility.

Learning Objectives:

1. Compare and contrast the response of the COVID-19 pandemic in the United States vs other developed countries.

2. Describe the multifaceted impact of the COVID-19 pandemic on diverse populations.

3. Apply 3 or more lessons learned to how we can respond to future pandemics.

We’ll discuss the rapid discovery efforts to identify human monoclonal antibody drugs that protect against COVID-19. We will review the technologies used to find antibodies, the optimal profile of protective antibody molecules, and the approach to testing in vivo. We will review the laboratory approach to identifying effective and synergistic combinations of antibodies that exhibit high potency and resist escape by variants of concern.

Learning Objectives: 

1.     Define the antigenic landscape on the SARS-CoV-2 spike protein.

2.     Explain current rational approaches to combination mAb therapy.

3.     Review the antibody correlates of protection for SARS-CoV-2.

We use COVID-19 cases, hospitalizations, and mortality data and a deterministic SEIR (susceptible, exposed, infectious and recovered) compartmental framework to model possible trajectories of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and the effects of non-pharmaceutical interventions in the United States at the state level. Our SEIR model uses several critical variables to produce these projections such as pneumonia seasonality, mobility, testing rates, population, density, mask use per capita, and vaccination levels and vaccines effectiveness. In making these forecasts, we aim to help policymakers plan for the days and months ahead, and take action to change the course of the pandemic for the better. We have developed three different scenarios that can help policymakers understand how different policy decisions, along with the availability of vaccines, could affect the trajectory of the pandemic in their location. With the surge of new variants, we have adopted our models to estimate the speed of their spread and their impact on vaccine effectiveness. Our results show that given the  available evidence on waning immunity and lower efficacy of vaccines preventing infection as compared to hospitalization and death, strategies to reduce  COVID-19  transmission  to  zero  are  unlikely to succeed. Ongoing COVID-19 transmission and burden on the health system are likely to extend past the forecast period and well into 2022 and beyond.

Learning objectives

1.    Recognize the drivers of Covid19 trends.

2.    List the short and long term scenarios given vaccine effectiveness and waning immunity.

3.    Discuss factors that would impact the trajectory.

Join me, an applied epidemiologist with boots on the ground, as we review key discoveries learned from the reopening of sports, entertainment and the arts. The four pillars of reopening include vaccination, ventilation, testing, and masking. Which safety policies are most closely related to staying open? 

Private businesses, including retail stores and corporate offices, have now adopted and adapted these strategies pioneered by sports leagues. Yet, the struggle continues as budget-impact and access to testing has limited businesses efforts to operate safe, in-person workplaces. How much are we willing to pay for faster test results? When will the Ct value from quantitative PCR results be endorsed for guiding the response to a positive case? Applied epidemiologists in the field have increased use of genomic sequencing for positive cases as part of workplace outbreak investigations - estimating the likelihood of transmission in the workplace. 

Hotly debated controversies remain. Can VIP cases end a 10-day isolation early with multiple PCR negative tests and return to work? How long might a case continue testing positive and when is it considered re-infection? We will connect the latest science with practical policy recommendations to protect health and accelerate economic recovery.  

Learning Objectives:

1.    Assess the cost of cancelling vs cost of prevention tradeoff for an upcoming public event.

2.    Define key safety pillars needed for successful in-person, recurring, large-group gatherings.

3.    Name the hottest controversial workplace policies under debate now.

By examining the host response to SARS-CoV-2 infection we gain valuable insights into viral pathogenesis and COVID-19 progression. MicroRNAs (miRNAs), a class of small (18-22nt), non-coding RNAs, often play central roles in the host-pathogen interface and have been recognised as promising biomarkers of infectious disease. In this study, we profiled the circulating miRNAs from 10 longitudinally sampled COVID-19 patients and their age and gender matched controls. We found 55 differentially expressed miRNAs in early-stage disease, including miRNAs with known pro- and anti-inflammatory roles. Machine learning also identified a three-miRNA signature of COVID-19 that predicted infection with 99.9% accuracy. This signature faded away as the patients recovered. When this three-miRNA signature was applied to ferrets (a common model of respiratory infections, including COVID-19), the signature predicted SARS-CoV-2 infection with 99.8% accuracy and could distinguish between SARS-CoV-2, influenza (H1N1), and uninfected controls with >95% accuracy.

This study demonstrates that SARS-CoV-2 infection results in a significant host miRNA response that aligns with our current knowledge of COVID-19 induced inflammation. By using a multivariate, machine learning approach, we have developed a robust miRNA biomarker signature of COVID-19. This signature could complement existing diagnostic tests by providing a new approach to detecting cases that might otherwise be missed. 

Severe SARS-CoV-2 infection often leads to development of acute respiratory distress syndrome (ARDS), with profound pulmonary patho-histological changes post-mortem. In this study, we utilized the spatial transcriptomic approach to focus on ARDS regions in SARS-CoV-2 subjects compared to other forms of virus-induced ARDS (H1N1), providing insights into regional or cell-specific differential gene regulation. We analyzed specific ARDS regions and cells of interest utilizing autopsy-derived lung tissue from patients with SARS-CoV-2 (n=3), H1N1 (n=3), and a dual infected individual (n=1). Enhanced gene signatures in alveolar epithelium, vascular tissue, and lung macrophages identified not only increased regional coagulopathy, but also increased extracellular remodeling, alternative macrophage activation, and squamous metaplasia of type II pneumocytes in SARS- CoV-2. Both the H1N1 and dual infected transcriptome demonstrated an enhanced antiviral response compared to SARS-CoV-2. Overall, these results challenge conventional wisdom and provide evidence for a more fibroproliferative ARDS phenotype in SARS-CoV-2 infection versus a more exudative inflammatory ARDS phenotype in H1N1 infection. This finding may explain the observation of COVID ARDS patients often displaying extended time requiring ventilator support. It is our hope that these pathways will improve our understanding of mechanisms leading to progressive worsening of gas exchange and increased mortality in SARS-CoV-2 related ARDS.  As a result, the potential for new therapeutic targets to alter the fibroproliferative response will present the potential to improve clinical outcomes in patients with progressive lung injury.

Learning Objectives:

1. Describe how spatial transcriptomics can be used to profile COVID-19 tissue autopsies.

2. Explain the differences seen in gene expression between SARS-CoV-2 infected lung samples and H1N1 infected lung samples.

3. Summarize the pathways involved in the fibroproliferative ARDS (Acute Respiratory Distress Syndrome) phenotype seen in SARS-CoV-2 infection.

Dr. John Moore, Professor of Microbiology and Immunology at Weill Cornell Medicine, a Vaccine and Virology researcher, will talk about SARS-CoV-2 vaccines and variants and other topical issues.

This presentation “SARS-CoV-2 Related Workflow and Solutions: Detection and Genotyping” will focus on strategies for the testing and detection of SARS-CoV-2, including multiplexed qPCR assays. We will also discuss genotyping and sequencing methods for surveillance, strain identification, and detection of key mutations that result in new and more infectious strains. Viral mutations can result in variants that are not detected, escape immune responses mounted by vaccines, and also generate drug resistance. RNA viruses have a higher degree of variance and are prone to mutate in response to vaccines and antiviral drugs. Constant surveillance and detection of mutations and variant strains are important to contain pandemics and to deploy new vaccines and antiviral drugs.

Learning Objectives:

1. Discuss genetic analysis platforms and technologies that can support SARS-CoV-2 research.

2. Describe how SARS-CoV-2 mutates and how variants emerge.

3. Break down how genotyping assays can complement sequencing strategies for SARS-CoV-2 surveillance.

Since late 2020, several prominent SARS-CoV-2 variants of concern have emerged, harboring specific mutations which increase viral transmissibility Delta variant) and which appear to reduce the efficacy of some current vaccines.  As a result, there is an elevated need for rapid scale-up of genomic surveillance to characterize circulating strains and detect newly emerging, potentially more harmful variants as early as possible.

Next-generation sequencing (NGS) is the most efficient and cost-effective technology for this purpose. NGS enables multiple samples to be processed in parallel and the entire viral genome to be sequenced at depth.  Nevertheless, current NGS solutions require complex, multi-step workflows, are challenging to automate and allow limited sample multiplexing. 

In this webinar, we will describe an accelerated workflow for SARS-CoV-2 sequencing that:

• Cuts viral amplification and library prep in half (to 4 hours) compared with current ARTIC-based approaches

• Enables twice the throughput per flow cell lane (multiplexing of up to 768 samples)

• Generates high-yield libraries with superior sequence uniformity and depth of coverage due to the tiling amplicon design of the solution

• Significantly reduces plasticware use 

SARS-CoV-2 testing is now facing increasing challenges in the face of an ongoing pandemic with the emergence of new variants and waning vaccine immunity. Increasing evidence supports the correlation between neutralizing antibody titers and protection from this dangerous virus. Recent studies show that less than 40% of immunocompromised and less than 70% of elderly (over 80 years of age) people who are fully vaccinated elicit these protective antibodies. Furthermore, Israel’s early vaccination program exclusively using the Pfizer vaccine has shown waning population immunity after about six months post-vaccination leading to a dramatic uptick in infections particularly from the Delta variant. Thus triggering a third booster shot for people over the age of 50 in that country. This talk explores the key questions associated with the healthcare implications of SARS-CoV-2 and how a new approach to testing may help in determining individual, neutralizing antibody response to vaccination.

Learning Objectives:

1. Explain the principles of a new cPass surrogate virus neutralization test (cPass sVNT) and how it compares to the gold standard live cell virus neutralization tests such as the plaque- and foci-reducing neutralization tests.

2. Contrast the more traditional and commonly employed SARS-CoV-2 IgG binding assays with the functional cPass sVNT. 

3. Discuss the variation in efficacy of current SARS-CoV-2 vaccines and uncertainties in vaccinated populations concerning protection.

In this session we will use a set of reads enriched for viral sequences and sequences from wastewater treatment plants. Specifically the aim is to assemble whole SARS-CoV-2 genomes from such samples and to perform whole genome alignments of such assemblies against reference sequence with automatic transfer of annotations. Further, statistical analysis of metagenomic data will be covered to compare groups of samples. All analysis will be carried out using QIAGEN CLC Genomics Workbench Premium.

Learning Objectives:

1. Discuss targeted viral profiling from a metagenomics sample extracted from wastewater.

2. Discuss reference based assembly from metagenomic reads and whole genome alignments.

3. Discuss statistical analysis of metagenomic profiles.

As the pandemic continues to evolve, new tools are needed to fight it. The greatest needs revolve around the ability to screen asymptomatic individuals for COVID-19 and to simultaneously test for COVID-19, Influenza, and RSV. 
Like diagnostic testing, screening for SARS-CoV-2 identifies infected individuals – however, screening tests are used when there is no reason to suspect infection. This includes screening of asymptomatic individuals without known exposure to the virus, but where there is a need to make decisions based on the results. Examples include screening in schools, places of business and high-risk environments, including aged care facilities, airports, and tradeshows.
According to experts, a highly sensitive RT-PCR test should be used for screening asymptomatic individuals without known exposure to SARS-CoV-2. This is critical to ensure the accuracy of testing as a 10-fold increase in LOD can increase false negative rate by 13%. Additionally, the ability to pool samples from asymptomatic individuals enables cost-effective testing. For accurate detection in pooled samples, a very sensitive RT-PCR assay is needed. 
As SARS-CoV-2 disease restrictions are being lifted, other respiratory diseases which were depressed due to social distancing are expected to return. Laboratories that routinely test for COVID-19 have been advised to consider a multiplex assay that can simultaneously detect multiple respiratory disease-causing pathogens. PerkinElmer’s PKamp™ Respiratory SARS-CoV-2 RT-PCR Panel enables detection and differentiation between SARS-CoV-2, influenza A, influenza B, and respiratory syncytial viruses using a single test, thereby helping labs manage potential surge in testing demand during the flu season.

Learning Objectives:

1. Discuss the difference between diagnostic testing and screening.

2. Discuss the limit of detection important in screening.

3. Explain how can syndromic respiratory disease panels help in the coming months.

I will discuss the development of the “Midnight” panel for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. We show that using a multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit and nanopore sequencing we produce high-quality assembled genomes with as few as 10 000 reads (∼5 Mbp of sequence data) in as little as 9 hours from patient sampling. This method cuts the hands-on time from sample to genome by more than half compared to the more standard ARTIC ligation-based Oxford Nanopore library preparation method at considerably lower costs. It achieves even coverage and is less prone to drop-outs, especially in the context of new COVID-19 variants, like Delta. It is currently in use by over 180 institutions in 35 countries, is one of two primary methods in use by Oxford Nanopore, has been modified for use on PacBio and Illumina platforms, and the original open access protocol has been accessed over 17,000 times. This method is also amenable to modification and use for other viruses. 

Learning Objectives:
1. Identify two reasons why sequencing the genome SARS-CoV2 (the virus that causes COVID-19) is important.
2. Describe the “midnight” method for whole genome sequencing of SARS-CoV-2.
3. Explain two advantages to using the “midnight” method.

SARS-CoV-2 is an emergent virus. Specifically how it will adapt to human hosts and populations with growing immunity is unknown. Coronaviruses acquire substitutions more slowly than other RNA viruses due to a proofreading RNA-dependent RNA polymerase. In the spike glycoprotein, we find that deletions contribute to the evolution of antigenic novelty. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including variants of concern. By altering entire stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution. 

Learning Objectives:
 
1. Define mechanisms for SARS-CoV-2 evolution 

2. Explain the impact of recurring SARS-CoV-2 mutations on protective antibodies 

In this talk, Dr. Adalja will discuss the role of diagnostic testing in infectious diseases. He will specifically address how improved diagnostic testing, in both home and hospital settings, can be thought of as a pandemic resiliency tool.

Learning Objectives:

1. Discuss the value of infectious disease diagnostics.

2. Recognize the importance of home diagnostics.

3. Identify how better diagnostics leads to more resiliency to pandemics.
 

Vaccination and infection are two different paths to immunity. Understanding human immune responses to SARS-CoV-2 RNA vaccines is of interest for a panoply of reasons. mRNA vaccines have demonstrated impressive protection from COVID-19; however, durability of immunity has been a major unknown. 

Given evidence that antibodies, CD4+ T cells, and CD8+ T cells can each participate in protective immunity against COVID-19, we measured acute and memory SARS-CoV-2 Spike-specific antibodies, CD4+ T cells and CD8+ T cells in the blood of subjects who received a low dose (25-µg) or standard dose (100-µg) mRNA-1273 COVID-19 vaccine. Vaccine-generated spike-specific memory CD4+ T cells 6 months post-boost were comparable in quantity and quality to COVID-19 cases, including the presence of T follicular helper cells and IFNγ-expressing cells. Spike-specific CD8+ T cells were generated in 88% of subjects, with equivalent memory at 6 months post-boost compared to COVID-19 cases. Lastly, subjects with pre-existing cross-reactive CD4+ T cell memory had increased CD4+ T cell and antibody responses to the vaccine, demonstrating the biological relevance of SARS-CoV-2–cross-reactive CD4+ T cells. In summary, the 25-µg-dose of mRNA-1273 vaccine induces durable and functional T cell and antibody memory at comparable magnitude to natural infection. This work expands our understanding of immune memory to mRNA vaccine in humans, the biological relevance of crossreactive T cells, and possible timing of boosters. 
 

Learning Objectives:

1. Discuss the durability of mRNA vaccine induced immunity.

2. Break down impact of pre-existing crossreactive memory on immune responses to SARS-CoV-2 proteins. 

The risk of mortality from COVID-19 follows a sharp age gradient, with older populations facing a thousand fold higher risk of death upon infection than children. At the same time, the COVID policy over the past year and a half has featured lockdowns – policies aimed at minimizing human interactions – that have caused enormous collateral damage, to whole populations without protecting older populations from infection. In this talk, I discuss an alternate strategy – the Great Barrington Declaration – for managing the pandemic, which features focused protection of vulnerable people and a end to COVID restrictions since the lockdowns harm the non-vulnerable more than COVID. I present evidence that countries which have used the incredibly effective COVID vaccines in service of focused protection of the elderly, have decoupled COVID cases from COVID deaths. I present evidence that lockdown policies have caused enormous harm to other important public health priorities, including childhood vaccination, cancer prevention, diabetes management and prevention of food insecurity. Finally, I present evidence that the lockdowns have failed in particular to protect minority and poor population in the US. 

Learning Objectives:

1. Break down how COVID-19 mortality increases sharply with age; there is a thousand fold difference in the mortality rate after infection between the youngest and oldest.

2. Explain how the lockdowns and COVID restrictions have had severe adverse effects on non-COVID public health priorities, including cancer screening and treatment in developed countries, and the prevention of hunger and poverty in poor countries.

3. Explain how the lockdowns have had an enormously unequal impact, protecting richer population from COVID mortality, while exposing poorer populations at high rates to COVID

COVID 19 is caused by a new coronavirus , SARS-CoV-2, which is highly infectious and can cause a wide spectrum of symptoms and affect multiple human systems. What we have learned from other viral infectious diseases is that typically the protection from reinfection is conferred by the development of neutralizing antibodies. These are antibodies that can bind to the virus in a way that they prevent the entry of the virus into the cell. Here we present a novel, high throughput neutralizing antibody test, the cPass™ SARS-Cov-2 Neutralization antibody test that can rapidly and efficiently detect neutralizing antibodies. The gold standard (virus neutralization assay) test for measuring neutralizing antibodies requires the use of live virus, cells, highly skilled operators, and complex safety laboratory procedures (biosafety level 3) that are generally less sensitive and require several days to obtain results. In contrast, the cPass™ Neutralization Antibody Detection Kit can be conducted within an hour in most labs, and is also amenable to high throughput and fully automated testing. In this presentation, we will review the performance and applications of this new technology. We will review applications for convalescent patients testing, convalescent plasma treatment testing and vaccine response analysis.

Learning Objectives:

1. Learn about methodologies for COVID-19 screening

2. Learn about the importance of neutralizing antibodies

3. Learn how the cPass SARS-COV-2 Neutralization antibody test is different than other serology tests

The Institute for Health Metrics and Evaluation (IHME) uses a hybrid modeling approach to generate Covid19 forecasts. The model incorporates elements of statistical and disease transmission models and is grounded primarily in real-time data instead of assumptions about how the disease will spread. The model accounts for several variables including mobility, mask wearing, testing, and the spread of the new variants. New variants have the potential to increase transmission, escape immunity from previous infections, and reduce the effectiveness of the vaccines. Our long-term projections show that there is a potential of a rise in cases and deaths due to the new variants. The future of the pandemic depends on the behavioral response in terms of vaccine confidence, mask wearing, and avoidance of situations that pose a high-risk for transmission.
 
Learning Objectives:

1. The seminar will help understand the future scenarios for the spread of the virus

2. The seminar will allow attendees to understand how IHME models covid19

3. The seminar will explain the impact of the new variants on the pandemic and how we can best respond to their challenge

Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates. To address this, we analyzed seropositivity in US adults who have not previously been diagnosed with COVID-19. Individuals with characteristics that reflect the US population were selected by quota sampling from volunteers. Enrolled participants provided medical, geographic, demographic, socioeconomic information, and dried blood samples. The majority (88.7%) of samples were collected between May 10th and July 31st, 2020. The highest undiagnosed seropositivity was detected in Black/African American participants, younger, female, Hispanic, and Urban residents, and lower undiagnosed seropositivity in those with chronic diseases. These data indicate that there were 4.8 undiagnosed cases for every diagnosed case of COVID-19, and an estimated 16.8 million undiagnosed cases by mid-July 2020.  Given the high point estimate of undiagnosed seropositivity in younger donors, lower point estimates in individuals with pre-existing conditions such as diabetes, and the vaccine rollout starting with older persons and those at risk, long-term study of naturally acquired immunity, vaccine acquired immunity, and vaccine boosted naturally acquired immunity will be necessary to fully understand the correlates of protection, durability of SARS-CoV-2 immunity, and the impact immunity will have long-term on the spread of SARS-CoV-2 and other future variants or novel coronaviruses. It is also clear from these data that novel coronaviruses can spread rapidly throughout human populations despite public health measures and we must therefore prepare for future novel coronaviruses and begin investigation into broadly protective countermeasures such as vaccines to mitigate this risk.

Learning Objectives:

1. Understand the spread of SARS-CoV-2 in the first 6 months of the pandemic, the limitations of testing, and how this impacts the overall epidemiologic data being used to direct public health measures

2. Understand what we can learn from these data and how we can alter our future pandemic responses to reduce the negative consequences of a pandemic

3. Understand the need for broadly protective vaccines/countermeasures, how we failed in the past, what research needs to be done, how novel vaccines they could be evaluated, and what real expectations are for them

Despite available vaccines and treatments, COVID-19 continues to impose a major burden in the world, as a leading cause of hospitalizations and deaths.  We and others have been working in te identification of novel SARS-CoV-2 inhibitors and vaccines that might have improved efficacy or that can be deployed quickly than those available at this moment.  I will present our preclinical studies on two promising countermeasures against COVID-19, one based on the use of inhibitors of translation as antivirals, the second based on the use of a negative strand RNA virus vector as vaccine.

Learning Objectives:

1. Strategies to repurpose drugs for the treatment of COVID-19

2. Research strategies to conduct preclinical studies on COVID-19 antivirals and vaccines

3. Use of Newcastle disease virus as a vaccine vector

The COVID19 pandemic continues to be a major epidemiological challenge across the globe.  Part of the challenge, often seen with viruses, is that the nucleic acid genome quickly mutates, producing new strain lineages.  These new lineages can spread more quickly, cause either milder or more severe symptoms, have decreased efficacy of therapeutic agents and can evade vaccine-induced immunity.  Importantly, they can also evade detection by nucleic acid sequence-based diagnostic tests, complicating epidemiological monitoring.  In this presentation, we illustrate strategies for monitoring changes in SARS-CoV-2 genome sequence.  These strategies include:  1) orthogonal testing of aberrant PCR results that may arise due to strain differences, 2) positive identification of highly transmissible variants of concern (B.1.1.7 and B.1.351), 3) monitoring newly arising variants in Spike (S) gene sequences, and 4) monitoring new variants that appear anywhere within the SARS-CoV-2 genome.  These surveillance tools facilitate tracking the spread of the virus at the population level, help assess the effectiveness of containment strategies, and contribute to the understanding evolution of this virus.

Learning Objectives:

1. Understand how to choose the right technology for SARS-CoV-2 surveillance

2. Learn to diagnose qPCR test drop-outs

3. Learn how to choose sequencing primers for a specific mutation

This presentation will focus on strategies for the design and validation of robust assays for the detection of SARS-CoV-2, including nucleic acid extraction, multiplexed qPCR assays, and interpretive software solutions. We will also present on strategies and methods for surveillance, strain identification, and detection of key mutations that result in new and more infectious strains. Viral mutations can result in variants that are not detected, escape immune responses mounted by vaccines, and also generate drug resistance. RNA viruses have a higher degree of variance and are prone to mutate in response to vaccines and antiviral drugs. Constant surveillance and detection of mutations and variant strains is important to contain pandemics and to deploy new vaccines and antiviral drugs.

Learning Objectives:

1. Learn how testing and detection is important to lower transmission rates and contain pandemics

2. Understand how mutations emerge

3. Learn about the effect of mutations on detection assays

As of March 2021, SARS-CoV-2 has infected 115 million people and caused over 2.56 million deaths. The emergence of mutants associated with changes to transmission of SARS-CoV-2 has shown that tracking and identification of SARS-CoV-2 variants is critical to establish an effective public health response.  Once a sample is detected as positive for COVID-19 using an RT-PCR assay, labs are encouraged to find whether the sample contains a Variant of Concern (VOC). NGS is ideal for this as its high resolution enables it to identify all mutations, known and unknown, providing insights to SARS-CoV-2 infection and transmission.

The NEXTFLEX® Variant-Seq™ SARS-CoV-2 workflow is optimized to easily identify all mutations in a SARS-CoV-2 sample. It utilizes an amplicon-based target enrichment workflow which offers many advantages over hybridization capture-based protocols, most notably speed, scalability, and cost.

Learning Objectives:

1. Understanding of the methods currently used to identify SARS-CoV-2 variants

2. NEXTFLEX® Variant-Seq™ SARS-CoV-2 workflow 

Dr. Jordan RoseFigura from Swift Biosciences will present on the technology created to enable this research that covers 99.7 % of the SARS-CoV-2 genome from limited viral titers. Including an overview of the elegant SNAP workflow, sophisticated primer design, data anaylsis workflow, as well as, how targeted pathogen sequencing can enable variant detection in S Gene dropouts in COVID-19 Samples. Learn how adding Swift Normalase® can save costs and time in order to scale large studies.

When SARS-CoV-2 reached the United States in late January 2020, Labcorp immediately began development of an RT-PCR test to aid in detection and diagnosis of COVID-19 in infected patients.  As a result of developing this assay, Labcorp has unprecedented access to positive SARS-CoV-2 samples nationwide and has leveraged that access to implement a comprehensive SARS-CoV-2 Sequencing Surveillance program.  This pipeline uses residual extraction material from positive samples and converts those samples into high throughput sequencing libraries using 1,200bp overlapping amplicons.  Sequencing proceeds on the Pacific Biosciences Sequel II using HiFi CCS reads.  Sequencing reads are used to generate a consensus sequence that is used to identify the lineage and clade of each sample that meets the minimum coverage criteria. To date, Labcorp has sequenced over 15,000 samples in real time and has submitted those sequences to public repositories in collaboration with the US Centers for Disease control.  Labcorp’s surveillance program has been able to track the spread of SARS-CoV-2 variants across the US, including the observation of the increased prevalence of B.1.1.7 and detection of the first case of B.1.351.  This work could serve as a model for future public and private collaborations with respect to national infectious disease surveillance.

Learning Objectives:

1. Understand the difference between RT-PCR testing and whole genome sequencing

2. Explain why sequencing based pandemic surveillance is so important to the national response to virus spread.

Developing an in vitro diagnostic device is often a complex and demanding process. Doing so in the midst of a pandemic and the IVD global supply chain stretched like never before, with project teams formed entirely via remote working and under intense time pressure takes this to another level. Clarigene: A pandemic diagnostic development story takes us through how Yourgene Health entered into the infectious disease space, including the major challenges and how they were overcome. Carefully working through market and customer needs enabled key design decisions to made, ultimately leading to a robust product being released onto the market. The implementation of the Clarigene SARS-CoV-2 test in the company’s service lab, including in house automation and development of wrap around sample tracking software, demonstrated the product to be a robust and scalable test that could be applied quickly and effectively into any laboratory setting. In the face of multiple mutations in the viral genome, enhanced post-market surveillance and risk mitigation planning is key to ensuring any SARS-CoV-2 test can be relied upon to perform as expected as new strains arise.

Learning Objectives:

1. Meeting customer needs through effective product design

2. Handling product development under difficult conditions

3. Monitoring viral genomes to ensure test performance is not impacted by random mutations

At UC Davis we have implemented rapid, inexpensive, high throughput testing for SARS-Cov-2 using technology repurposed from the agricultural biotechnology sector.  As part of Healthy Davis Together, this is providing at least weekly testing for the campus and the City of Davis.   The workflow involves testing saliva samples from asymptomatic individuals without RNA extraction.  To date, we have processed over 400,000 tests and identified more than 1,700 positive individuals.  The IntelliQube qPCR machine is not the rate limiting step, which provides the opportunity for high throughput genotyping of all positive samples for variants of SARS-CoV-2.  Evolution of the virus is inevitable and it is critical to monitor for variants of concern that have higher transmissibility and/or reduce the effectiveness of vaccines.  Genotyping using SNPs that discriminate between known variants of concern is more efficient, less expensive, technically less demanding, and importantly much more rapid than sequencing.  It will not, however, discover new variants and is therefore complementary to sequencing.  In collaboration with LGC, we have developed and deployed 14 SNP assays that can distinguish all the current variants of concern and interest in a redundant fashion.  All positive samples are assayed and genotypes assigned within a few days of sample collection.  Non-wildtype genotypes are validated by sequencing.  This provides rapid resulting to the county health authorities.  In summary, robust genotyping technology is available for monitoring large numbers of positive samples on a global scale; this will be particularly important in geographical areas where sequencing is not feasible.  The regulatory framework for this is more challenging than the technical aspects.

Learning Objectives:

1. Why is it important to monitor for variants of SARS-CoV-2?

2. What are the relative advantages of SNP genotyping and sequencing for surveillance?

Over a year into the COVID-19 pandemic, key vulnerable populations in the United States and across the world lack access to effective vaccines. IDRI has developed technology that addresses some of the most important unmet vaccine needs. Our technology is proven to make RNA vaccines stable at room temperature for nearly a year, enables safe and highly-effective protein vaccines that provide durable protection against current and future COVID mutations, and allows for the advancement of vaccines that will be suitable for young children. These discoveries can help support the global effort to end COVID-19 and reduce the burden of the inevitable next pandemic.

Learning Objectives:

1. Understand limitations in current vaccines against SARS-CoV-2 that compromise universal access, durability and broadly protective immune responses

2. Become familiar with the technology behind self-amplifying / self-adjuvanting RNA vaccines delivered by a novel nanostructured lipid carrier, which generate potent immune responses and are stable at room temperature for nearly a year

3. Explore the use of vaccine adjuvant formulations as a method to generate durable and broadly-protective immune responses against coronaviruses.

The global pandemic of Coronavirus disease 2019 (COVID-19), caused by Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has highlighted the importance of surveillance efforts to closely monitor the transmission and evolution of viral pathogens. I will present how the Mount Sinai Health System Pathogen Surveillance Program has applied high-throughput sequencing of SARS-CoV-2 genomes from COVID-19 patients, in combination with molecular epidemiology, to identify the timing and origins of early introductions of SARS-CoV-2 in the New York City metropolitan area and its continued spread. NYC was one of the first affected large cities in the world and an early epicenter of the pandemic. I will further outline how genomic technologies can be applied to precisely delineate outbreaks in quarantine and healthcare settings.

Learning objectives:

1. Understand how we can use next-generation sequencing to track the spread and diversity of SARS-CoV-2

2. Understand how limitations in testing obscured our view of early viral introductions 

3. Identify and evaluate the contribution of asymptomatic carriers in the transmission of SARS-CoV-2

Despite a continuous decline of corona virus cases, the broad rollout of multiple vaccines, and the start of a return to normalcy, concerns of SARS-CoV-2 outbreaks continue to linger on the minds of scientists, health organizations, and policymakers throughout the world. The knowledge that the virus has and will continue to mutate prompts a desire to not only understand if people are sick, but also what specific strain of the virus they are sick with.  Genomics is an essential tool to answer this question.  It provides a comprehensive look into the details of the virus, it’s history, and possibly even insights into the future. This session will demonstrate the importance of understanding genomic variation within the SARS-CoV-2 genome and will explore the potential for leveraging it to more effectively monitor the spread and impact of the virus as it continues to evolve.

Learning Objectives:

1. Understand how genomic variation can impact viral properties.

2. Understand role of genomics in infectious disease surveillance.

Vaccines to prevent COVID-19 were developed within 1 year after the identification of SARS-CoV-2 as the causative virus. There are now 3 vaccines that are FDA approved via Emergency Use Authorization. This talk will highlight how one of those vaccines was developed. It will focus on how rapid development of the vaccines were attained while still testing them rigorously for safety. It will also show how these vaccines work as well as present safety, efficacy, and immune data. It will end with a brief discussion on which vaccines have been developed and shown to be effective in preventing COVID-19 across the world.

Learning Objectives: 

1. Understand how mRNA vaccines work

2. Understand how COVID-19 vaccines were approved so rapidly without impacting their safety

This talk goes over the importance of face masks as a pillar of COVID-19 pandemic control. First, we review the epidemiologic evidence for how face masks reduce COVID-19 transmission from studies in the United States since the beginning of the pandemic.  We then discuss an emerging hypothesis that viral inoculum or dose is related to severity of disease so that face masks may also increase the proportion of asymptomatic infection (if infection occurs) by reducing viral dose. Finally this talk discusses the physical science properties of masks and makes recommendations for basic and maximal protection masks for the public.

Learning Objectives:

1. To review the epidemiologic data on how face masks reduce COVID-19 transmission

2. To explore the hypothesis that reducing the viral inoculum (via face masks) will lead to less severe disease if infected

3. To review the type of face masks most protective for the public

The 2020 SARS-CoV-2 pandemic is now the 5th respiratory virus pandemic since 1918.  No matter the time in history that these pandemics occur and no matter the severity we see public health efforts and scientists stymied in their efforts to truly change the course of these pandemics.  The reasons for this are numerous as there are so many unanswered questions regarding respiratory virus infections that lead to many of the failed, confusing, and sometimes harmful actions taken by governments, health officials, and physicians/scientists.  In order to address the current and future pandemics we must work hard to better understand the correlates of protection of respiratory viruses.  During the early stage of this pandemic we started a trial to look at the prevalence of SARS-CoV2 antibody in a nationwide sampling of individuals who were not diagnosed with COVID19.  The goal of this study was to achieve a highly representative sample that could be used to estimate the true prevalence nationwide and in different groups based on multiple demographic and other factors.  This study performed April to August, gave us the opportunity to take an early sample and then currently follow up at 6 and 12 months to assess change over time, longevity of response, and begin to probe questions regarding correlates of protection.  This study sets the stage for much more work and raises questions that will need to be addressed in future studies. With focused efforts and thoughtful science, we can achieve a much better understanding of respiratory viruses and the correlates of protection.  This will require significant collaboration, communication, and of course funding.  It is important that we try to get this right so that we are better prepared for the next pandemic and do not find ourselves still in the same situation we have been in during every pandemic since 1918.

Learning Objectives:

1. Define SARS-CoV-2 immunity, antibody testing, and discuss what is known about the meaning of these tests

2. Identify challenges in doing research during social distancing and demonstrate methods to overcome those challenges

3. Explain the findings of the NIH serosurvey in terms of prevalence of SARS-CoV-2 immunity by geography and demographic groups

To execute COVID-19 testing strategies effectively, labs need to procure reliable components of the workflow without interruption – from reagents to equipment and consumables at the scale they need, when they need them. PerkinElmer has more than 20 years of experience in optimizing and successfully delivering complete workflows suitable to meet various demands. The company’s comprehensive SARS-CoV-2 offerings span automated RNA extraction, liquid handling, nucleic acid tests and immunoassays. PerkinElmer’s RT-PCR kit for SARS-CoV-2 detection in combination with chemagic™ Viral DNA/RNA 300 Kit H96 and the chemagic™ 360 instrument delivers the most sensitive COVID-19 diagnostic test in the market. Labs now also have the option to accept saliva specimens, asymptomatic samples and implement pooling using the CE-marked PerkinElmer SARS-CoV-2 Real-time RT-PCR Assay. These critical advancements have been made possible by PerkinElmer’s robust chemistry and stringent manufacturing systems. Building off this strong foundation, PerkinElmer’s new CE-marked PKamp™ Respiratory SARS-CoV-2 RT-PCR Panel enables detection and differentiation between SARS-CoV-2, influenza A, influenza B, and respiratory syncytial viruses using a single test, to help labs manage the surge in testing demand during the flu season.

Learning Objectives:

1. Why is the Limit of Detection (LOD) of an RT-PCR assay important for COVID-19 testing?

2. How are technical enhancements improving testing efficiency?

3. What options are available to manage the surge in testing demand during the flu season?

Dynamic models of infectious disease systems are often used to study the epidemiological characteristics of disease outbreaks, the ecological mechanisms and environmental conditions affecting transmission, and the suitability of various mitigation and intervention strategies.  In recent years these same models have been employed to generate probabilistic forecasts of infectious disease incidence at the population scale.  Here I present research from my own group describing application of model systems and combined model-inference frameworks to the study of SARS-CoV-2.

Learning Objectives:

1. Define undocumented v. asymptomatic infection

2. Identify epidemiological characteristics supporting pandemic spread of SARS-CoV-2

3. Explain the structure of model-inference systems depicting infectious disease transmission

Cases and deaths continue to increase steadily in most states. The pace of increase is faster than we expected, leading us to revise upward IHME forecast of deaths and cases into the future. Our forecast assumes that states will re-impose social distancing mandates as the daily death rate exceeds 8 per million. If they do not, the death toll could be much higher. Hospital systems in most states will be under severe stress during December and January even in our best scenario. IHME has substantially revised the infection-fatality rate (IFR) used in the model. We have now accumulated considerable empirical evidence that suggests that 1) the IFR has been declining since March/April due to improvements in the clinical management of patients, and 2) the IFR varies as a function of the level of obesity in a community. Even with the improvement in IFR, the seasonality of COVID-19 with the winter months will results in a rise of cases and deaths. Vaccines will improve the situation in 2021 but will not impact the situation in the coming 2 months. Increasing mask use to 95% can save many lives.

Learning Objectives:

1. What are the drivers of COVID-19 surge in the U.S.?

2. What are the projected numbers of cases and deaths?

3. What are the measures to contain the virus?

When producing a quality vaccine, all manufacturers must confirm the purity as well as the stability of their formulation and final product. Sample quantity and measurement time are often the throughput bottlenecks encountered during the process. As PerkinElmer’s LabChip GXII Touch addresses these specific gaps, we’ve developed a literature-centric webinar.

Learning Objectives:

1. The vaccine development and manufacturing process

2. The key applications of microfluidic CE in vaccine process development

The University of Louisville Infectious Diseases Laboratory (IDL) is a high-complexity, CLIA-certified laboratory in Louisville, KY. The IDL adopted the Luminex ARIES® platform in 2016 for diagnostic testing to increase throughput while minimizing the risk of amplicon contamination. Our familiarity with the ARIES platform allowed us to pursue FDA Emergency Use Authorization for a duplex PCR assay detecting the N1 and N3 targets of the SARS-CoV-2 genome. This presentation outlines our methods, quality control material selection, the populations tested, the challenges we faced, and the future for the laboratory developed SARS-CoV-2 duplex PCR assay.

Learning Objectives:

1. Learn how a lab responded to COVID-19

2. Understand how to run a SARS-CoV-2 test on the ARIES® System

3. Gain knowledge and an understanding of creating a Laboratory Developed Test (LDT) on the ARIES® System

As we have all heard many times on the news, that when a COVID-19 patient gets infected they eventually develop an immune response and generate antibodies to the SARS-CoV-2 virus. However not all antibodies are created equal. Some of these antibodies simply bind to the viral proteins, while others bind in such way that they also have the ability to block the virus from infecting the cells. These antibodies are commonly referred to as neutralizing antibodies. While there are many kits on the market that detect SARS-CoV-2 binding antibodies, here we present performance data for the cPass SARS CoV-2 Neutralization Antibody Test that is FDA EUA authorized and has been shown to be equivalent to live virus tests to detect neutralizing antibodies in clinical studies. We will also share the comparison of the results to other antibody tests and discuss the differences. We will also present data on the quantitative use of the technology that can measure neutralizing antibody levels and it’s potential utility.

Learning Objectives:

1. Brief overview of SARS CoV-2 infection mechanism

2. Description of cPass™ SARS-CoV-2 Neutralization Antibody Test, its advantages and comparative data with live cell neutralization and other serology tests

3. Quantitative protocol for the Neutralization antibody test and its application to samples from recovered SARS CoV-2 patients

This drug development program is designed to create a family of broad-spectrum, pan-coronaviral drugs that respectively inhibit multiple key enzymes required for viral replication. By targeting multiple gene products simultaneously we hope to eliminate/minimize the development of treatment-resistant viral strains as was successfully done when HAART (highly active anti-retroviral therapy) was introduced for HIV-1 disease.  We employ a pipeline-based drug development process that includes multiple feedback loops between and among both in silico and laboratory-based processes for the generation of highly effective and mutation-resistant pharmaceuticals.   As part of our process to minimize the risk of the evolution of escape mutants, we begin our drug design using a suite of artificial intelligence-based machine-learning algorithms that are proven to: 1) predict future evolution (mutations) of the target viral enzymes in silico –  these sequences are added to the extant set of all protein structure files from the -coronaviruses that correspond to each of our target enzymes;  2) perform protein structure overlays of all available structures for each target enzyme to determine the most highly conserved active site morphologies; 3) prepare a 3-D grid of the conserved (consensus) active site for each target enzyme;  4) using a 3-step in silico funnel process, with increased-stringency at each step, run each consensus target active-site against multiple large druggable compound libraries, including all FDA-approved drugs, to obtain ‘hit’ compounds.  These ‘hit’ compounds are then simultaneously moved into: a) our in silico molecular dynamics pipeline to identify and characterize the active-site interacting groups (molecular domains) which will be used as one of the inputs into our structure-activity relationship (SAR) modeling to rationally build derivative compounds with greater affinities; and b) our three-phase laboratory biophysical-biochemical pipeline consisting of (i) surface plasmon resonance for protein binding kinetics, (ii) functional enzyme inhibition studies, and (iii) isothermal titration calorimetry and microscale thermophoresis to obtain precise stoichiometry and binding affinities under multiple liquid-phase parameters.  Hit compounds meeting both preset biophysical and biochemical criteria will be moved as “leads” into the antiviral testing arm of the pipeline.  Those compounds showing promise, but without high enough binding scores or IC50 values will be moved in the SAR pipeline for the development of rationally-designed derivatives.  Results from the SAR studies will be screened for their ease/predicted yields of synthesis, and then process-specific software will be used to augment protocols for their organic syntheses.  Lead compounds will be evaluated individually, and as cocktails of two and three compounds targeting different enzymes, for: 1) human cell toxicity; 2) SARS-CoV-2 virological studies using Calu-3 cells and human airway epithelial cells; and 3) in a physiologically relevant lung-on-a-chip system. Emergence of viral escape mutants in response to lead compounds will be sequenced and inform the synthesis of escape-resistant antiviral drugs. Finally, the prophylactic/therapeutic in vivo antiviral efficacy of lead compounds will be determined in animal models of coronavirus infection and pathogenesis.

Learning Objectives:

1. Learn applications of deep-learning algorithms and machine-learning techniques to help with the design of escape-resistant drugs for infectious agents

2. Learn targeting strategies to minimize the evolution of escape mutants

Learning Objectives:

1. Vaccine discovery: Understand the different types of vaccines for COVID-19 in development and how they will work to protect from SARS-CoV-2

2. Vaccine development: Learn how clinical testing of COVID-19 vaccines could get shortened from 5-7 years to 1.5-2 years without compromising evaluation of their safety

3. Vaccine distribution: Learn what is meant by targeted vaccines, ring vaccination and herd immunity

Antibody tests are important tools to assess the efficacy of vaccine candidates and to derive suitable vaccination modalities. High specificity and sensitivity are of great importance for the quality of an antibody test. Over the past five months, BOKU has been working intensively on the production of various SARS CoV-2 antigens in different biotechnological production systems. The aim was to identify antigen variants for the improved detection of SARS CoV-2 antibodies and to develop sustainable production processes for their high-quality supply. In order to rapidly screen a wide range of antigen candidates generated in different expression platforms, BOKU closely collaborated with the University of Veterinary Medicine Vienna. There, all BOKU antigens were pre-assessed in ELISA assays with a panel of pre-COVID control sera and selected sera of COVID19 patients. In addition, all proteins were also tested for SARS CoV-2 antibodies with the Luminex platform at the Austrian Institute of Technology and the Medical University Vienna. Based on the immunoassay results as well as antigen production yield and suitability for process scale-up, a truncated variant of the SARS CoV-2 spike receptor-binding domain (RBD) produced in a human cell line and the viral nucleocapsid protein (NP), produced in bacteria, were selected for further assay development. BOKU established complex multi-step purification processes and analytics with multiple antigen batches to ensure that the high-quality standards required for diagnostic protein reagents are always met. For prolonged antigen and test supply, two Viennese companies, that already provided knowledge and technology in the development phase, are now commercializing the diagnostic antigens and serological tests. Technoclone GmbH optimized the ELISA protocol and now offers both the RBD and NP ELISA Test “made in Austria”. EnGenes Biotech GmbH now commercially produces and distributes SARS CoV-2 antigens. The excellent interaction between the cooperating universities, research institutions and companies in this unique cross competence approach has paid off, as the tests achieved excellent scores in clinical validations performed at the Department of Laboratory Medicine at MedUni Vienna. The tests not only allow for highly specific and sensitive detection of SARS CoV-2 antibodies, the RBD test results also correlate well with the titers of neutralizing antibodies present in sera of COVID19 patients.

Learning Objectives:

1. Quantitative SARS-CoV2 Antibody tests, basted on SARS-CoV2 receptor binding domain and highly pure nucleocapsid protein for vaccination monitoring

2. Antigen quality assessment compared with both ELISA and LUMINEX in over 2000 sampels

3. Increased Specificity and Sensitivity by applying a combined two test strategy

SARS-CoV-2 had spread with speed unknown in recent history across the globe, sickening >50M people and killing over 1M.  By far the most of the severe cases and deaths were registered amongst adults older than 65, and often older than 50 years. We will discuss what makes this virus so well suited to disperse and infect so many and be so dangerous to older adults.

Learning Objectives:

1. Discuss what is SARS-CoV-2 and how is it different from other coronaviruses

2. Delineate the disease that this virus produces and what is unexpected in it

3. Review the immune response to this virus in adult and older populations, including  duration of immunity, and discuss potential immune vulnerability and protection by vaccination

Next-Generation Sequencing (NGS) has been a key technology during the COVIID-19 pandemic and has helped researchers characterize the SARs-CoV-2 genome, perform strain-typing for molecular epidemiology, study host genetics to identify patients with elevated genetic risk, determine effects of co-infections, and monitor host immune response.   In this talk we will give an overview of the key methods used to study the SARS-CoV-2 RNA genome as well as other respiratory pathogens.  We will compare the three main NGS methods for studying RNA viruses: shotgun meta-transcriptome sequencing, targeted RNA enrichment and PCR amplicon methods.  Finally, we will discuss how NGS can be used as a surveillance tool in the future to help control future breakouts.

Learning Objectives:

1. NGS enables precision diagnosis and characterization of respiratory pathogens

2. NGS can be used to understand host genetics, inflammatory and immune response Surveillance using

3. NGS will be critical to identify and control future pandemics

In this talk, Dr. Adalja will discuss the coronavirus family in general highlighting its history. Emphasis will be placed on why this viral family has pandemic potential.

Learning Objectives:

1. Understand the spectrum of illness caused by various coronaviruses

2. Recognize features of infectious pathogens that confer pandemic potential

The fast spread and deadliness of SARS-CoV-2 has sparked much interest in understanding the underlying genomics and evolutionary patterns of this 30,000bp Coronavirus. Since the first reported case on January 19th, 2020, over 200,000 genomes are now available. Within this large set of SARS-CoV-2 genomic data, thousands of mutations have been, including the D614G mutation that now is found in nearly all genomes and mink-associated variants. In this talk, I will take a deep dive into the intrahost and interhost diversity of the virus responsible for the COVID-19 pandemic. Specifically, I will discuss within-host minor variants and consensus-level variants that are found across hosts and describe population-wide structural variations that highlight this underexplored intrahost diversity. Implications of these findings include improved transmission cluster identification  and better understanding of how SARS-CoV-2 is changing over time.

Learning Objectives:

1. Differentiating consensus-level vs within-host variation of SARS-CoV-2

2. Discovering the utility of genomic variants on tracking SARS-CoV-2 transmission

3. Understanding of how SARS-CoV-2 is changing over time

The United States has had the worst response to COVID-19 among any country in the world. We are approaching nearly 200K deaths and more than 6 million known infections. The US government’s response to the pandemic from early on was a mixture of denial and incompetence. This includes a failure to set up an effective testing infrastructure to let the nation identity who was infected and who was not; downplaying the seriousness of the infection like comparing it with the flu when everyone knew it was far more deadly; the large campaign of misinformation through platforms like Facebook and much of the misinformation being augmented by our federal political leaders has led to a dramatically uneven response across the nation. As we look towards the fall and winter, despite progress on therapeutics and vaccines on the horizon, we will need a coordinated and effective federal response if we are to avoid hundreds of thousands of people dying from this disease.

Learning Objectives:

1. To understand the role of the US federal government in testing and other disease containment strategies

2. To understand how US federalism led to a diversity of responses and outcomes in this pandemic

The forecast IHME released on March 26, 2020, was geared to helping hospitals plan for a surge in demand for their resources (e.g., beds, ICUs, ventilators) to fight COVID-19. With many locations seeing a second peak of COVID-19 infections and deaths, attention is now on how best to prevent and manage a resurgence of the disease while safely enabling people to get back to work and school. To help with policy decisions, IHME is now providing a reference scenario and two additional forecasts for daily and total deaths. In this seminar, we will provide and Introduction to the IHME model, its limitations, projections for our region, how can the countries use these estimates, and looking ahead.

Learning Objectives:

1. The main drivers of the increased cases and deaths?

2. How we could control this pandemic

3. The scenarios for this coming winter and the impact of seasonality

Part I:  Introduction and history coronaviruses dating back to the 1980s and coronavirus biology. I will describe the coronavirus life cycle pointing steps that may serve as targets of antiviral therapies that may effective against most if not all coronaviruses.

Part II. Coronaviruses are highly effective in antagonizing host innate immune responses, more specifically interferon (IFN) induction and signaling pathways. MERS-CoV and SARS-CoV fail to induce IFN early in infections of humans and in mouse models while IFN production in late disease may be pathogenic. Antagonism of host responses is carried out through expression of multiple viral accessory proteins as well as conserved replicase encoded proteins, sometimes with redundant activities. Our lab focuses on the double-stranded RNA induced antiviral pathways: type I and types III IFNs, oligoadenylate synthetase-ribonuclease (OAS-RNase L) and protein kinase R (PKR). Activation of these pathways leads to inhibition of viral replication, shut down of protein synthesis and apoptotic cell death. I will discuss coronavirus antagonism of these pathways using examples from our previous studies of the betacoronaviruses murine coronavirus MHV and MERS-CoV and recent data on SARS-CoV-2.

Learning Objectives:

1. Coronaviruses enter cells by two pathways, at the plasma membrane fusion or through endosomes

2. Coronaviruses encode 16 conserved non-structural proteins in the replicase locus, potential targets for pan coronavirus antivirals

3. Coronaviruses are adept at antagonizing activation of dsRNA induced antiviral pathways, including interferon signaling, OAS-RNase L and PKR

PerkinElmer is a global leader in the development of instrumentation and probes for small animal non-invasive imaging, including optical and µCT imaging. Through optical imaging, we have developed a technology which allows biological processes, including gene expression that is temporally and spatially defined, to be non-invasively monitored both longitudinally and in real-time. Genes encoding optical reporters, luciferases and fluorescent proteins, are engineered into cells and pathogens (e.g., bacteria, viruses), or directly into animals (e.g., monitoring host responses) to enable the generation of light that can be visualized through the tissues of a live animal. PerkinElmer has optimized this technique to allow true three-dimensional optical imaging and tomographic multimodality imaging (e.g., through co-registration of optical imaging with µCT and MRI). Furthermore, this technique is equally applicable to imaging of fluorescent dyes and particles, allowing fluorescently tagged biological events (e.g., tracking of antibodies, peptides and viral capsids) to be monitored both independently and in combination with genetically tagged events. An overview of optical imaging in viral and bacterial disease research will be presented, showing how this approach can be used to refine and improve fundamental biological research, as well as drug development and clinical translation strategies.

Learning Objectives:

1. Understand the principle of non-invasive preclinical optical imaging as it relates to infectious disease research

2. Recognize different molecular imaging techniques for visualizing host-pathogen interactions

In recent months, we have seen a large part of the global scientific community shift to infectious disease research. In response, researchers are exploring safer and easier methods to handle, isolate, and analyze cells from hazardous materials. Mitigating risk while achieving highly pure, viable cells is essential to understanding the immune system’s role in COVID-19 infection and recovery. When it comes to cell sorting, samples, such as SARS-CoV-2 convalescent samples, virus-infected human cells (e.g., from HIV-positive donors), or bacteria, can escape the fluidic system of a traditional droplet-based cell sorter as aerosols.  Our multi-parametric cell sorting platform offers a solution with its unique closed, single-use, and disposable sorting cartridge. This cartridge provides an increased level of biocontainment and can mitigate the risk when implementing a fluorescent-activated cell sorter in BSL-3 or BSL-2+ level laboratories.

Learning Objectives:

1. Scientists utilizing cell sorting to obtain high quality cell populations from biohazardous samples

2. Mitigating risk while sorting hazardous samples though leveraging a microfluidic-based fluorescent-activated cell sorter

3. GMP-compliant cell sorting options available for your translational research

Learning Objectives:

1. Drug Repurposing Strategies for SARS-CoV2

2. Validation pipeline for SARS-CoV-2 antiviral

3. Outlook for SARS-CoV-2 therapeutics

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has killed hundreds of thousands of people, including >23,000 in New York City (NYC) alone. The pandemic’s sudden emergence highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, clinical data from 50,821 patients shows evidence of a protective impact of patients taking ACE inhibitors, which is distinct from other drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive new SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Learning Objectives:

1. List several ways to profile the SARS-CoV-2 virus'

2. Describe the host and viral responses from infection for SARS-CoV-2

Infectious diseases, such as COVID-19, are challenging to study in animal models due to species differences, and conventional 2D cell-based systems lack the complexity to appropriately model the disease or immune response in humans. Organs-on-Chips offer a human relevant system that can recreate key disease phenotypes in a more physiological microenvironment due to their complex 3D architecture and mechanical forces induced by flow and stretch. In this webinar, we discuss how the Airway Lung-Chip and Alveolus Lung-Chip can be used to study viral infection and accelerate the development of new therapeutics.

Learning Objectives:

1. Learn how Organs-on-Chips technology can be applied to recreate key aspects of pulmonary physiology, specifically the creation of Airway and Alveolus Lung-Chip models

2. Review data demonstrating how the Airway Lung-Chip can be used to study viral infection and evaluate the efficacy of therapeutic interventions

Next-generation sequencing (NGS) is the primary technology used to identify genomic targets for vaccine development, detect emerging viral strains and monitor transmission patterns. Enhanced options for NGS on Illumina systems from the Invitrogen Collibri portfolio of library prep technology now make it possible to identify multiple potentially pathogenic strains of a disease and understand the rate of evolution quickly, with improved precision.

Learning Objectives:

1. Learn how to enable rapid sequencing SARS-CoV-2 samples for real-time monitoring of transmission patterns and emerging strains

2. Why do some people become severely ill compared to those who do not, even when infected with the same viral strain? Learn about new tools to investigate differences in gene expression among these groups

Therapeutic antibody can provide key protection or lifesaving treatment for those who haven't been or can’t be vaccinated, or when vaccines don’t “take". We galvanized a Gates- and NIAID-funded consortium to understand which antibodies are most protective and why, to learn which in vitro assays best correlate with in vivo success, and to broadly mobilize therapeutics where needed.

Learning Objectives:

1. The different mechanisms by which antibodies protect against viral infection

2. How a multidisciplinary, multi-investigator study can offer new information

Choosing the right solution for your laboratory’s SARS-CoV-2 testing needs can be a difficult decision. With the dynamic demand on labs, making the wrong choice could be catastrophic. In this presentation, we will be discussing the critical factors to consider when choosing the set up for your testing needs:

• Assay sensitivity and reliability

• Availability of reagents

• Throughput and labor requirements

• Sample-to-solution workflow

• Support

Learning Objectives:

1. Specialized work flows required for launching a RT-PCR COVID-19 assay

2. Validation of COVID-19 RT-PCR assays following FDA guidance

3. Requirements and process for submitting for EUA approval

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the cause of Coronavirus Disease 2019 (COVID-19) and responsible for the current pandemic.  Here, we present an in-depth study of SARS-CoV-2 infection, associated disease, transmission and reinfection dynamics in domestic cats.  Six 4- to 5-month-old cats were challenged with SARS-CoV-2 via intranasal and oral routes simultaneously.  One day post challenge (DPC), two sentinel contact cats were co-mingled with the principal infected animals.  Animals were monitored for clinical signs, clinicopathological abnormalities (blood cell counts, serum biochemistry) and viral shedding throughout a 21 DPC observation period.  On 21 DPC, three cats were reinfected with SARS-CoV-2. Animals were sacrificed and post mortem examinations performed at 4, 7, 21 DPC and 4 days post second challenge (DP2C) to investigate disease progression in various organ systems and tissues.  Viral RNA was not detected in blood but transiently in nasal, oropharyngeal and rectal swabs in principal infected, sentinel and reinfected animals, as well as in bronchoalveolar lavage fluid at 4 and 7 DPC and in various organs/tissues of primary infected and reinfected animals.  Lung lesions associated with the presence of viral RNA and antigen were observed in primary infected cats on 4 and 7 DPC, but not on 21 DPC and 4 DP2C. Serology showed that both, principal and sentinel cats developed SARS-CoV-2-specific and neutralizing antibodies to SARS-CoV-2 starting at 7 DPC or 10 DPC, respectively. All animals were clinically asymptomatic during the course of the study; primary infected but not reinfected cats were capable of transmitting SARS-CoV-2 to contact animals within 2 days of comingling. The results of this study are critical: (i) for our understanding of the clinical course of SARS-CoV-2 in a naturally susceptible host species; (ii) for evaluating whether a SARS-CoV-2 infection can protect against reinfection; (iii) for the development of an alternative preclinical COVID-19 animal model; and (iv) for risk assessment of SARS-CoV-2 infections in felines and transmission to other animals and humans.

Learning Objectives:

1. Be aware of SARS-CoV-2 infections in companion animals

2. How to diagnose SARS-CoV-2 infections in companion animals

COVID-19 has developed into a crisis of global proportions. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms driving high infectivity, broad tissue tropism and severe pathology. SARS-CoV-2 is decorated by multiple copies of a glycoprotein, called Spike, which is key to infectivity. Using cryo-electron microscopy and cloud computing, we discovered a potentially druggable pocket within the SARS-CoV-2 Spike, which appears to be likewise present in the highly pathogenic coronaviruses that caused the previous SARS and MERS outbreaks. Our discovery provides, for the first time, a structural link between COVID-19 pathology and the virus itself, setting the stage for developing new therapeutic interventions to combat and defeat COVID-19.

Learning Objectives:

1. Learn about the high-tech science technologies and techniques being used to defeat the global COVID-19 epidemic

2. Learn about a novel discovery of a druggable pocket in SARS-CoV-2 spike protein for drug development

There are an urgent need for antivirals to treat the newly emerged SARS-CoV-2. We set out to develop cell-based screens to repurpose existing drugs for use against SARS-CoV-2. Our goal was to identify both direct-acting and host-targeted antivirals. We have screened an in-house repurposing library of ~3,000 drugs in three distinct cell types permissive to SARS-CoV-2 infection: monkey kidney cells (Vero), human hepatocytes (Huh7.5) and human lung epithelial cells (Calu-3). There were 6 actives in Vero, 33 in Huh7.5 and 88 in Calu-3, with little overlap. While direct-acting antivirals such as remdesivir are active in all three cell types, we found few antivirals that were broadly active suggesting that the host dependencies are distinct in different cell types. Indeed, exploring entry pathways  revealed that in in lung epithelial Calu-3 cells entry is pH-independent and cathepsin-independent but requires TMPRSS2,. In contrast entry in Vero and Huh7.5 cells requires low pH and triggering by acid-dependent cathepsin proteases and is independent of TMPRSS2. Moreover, we found 9 drugs are antiviral in both hepatocytes and lung cells, 7 of which have been tested in humans, and 3 are FDA approved including Cyclosporine which we found is targeting Cyclophilin rather than Calcineurin for its antiviral activity revealing essential host targets that have the potential for rapid clinical implementation Specifically, I will discuss antiviral screening strategies and validation paradigms and discuss the implications of the cell type specificity. In addition, I will discuss some of our antivirals and mechanisms by which they function to block SARS-CoV-2 infection.

Learning Objectives:

1. Strategies for antiviral screening

2. Importance of cell types in antiviral discovery

3. Cellular dependencies of SARS-CoV-2 in the lung epithelium

The COVID-19 pandemic has resulted in demand for population scale pathogen screening. The most sensitive and reliable method for detecting SARS-CoV-2 remains reverse transcription PCR (RT-PCR). However, current platforms for SARS-CoV-2 RNA detection have not yet met the demand for large scale, rapid testing. Here, we present an ultra-fast PCR platform, NEXTGENPCR, which accelerates RT-PCR assays. The NEXTGENPCR machine provides a small footprint capable of running PCR in 96 or 384 well plates in less than 10 minutes; and RT-PCR in less than 16 minutes. Come learn how you can accelerate RT-PCR for direct detection or sequencing applications.

Learning Objectives:

1. Understand how NEXTGENPCR accelerates SARS-CoV-2 assays and chemistries

2. Considerations for setting up an efficient workflow to process >1,000 per hour

3. Understand how accelerated cycling yields equivalent assay performance

As part of a large collaborative effort, we have used systems biology approaches to identify host factors that participate in SARS-CoV-2 replication.  Protein-protein interactions maps between viral and host proteins and  global landscapes on protein phosphorylation changes taking place in SARS-CoV-2 infected cells were used as guides for the identification of host processes that could be targeted for antiviral therapeutic intervention. Drugs known to interact with these host processes and with known clinical profiles were tested for their ability to inhibit SARS-CV-2 replication in tissue culture.   As a result, we found several promising therapeutic candidates to be evaluated in vivo for the treatment of COVID-19.

Learning Objectives:

1. Understand the concept of drug re-purposing

2. Gain insights on the use of system biology approaches for the discovery of antivirals

3. Gain insights on the host-virus protein interactions contributing to SARS-CoV-2 replication

This presentation will discuss the use of the FDA EUA process to implement SARS-CoV-2 assays to address the COVID-19 pandemic.  The use of a team-based approach, through an Incident Command structure, to optimally address all the operational challenges in validating, implementing and maintaining SARS-CoV-2 testing for the patient population in a large tertiary care referral center.  The presentation we review a comparison of five SARS-CoV-2 assays.   Evaluation of the changes in viral load thoughout the time course of COVID-19 infections will be reviewed, and how this related back to the five test comparison will be discussed.  The importance of the population tested (i.e. high versus low prevalence) will be reviewed, as diagnostic tests are being used as screening tests.  The presentation will review the testing of saliva as an alternate diagnostic specimen, and will explain the benefits and limitations of pool testing of diagnostic specimens.  In conclusion, the presentation will describe how testing is integrated with mitigation strategies necessary to curtail the COVID-19 pandemic.

Learning Objectives:

1. Describe the optimal uses for the various types of SARS-CoV-2 tests (i.e. antigen, antibody, & different nucleic acid amplification assays)

2. Discuss the molecular detection of SARS-CoV-2 during COVID-19 convalescence

3. Discuss the impact of utilizing a test with high (95%) specificity in a diagnostic setting versus screening setting

4. Review the benefits and limitations of testing alternate specimen types (e.g. saliva) and utilizing alternate testing strategies (e.g. pooling) for the detection of SARS-CoV-2

As the spread of infectious diseases, current pandemic, and growing antimicrobial resistance (AMR) continues globally, next-generation sequencing (NGS) became a tool to diagnose infectious diseases. The rapid identification of pathogens providing key information on species, strains, genetic variants and geographic origin, NGS and artificial intelligence-based approach enables emerging pathogen and strain identification, patient risk stratification, AMR tracking, clinical interpretation and outcome prediction.

Learning Objectives:

1. Understanding the next-generation sequencing (NGS) and how NGS can be used to fight against infectious diseases and the current pandemic

2. Facilitate in-depth knowledge about harnessing microbial genetic information to develop breakthrough diagnostic and surveillance tools

3. Leverage insights gathered from the microbiome and virome to fight against infectious diseases through the development of precision diagnostics

4. Understanding how NGS and the SARS-CoV-2 viral genome can be used for pandemic surveillance

Next-generation sequencing (NGS) is the primary technology used to identify genomic targets for vaccine development, detect emerging viral strains and monitor transmission patterns. Enhanced options for NGS on Illumina systems from the Invitrogen Collibri portfolio of library prep technology now make it possible to identify multiple potentially pathogenic strains of a disease and understand the rate of evolution quickly, with improved precision. The most current application of NGS technology is to rapidly map differences in gene expression profiles to research variance in immune response among infected individuals.

Learning Objectives:

1. Considerations to choose between RNA-seq and whole-genome sequencing when studying RNA viruses

2. Criteria to choose among three RNA sequencing methods

3. Tools to improve the quality of viral sequencing data

With more than 6 million infections and more than 300,000 deaths (as of end of May 2020), the current COVID-19 pandemic has led to large scale lockdown around the world to prevent further spread of the disease.

From the initial effort of rapid diagnosis and containment, the international community is now facing the challenge of an effective and pragmatic “exit” strategy to balance the public health risk versus the huge economic losses as a result of the travel ban and lockdown measures globally.

Among the many challenges of onging COVID-19 investigation and repsonses, the follwong three stands out as the most pressing: 1) A good understanding of protective immunity and longevity of immunity to better advise/design “exit” strategy and policy; 2) Rapid development and deployment of COVID-19 vaccine(s) and a reliable testing platform capable of assessing and monitoring vaccine efficacy en masse; and 3) Investigation of virus origin and the early animal-to-human transmission events to prevent future outbreaks.

Serology will play a key role in all three areas. In this presentation, different serological platforms currently used for COVID-19 testing will be reviewed and compared together with the introduction of a novel platfom, the surrogate virus neutralization test (sVNT), that we have developed recently.

Learning Objectives:
1. Challenges for next phase of COVID-19 outbreak

2. Role of serology in meeting some of these challenges

Coronavirus disease 2019 (Covid-19) is a global pandemic that has impacted the lives of the entire world’s population. Accurate and effective testing mechanisms to identify those with active infections or have convalesced is necessary to properly monitor and control this infectious agent. To this end, we have recently developed a serological method for assessment of an immune response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen based on simultaneous evaluation of four viral antigens, including the Spike, Nucleocapsid, Membrane, and Envelope glycoproteins, and built on the Luminex immunobead platform. Validation studies against 1042 patients have provided test performance characteristics of 100% Sensitivity, 99.6% Specificity, and 99.62% overall accuracy, relative to PCR-based assignments. This quantitative method is highly effective in applications that include diagnosis of those with past infections (symptomatic or asymptomatic), epidemiological studies/ guidance for policy decisions, monitoring titers during vaccine trials, and rationalized donor selection for therapeutic ‘convalescent plasmapheresis’ strategies.

Learning Objectives:

1. To understand the best testing strategy to survey COVID-19 in population in order to constrain the disease and prepare for safe reopening

2. To understand the advantage of multiplexing technology to improve testing accuracy and sensitivity