Beyond Costs: Pragmatic Considerations for Pooling of SARS-CoV-2 Test Samples for Nursing Home Surveillance.

Pooling of samples can increase throughput and reduce costs for large-scale SARS-CoV-2 testing when incidence is low. In a cross-sectional study of serial SARS-CoV-2 sampling of staff and residents at three nursing homes, laboratory labor constraints limited the feasibility of pooling prior to the maximal incidence that favored cost savings. IMPORTANCE This study highlights the pragmatic considerations surrounding SARS-CoV-2 sample pooling beyond accuracy and costs. We performed a cost analysis to determine the percent positivity at which pooling would reduce costs versus single testing. We found that the need for a stable amount of daily work hours staffed by a highly trained workforce was a major limitation in pooling as test positivity increased. For the COVID-19 pandemic and future pandemic threats, laboratories should carefully consider the thresholds at which sample pooling is beneficial, with a particular focus on the impact on laboratory staff.

A Protein Microarray-Based Respiratory Viral Antigen Testing Platform for COVID-19 Surveillance.

High-throughput and rapid screening testing is highly desirable to effectively combat the rapidly evolving COVID-19 pandemic co-presents with influenza and seasonal common cold epidemics. Here, we present a general workflow for iterative development and validation of an antibody-based microarray assay for the detection of a respiratory viral panel: (a) antibody screening to quickly identify optimal reagents and assay conditions, (b) immunofluorescence assay design including signal amplification for low viral titers, (c) assay characterization with recombinant proteins, inactivated viral samples and clinical samples, and (d) multiplexing to detect a panel of common respiratory viruses. Using RT-PCR-confirmed SARS-CoV-2 positive and negative pharyngeal swab samples, we demonstrated that the antibody microarray assay exhibited a clinical sensitivity and specificity of 77.2% and 100%, respectively, which are comparable to existing FDA-authorized antigen tests. Moreover, the microarray assay is correlated with RT-PCR cycle threshold (Ct) values and is particularly effective in identifying high viral titers. The multiplexed assay can selectively detect SARS-CoV-2 and influenza virus, which can be used to discriminate these viral infections that share similar symptoms. Such protein microarray technology is amenable for scale-up and automation and can be broadly applied as a both diagnostic and research tool.

Whole Genome Sequencing (WGS) for COVID-19 Outbreak Evaluations – How Much Does It Add to Bootstrap Epidemiology & Contact Tracing?

Background Epidemiologic investigations are foundational in outbreak evaluations but are unable to fully capture the innumerable interactions that lead to exposure. Whole Genome Sequencing (WGS) offers clonality information that can suggest potential transmission links but is costly and resource intensive. We compared COVID-19 exposure source as determined by contact tracing investigations with linkages inferred by WGS data for a COVID-19 outbreak among healthcare workers (HCWs) and patients. Methods Contact tracing investigations were conducted for HCWs identified in three COVID-19 hospital clusters and included interviews to assess exposure history and infection prevention breaches and categorized as either: Community, HCW-to-HCW, Patient-to-HCW, HCW-to-Patient, or Unknown. WGS evaluations were completed for 45 (34 HCWs,11 patients) COVID-19 positive samples (Quiagen EZ1 RNA extraction, Illumina Nextera FLex library/Illumina NextSeq 500). Exposure source determinations were reevaluated using WGS data. Agreement between the two strategies were described as percentage and compared using Cohen's Kappa. Results Among 45 samples submitted, 37 were successfully sequenced, and19 (51%,17 HCWs and 2 patients) were identified as potentially linked clonal Epsilon (B.1.429) COVID-19 variant strains. WGS identified 13 identical and 6 closely related strains that suggested linkages between 15 HCW-HCW, 2 HCW-Patient, 1 community, and 1 unknown transmission. Contact tracing categorized the 19 cases as: 8 HCW-HCW, 1 Patient-HCW, 3 Community, and 7 Unknown. After incorporating WGS data, these were reclassified as 9 HCW-HCW, 5 Community, and 5 Unknown. Combining contact tracing with WGS information resulted in 6 (32%) reclassifications;agreement between the two strategies was 58% (Cohen's kappa=0.19), identifying 1 previously unrecognized 1 HCW-HCW and 2 community cases. While contact tracing had suggested 1 patient-HCW transmission, WGS results did not show matching strains. Conclusions WGS can improve the precision of COVID-19 outbreak investigation of transmission links in almost one third of cases.

Genome-Wide B Cell, CD4+, and CD8+ T Cell Epitopes That Are Highly Conserved between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines.

Over the last two decades, there have been three deadly human outbreaks of coronaviruses (CoVs) caused by SARS-CoV, MERS-CoV, and SARS-CoV-2, which has caused the current COVID-19 global pandemic. All three deadly CoVs originated from bats and transmitted to humans via various intermediate animal reservoirs. It remains highly possible that other global COVID pandemics will emerge in the coming years caused by yet another spillover of a bat-derived SARS-like coronavirus (SL-CoV) into humans. Determining the Ag and the human B cells, CD4+ and CD8+ T cell epitope landscapes that are conserved among human and animal coronaviruses should inform in the development of future pan-coronavirus vaccines. In the current study, using several immunoinformatics and sequence alignment approaches, we identified several human B cell and CD4+ and CD8+ T cell epitopes that are highly conserved in 1) greater than 81,000 SARS-CoV-2 genome sequences identified in 190 countries on six continents; 2) six circulating CoVs that caused previous human outbreaks of the common cold; 3) nine SL-CoVs isolated from bats; 4) nine SL-CoV isolated from pangolins; 5) three SL-CoVs isolated from civet cats; and 6) four MERS strains isolated from camels. Furthermore, the identified epitopes: 1) recalled B cells and CD4+ and CD8+ T cells from both COVID-19 patients and healthy individuals who were never exposed to SARS-CoV-2, and 2) induced strong B cell and T cell responses in humanized HLA-DR1/HLA-A*02:01 double-transgenic mice. The findings pave the way to develop a preemptive multiepitope pan-coronavirus vaccine to protect against past, current, and future outbreaks.

Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score.

Effective methods for predicting COVID-19 disease trajectories are urgently needed. Here, enzyme-linked immunosorbent assay (ELISA) and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide range of disease states. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the intensive care unit (ICU), requirement for ventilators, or death. Importantly, anti-Ep9 antibodies can be detected within 6 days post-symptom onset and sometimes within 1 day. Furthermore, anti-Ep9 antibodies correlate with various comorbidities and hallmarks of immune hyperactivity. We introduce a simple-to-calculate, disease risk factor score to quantitate each patient's comorbidities and age. For patients with anti-Ep9 antibodies, scores above 3.0 predict more severe disease outcomes with a 13.42 likelihood ratio (96.7% specificity). The results lay the groundwork for a new type of COVID-19 prognostic to allow early identification and triage of high-risk patients. Such information could guide more effective therapeutic intervention.IMPORTANCE The COVID-19 pandemic has resulted in over two million deaths worldwide. Despite efforts to fight the virus, the disease continues to overwhelm hospitals with severely ill patients. Diagnosis of COVID-19 is readily accomplished through a multitude of reliable testing platforms; however, prognostic prediction remains elusive. To this end, we identified a short epitope from the SARS-CoV-2 nucleocapsid protein and also a disease risk factor score based upon comorbidities and age. The presence of antibodies specifically binding to this epitope plus a score cutoff can predict severe COVID-19 outcomes with 96.7% specificity.

Genome-Wide Asymptomatic B-Cell, CD4 + and CD8 + T-Cell Epitopes, that are Highly Conserved Between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Immune Targets for Pre-Emptive Pan-Coronavirus Vaccines.

Over the last two decades, there have been three deadly human outbreaks of Coronaviruses (CoVs) caused by emerging zoonotic CoVs: SARS-CoV, MERS-CoV, and the latest highly transmissible and deadly SARS-CoV-2, which has caused the current COVID-19 global pandemic. All three deadly CoVs originated from bats, the natural hosts, and transmitted to humans via various intermediate animal reservoirs. Because there is currently no universal pan-Coronavirus vaccine available, two worst-case scenarios remain highly possible: (1) SARS-CoV-2 mutates and transforms into a seasonal "flu-like" global pandemic; and/or (2) Other global COVID-like pandemics will emerge in the coming years, caused by yet another spillover of an unknown zoonotic bat-derived SARS-like Coronavirus (SL-CoV) into an unvaccinated human population. Determining the antigen and epitope landscapes that are conserved among human and animal Coronaviruses as well as the repertoire, phenotype and function of B cells and CD4 + and CD8 + T cells that correlate with resistance seen in asymptomatic COVID-19 patients should inform in the development of pan-Coronavirus vaccines 1 . In the present study, using several immuno-informatics and sequence alignment approaches, we identified several human B-cell, CD4 + and CD8 + T cell epitopes that are highly conserved in: ( i ) greater than 81,000 SARS-CoV-2 human strains identified to date in 190 countries on six continents; ( ii ) six circulating CoVs that caused previous human outbreaks of the "Common Cold"; ( iii ) five SL-CoVs isolated from bats; ( iv ) five SL-CoV isolated from pangolins; ( v ) three SL-CoVs isolated from Civet Cats; and ( vi ) four MERS strains isolated from camels. Furthermore, we identified cross-reactive asymptomatic epitopes that: ( i ) recalled B cell, CD4 + and CD8 + T cell responses from both asymptomatic COVID-19 patients and healthy individuals who were never exposed to SARS-CoV-2; and ( ii ) induced strong B cell and T cell responses in "humanized" Human Leukocyte Antigen (HLA)-DR/HLA-A*02:01 double transgenic mice. The findings herein pave the way to develop a pre-emptive multi-epitope pan-Coronavirus vaccine to protect against past, current, and potential future outbreaks.