Teicoplanin derivatives block spike protein mediated viral entry as pan-SARS-CoV-2 inhibitors.

The rapid emergence of highly transmissible SARS-CoV-2 variants poses serious threat to the efficacy of vaccines and neutralizing antibodies. Thus, there is an urgent need to develop new and effective inhibitors against SARS-CoV-2 and future outbreaks. Here, we have identified a series of glycopeptide antibiotics teicoplanin derivatives that bind to the SARS-CoV-2 spike (S) protein, interrupt its interaction with ACE2 receptor and selectively inhibit viral entry mediated by S protein. Computation modeling predicts that these compounds interact with the residues in the receptor binding domain. More importantly, these teicoplanin derivatives inhibit the entry of both pseudotyped SARS-CoV-2 Delta and Omicron variants. Our study demonstrates the feasibility of developing small molecule entry inhibitors by targeting the interaction of viral S protein and ACE2. Together, considering the proven safety and pharmacokinetics of teicoplanin as a glycopeptide antibiotic, the teicoplanin derivatives hold great promise of being repurposed as pan-SARS-CoV-2 inhibitors.

Cancer and COVID-19 Vaccines on Twitter:The Voice and Vaccine Attitude of Cancer Community.

We investigate social media discourses on the relationship between cancer and COVID-19 vaccines focusing on the key textual topics, themes reflecting the voice of cancer community, authors who contribute to the discourse, and valence toward vaccines. We analyzed 6,427 tweets about cancer and COVID-19 vaccines, posted from when vaccines were approved in the U.S. (December 2020) to the February 2022. We mixed quantitative text mining, manual coding and statistical analysis, and inductive qualitative thematic analysis. Nearly 16% of the tweets posted by a cancer community member mentioned about refusal or delay of their vaccination at the state/local level during the initial rollout despite the CDC's recommendation to prioritize adults with high-risk medical conditions. Most tweets posted by cancer patients (pro = 82.4% vs. anti = 5.1%) and caregivers (pro = 89.2% vs. anti = 4.2%) showed positive valence toward vaccines and advocated for vaccine uptake increase among cancer patients and the general population. Vaccine hesitancy, self-reported adverse events, and COVID-19 disruption of cancer treatment also appeared as key themes. The cancer community called for actions to improve vaccination procedures to become safe and accessible especially for elderly cancer patients, develop COVID-19 vaccines suitable for varying type, stage, and treatment of cancer, and advance cancer vaccines. Future research should continue surveilling conversations around continuous impacts of COVID-19 interference with the cancer control continuum, beyond vaccination, focusing on the voice and concern of cancer community.

SARS-CoV-2 hijacks cellular kinase CDK2 to promote viral RNA synthesis.

The coronavirus disease 2019 (COVID-19) pandemic has devastated global health. Identifying key host factors essential for SARS-CoV-2 RNA replication is expected to unravel cellular targets for the development of broad-spectrum antiviral drugs which have been quested for the preparedness of future viral outbreaks. Here, we have identified host proteins that associate with nonstructural protein 12 (nsp12), the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 using a mass spectrometry (MS)-based proteomic approach. Among the candidate factors, CDK2 (Cyclin-dependent kinase 2), a member of cyclin-dependent kinases, interacts with nsp12 and causes its phosphorylation at T20, thus facilitating the assembly of the RdRp complex consisting of nsp12, nsp7 and nsp8 and promoting efficient synthesis of viral RNA. The crucial role of CDK2 in viral RdRp function is further supported by our observation that CDK2 inhibitors potently impair viral RNA synthesis and SARS-CoV-2 infection. Taken together, we have discovered CDK2 as a key host factor of SARS-CoV-2 RdRp complex, thus serving a promising target for the development of SARS-CoV-2 RdRp inhibitors.

Identification of the pathogenic relationship between Long COVID and Alzheimer's disease by bioinformatics methods (preprint)

Background The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an unprecedented global health crisis. Although many Corona Virus Disease 2019 (COVID-19) patients have recovered, the long-term consequences of SARS-CoV-2 infection are unclear. Several independent epidemiological surveys and clinical studies have found that SARS-CoV-2 infection and Long COVID are closely related to Alzheimer's disease (AD). This could lead to long-term medical challenges and social burdens following this health crisis. However, the mechanism between Long COVID and AD is unknown.Methods Genes associated with Long COVID were collected from the database. Two sets of AD-related clinical sample datasets were collected in the Gene Expression Omnibus (GEO) database by limiting screening conditions. After identifying the differentially expressed genes (DEGs) of AD, the significant overlapping genes of AD and Long COVID were obtained by taking the intersection. Then, four kinds of analyses were performed, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analysis, protein-protein interaction (PPI) analysis, identification of hub genes, hub gene verification and transcription factors (TFs) prediction.Results A total of 197 common genes were selected for subsequent analysis. GO and KEGG enrichment analysis showed that these genes were mainly enriched in multiple neurodegenerative disease related pathways. In addition, 20 important hub genes were identified using cytoHubba. At the same time, these hub genes were verified in another data set, where 19 hub gene expressions were significantly different in the two diseases and 6 hub genes were significantly different in AD patients of different genders. Finally, we collected 9 TFs that may regulate the expression of these hub genes in the Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining (TRUSST) database and verified them in the current data set.Conclusion This work reveals the common pathways and hub genes of AD and Long COVID, providing new ideas for the pathogenic relationship between these two diseases and further mechanism research.

SARS-CoV-2 hijacks cellular kinase CDK2 to promote viral RNA synthesis.

The coronavirus disease 2019 (COVID-19) pandemic has devastated global health. Identifying key host factors essential for SARS-CoV-2 RNA replication is expected to unravel cellular targets for the development of broad-spectrum antiviral drugs which have been quested for the preparedness of future viral outbreaks. Here, we have identified host proteins that associate with nonstructural protein 12 (nsp12), the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 using a mass spectrometry (MS)-based proteomic approach. Among the candidate factors, CDK2 (Cyclin-dependent kinase 2), a member of cyclin-dependent kinases, interacts with nsp12 and causes its phosphorylation at T20, thus facilitating the assembly of the RdRp complex consisting of nsp12, nsp7 and nsp8 and promoting efficient synthesis of viral RNA. The crucial role of CDK2 in viral RdRp function is further supported by our observation that CDK2 inhibitors potently impair viral RNA synthesis and SARS-CoV-2 infection. Taken together, we have discovered CDK2 as a key host factor of SARS-CoV-2 RdRp complex, thus serving a promising target for the development of SARS-CoV-2 RdRp inhibitors.

Rapid Genotyping of SARS-CoV-2 Strains Alpha, Delta, Omicron BA.1, Omicron BA.2, Omicron BA.2.12.1, and Omicron BA.4/BA.5 Using ARMS- PCR and Molecular Beacon Technology (preprint)

Background SARS-CoV-2 subtypes Alpha, Delta, Omicron BA.1, Omicron BA.2, Omicron BA.2.12.1, and Omicron BA.4/BA.5 have significant differences in transmission and immune escape ability. Currently, no effective detection methods are available for these subtypes. Routine detection methods are prone to missed detection.Methods In this study, a rapid detection method based on ARMS-PCR and molecular beacon probes was developed for the identification of SARS-CoV-2 subtypes Alpha, Delta, Omicron BA.1, Omicron BA.2, Omicron BA.2.12.1, and Omicron BA.4/5. Specific primers and probes were designed and validated using gel electrophoresis, real-time fluorescence quantitative PCR, and molecular hybridization.Results ARMS-PCR and molecular beacon probe-based assays can be applied in RT-PCR and fluorescence assays to differentiate SARS-CoV-2 subtypes Alpha, Delta, Omicron BA.1, Omicron BA.2, Omicron BA.2.12.1, and Omicron BA.4/5.Conclusions In the present study, we developed a simple, rapid and accurate detection method based on ARMS-PCR and molecular beacon probes for rapid genotyping of SARS-CoV-2 subtypes Alpha, Delta, Omicron BA.1, Omicron BA.2, Omicron BA.2.12.1, and Omicron BA.4/5. It can be used in real-time fluorescence quantitative PCR and molecular hybridization to identify subtypes of COVID-19, effectively improving the detection rate to provide guidance for disease prevention and treatment.

Temporal Events Detector for Pregnancy Care (TED-PC): A rule-based algorithm to infer gestational age and delivery date from electronic health records of pregnant women with and without COVID-19.

OBJECTIVE: Identifying the time of SARS-CoV-2 viral infection relative to specific gestational weeks is critical for delineating the role of viral infection timing in adverse pregnancy outcomes. However, this task is difficult when it comes to Electronic Health Records (EHR). In combating the COVID-19 pandemic for maternal health, we sought to develop and validate a clinical information extraction algorithm to detect the time of clinical events relative to gestational weeks. MATERIALS AND METHODS: We used EHR from the National COVID Cohort Collaborative (N3C), in which the EHR are normalized by the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). We performed EHR phenotyping, resulting in 270,897 pregnant women (June 1st, 2018 to May 31st, 2021). We developed a rule-based algorithm and performed a multi-level evaluation to test content validity and clinical validity, and extreme length of gestation (<150 or >300). RESULTS: The algorithm identified 296,194 pregnancies (16,659 COVID-19, 174,744 without COVID-19) in 270,897 pregnant women. For inferring gestational age, 95% cases (n = 40) have moderate-high accuracy (Cohen's Kappa = 0.62); 100% cases (n = 40) have moderate-high granularity of temporal information (Cohen's Kappa = 1). For inferring delivery dates, the accuracy is 100% (Cohen's Kappa = 1). The accuracy of gestational age detection for the extreme length of gestation is 93.3% (Cohen's Kappa = 1). Mothers with COVID-19 showed higher prevalence in obesity or overweight (35.1% vs. 29.5%), diabetes (17.8% vs. 17.0%), chronic obstructive pulmonary disease (0.2% vs. 0.1%), respiratory distress syndrome or acute respiratory failure (1.8% vs. 0.2%). DISCUSSION: We explored the characteristics of pregnant women by different gestational weeks of SARS-CoV-2 infection with our algorithm. TED-PC is the first to infer the exact gestational week linked with every clinical event from EHR and detect the timing of SARS-CoV-2 infection in pregnant women. CONCLUSION: The algorithm shows excellent clinical validity in inferring gestational age and delivery dates, which supports multiple EHR cohorts on N3C studying the impact of COVID-19 on pregnancy.

A Versatile Biomimic Nanotemplating Fluidic Assay for Multiplex Quantitative Monitoring of Viral Respiratory Infections and Immune Responses in Saliva and Blood.

The last pandemic exposed critical gaps in monitoring and mitigating the spread of viral respiratory infections at the point-of-need. A cost-effective multiplexed fluidic device (NFluidEX), as a home-test kit analogous to a glucometer, that uses saliva and blood for parallel quantitative detection of viral infection and body's immune response in an automated manner within 11 min is proposed. The technology integrates a versatile biomimetic receptor based on molecularly imprinted polymers in a core-shell structure with nano gold electrodes, a multiplexed fluidic-impedimetric readout, built-in saliva collection/preparation, and smartphone-enabled data acquisition and interpretation. NFluidEX is validated with Influenza A H1N1 and SARS-CoV-2 (original strain and variants of concern), and achieves low detection limit in saliva and blood for the viral proteins and the anti-receptor binding domain (RBD) Immunoglobulin G (IgG) and Immunoglobulin M (IgM), respectively. It is demonstrated that nanoprotrusions of gold electrodes are essential for the fine templating of antibodies and spike proteins during molecular imprinting, and differentiation of IgG and IgM in whole blood. In the clinical setting, NFluidEX achieves 100% sensitivity and 100% specificity by testing 44 COVID-positive and 25 COVID-negative saliva and blood samples on par with the real-time quantitative polymerase chain reaction (p < 0.001, 95% confidence) and the enzyme-linked immunosorbent assay.

Analysis of Residential Segregation and Racial and Ethnic Disparities in Severe Maternal Morbidity Before and During the COVID-19 Pandemic.

Importance: Persistent racial and ethnic disparities in severe maternal morbidity (SMM) in the US remain a public health concern. Structural racism leaves women of color in a disadvantaged situation especially during COVID-19, leading to disproportionate pandemic afflictions among racial and ethnic minority women. Objective: To examine racial and ethnic disparities in SMM rates before and during the COVID-19 pandemic and whether the disparities varied with level of Black residential segregation. Design, Setting, and Participants: A statewide population-based retrospective cohort study used birth certificates linked to all-payer childbirth claims data in South Carolina. Participants included women who gave birth between January 2018 and June 2021. Data were analyzed from December 2021 to February 2022. Exposures: Exposures were (1) period when women gave birth, either before the pandemic (January 2018 to February 2020) or during the pandemic (March 2020 to June 2021) and (2) Black-White residential segregation (isolation index), categorizing US Census tracts in a county as low (<40%), medium (40%-59%), and high (≥60%). Main Outcomes and Measures: SMM was identified using International Statistical Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) codes developed by the US Centers for Disease Control and Prevention. Multilevel logistic regressions with an interrupted approach were used, adjusting for maternal-level and facility-level factors, accounting for residential county-level random effects. Results: Of 166 791 women, 95 098 (57.0%) lived in low-segregated counties (mean [SD] age, 28.1 [5.7] years; 5126 [5.4%] Hispanic; 20 523 [21.6%] non-Hispanic Black; 62 690 [65.9%] White), and 23 521 (14.1%) women (mean [SD] age, 28.1 [5.8] years; 782 [3.3%] Hispanic; 12 880 [54.8%] non-Hispanic Black; 7988 [34.0%] White) lived in high-segregated areas. Prepandemic SMM rates were decreasing, followed by monthly increasing trends after March 2020. On average, living in high-segregated communities was associated with higher odds of SMM (adjusted odds ratio [aOR], 1.61; 95% CI, 1.06-2.34). Black women regardless of residential segregation had higher odds of SMM than White women (aOR, 1.47; 95% CI, 1.11-1.96 for low-segregation; 2.12; 95% CI, 1.38-3.26 for high-segregation). Hispanic women living in low-segregated communities had lower odds of SMM (aOR, 0.48; 95% CI, 0.25-0.90) but those living in high-segregated communities had nearly twice the odds of SMM (aOR, 1.91; 95% CI, 1.07-4.17) as their White counterparts. Conclusions and Relevance: Living in high-segregated Black communities in South Carolina was associated with racial and ethnic SMM disparities. During the COVID-19 pandemic, Black vs White disparities persisted with no signs of widening gaps, whereas Hispanic vs White disparities were exacerbated. Policy reforms on reducing residential segregation or combating the corresponding structural racism are warranted to help improve maternal health.

Curating a knowledge base for individuals with coinfection of HIV and SARS-CoV-2: a study protocol of EHR-based data mining and clinical implementation.

INTRODUCTION: Despite a higher risk of severe COVID-19 disease in individuals with HIV, the interactions between SARS-CoV-2 and HIV infections remain unclear. To delineate these interactions, multicentre Electronic Health Records (EHR) hold existing promise to provide full-spectrum and longitudinal clinical data, demographics and sociobehavioural data at individual level. Presently, a comprehensive EHR-based cohort for the HIV/SARS-CoV-2 coinfection has not been established; EHR integration and data mining methods tailored for studying the coinfection are urgently needed yet remain underdeveloped. METHODS AND ANALYSIS: The overarching goal of this exploratory/developmental study is to establish an EHR-based cohort for individuals with HIV/SARS-CoV-2 coinfection and perform large-scale EHR-based data mining to examine the interactions between HIV and SARS-CoV-2 infections and systematically identify and validate factors contributing to the severe clinical course of the coinfection. We will use a nationwide EHR database in the USA, namely, National COVID Cohort Collaborative (N3C). Ultimately, collected clinical evidence will be implemented and used to pilot test a clinical decision support prototype to assist providers in screening and referral of at-risk patients in real-world clinics. ETHICS AND DISSEMINATION: The study was approved by the institutional review boards at the University of South Carolina (Pro00121828) as non-human subject study. Study findings will be presented at academic conferences and published in peer-reviewed journals. This study will disseminate urgently needed clinical evidence for guiding clinical practice for individuals with the coinfection at Prisma Health, a healthcare system in collaboration.

Changes in inpatient admissions before and during COVID-19 outbreak in a large tertiary hospital in Shanghai.

Background: The coronavirus disease 2019 (COVID-19) outbreak caused a significant strain on healthcare resources and utilization worldwide. However, the impact of COVID-19 outbreak on patient hospitalization was barely known. This study aimed to determine the impact of the outbreak on the pattern of inpatient hospital admissions to help allocate health care resources during a pandemic. Methods: This retrospective study included patients who were hospitalized in a tertiary teaching hospital in Shanghai between 1 January and 30 April across the years 2017 to 2020. The number of hospitalizations during the study period from 2017 to 2020 were 30,605, 31,464, 32,812 and 24,163, respectively. Changes in patient volumes and the frequency of the International Classification of Diseases and Related Health Problem Tenth Edition (ICD-10) codes before and after the onset of the COVID-19 outbreak were analyzed and presented as absolute and relative differences with 95% confidence intervals between periods of different years. Results: Overall inpatient hospital admissions decreased by 26.35% between January and April 2020, compared to the same period in 2019. The average age of patients in 2020 was higher compared to those from 2017 to 2019. Conversely, the proportions of self-paying patients and non-local patients were significantly lower between January and April 2020 compared to the same period in the previous three years. The top five ICD-10 codes remained common before and during the pandemic. Admissions associated with antineoplastic radiation therapy, chemotherapy, and immunotherapy increased in frequency and proportion by 2020 (difference, 5.6%, 95% CI: 4.4% to 6.8%), and increased proportions were observed for liver and intrahepatic bile duct malignancies (2.18%, 95% CI: 1.15% to 3.21%), cerebral infarction (2.27%, 95% CI: 0.54% to 4.00%), and chronic kidney disease (3.56%, 95% CI: 1.79% to 5.33%). Conclusions: There was a significant reduction in the number of inpatients and a marked change in admission diagnoses during the COVID-19 outbreak. Our findings are useful for making informed decisions on hospital management and reallocation of available health care resources during a pandemic.

Human KIR+CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19 (preprint)

Previous reports show that Ly49+CD8+ T cells can suppress autoimmunity in mouse models of autoimmune diseases. Here we find a markedly increased frequency of CD8+ T cells expressing inhibitory Killer cell Immunoglobulin like Receptors (KIR), the human equivalent of the Ly49 family, in the blood and inflamed tissues of various autoimmune diseases. Moreover, KIR+CD8+ T cells can efficiently eliminate pathogenic gliadin-specific CD4+ T cells from Celiac disease (CeD) patients' leukocytes in vitro. Furthermore, we observe elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 and influenza-infected patients, and this correlates with disease severity and vasculitis in COVID-19. Expanded KIR+CD8+ T cells from these different diseases display shared phenotypes and similar T cell receptor sequences. These results characterize a regulatory CD8+ T cell subset in humans, broadly active in both autoimmune and infectious diseases, which we hypothesize functions to control self-reactive or otherwise pathogenic T cells.

Post-vaccination SARS-COV-2 among healthcare workers in New Jersey: a genomic epidemiological study (preprint)

ABSTRACT Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called Variants of Concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated healthcare professionals (HCP). Our post-vaccination COVID-19 symptoms-based surveillance program among HCPs in a 17-hospital network, identified all vaccinated HCP who tested positive for COVID-19 after routine screening or after self-reporting. From 01/01/2021 to 04/30/2021, 23,687 HCP received either mRNA-1273 or BNT162b2 mRNA vaccine. All available post-vaccination SARS-CoV-2 samples and a random collection from non-vaccinated patients during the similar timeframe were subjected to VOC screening and whole genome sequencing (WGS). 62% (23,697/37,500) of HCPs received at least one vaccine dose, with 95% (22,458) fully vaccinated. We detected 138 (0.58%, 138/23,697) COVID-19 cases, 105 among partially vaccinated and 33 (0.15%, 33/22,458) among fully vaccinated. Five partially vaccinated required hospitalization, four with supplemental oxygen. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; concurrent non-vaccinated samples was 37% (523/1404) and 20% (284/1394), respectively. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). WGS analysis from vaccinated and non-vaccinated individuals indicated highly congruent phylogenies. We did not detect an increased frequency of any RBD/NTD polymorphism between groups (P>0.05). Our results support robust protection by vaccination, particularly among recipients of both doses. Despite VOCs accounting for over 40% of SARS-CoV-2 from fully vaccinated individuals, the genomic diversity appears to proportionally represent those among non-vaccinated populations. IMPORTANCE A number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants, with high transmission potential and immune evasion properties, the so-called Variants of Concern (VOC), continues to be a major concern. Whether these VOCs alter the efficacy of the administered vaccines is of great concern, and a critical question to study. We describe the initial genomic epidemiology of SARS-CoV-2 recovered from vaccinated healthcare professionals and probe specifically for VOC enrichment. Our findings support the high-level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the non-vaccinated population. Thus, we do not find evidence of VOC enrichment among vaccinated groups. Overall, the genomic diversity of SARS-CoV-2 recovered post-vaccination appears to proportionally represent the observed viral diversity within the community.

CD147 antibody specifically and effectively inhibits infection and cytokine storm of SARS-CoV-2 variants (preprint)

SARS-CoV-2 and its variants are raging worldwide. Unfortunately, the global vaccination is not efficient enough to attain a vaccine-based herd-immunity and yet no special and effective drug is developed to contain the spread of the disease. Previously we have identified CD147 as a novel receptor for SARS-CoV-2 infection. Here, we demonstrated that CD147 antibody effectively inhibits infection and cytokine storm caused by SARS-CoV-2 variants. In CD147KO VeroE6 cells, infections of SARS-CoV-2, its variants (B.1.1.7, B.1.351) and pseudovirus mutants (B.1.1.7, B.1.351, B.1.525, B.1.526 (S477N), B.1.526 (E484K), P.1, P.2, B.1.617.1, B.1.617.2) were decreased. Meanwhile, CD147 antibody effectively blocked the entry of variants and pseudomutants in VeroE6 cells, and inhibited the expression of cytokines. A model of SARS-CoV-2-infected hCD147 transgenic mice was constructed, which recapitulated the features of exudative diffuse alveolar damage and dynamic immune responses of COVID-19. CD147 antibody could effectively clear the virus and alveolar exudation, resolving the pneumonia. We found the elevated level of cyclophilin A (CyPA) in plasma of severe/critical cases, and identified CyPA as the most important proinflammatory intermediate causing cytokine storm. Mechanistically, spike protein of SARS-CoV-2 bound to CD147 and initiated the JAK-STAT pathway, which induced expression of CyPA. CyPA reciprocally bound to CD147, triggered MAPK pathway and consequently mediated the expression of cytokine and chemokine. In conclusion, CD147 is a critical target for SARS-CoV-2 variants and CD147 antibody is a promising drug to control the new wave of COVID-19 epidemic.

Emergence of multiple SARS-CoV-2 antibody escape variants in an immunocompromised host undergoing convalescent plasma treatment (preprint)

SARS-CoV-2 Variants of Concerns (VOC), e.g., B.1.351 (20H/501Y.V2) and P1 (20J/501Y.V3), harboring N-terminal domain (NTD) or the receptor-binding domain (RBD) (e.g., E484K) mutations, exhibit reduced in vitro susceptibility to convalescent serum, commercial antibody cocktails, and vaccine neutralization, and have been associated with reinfection. The accumulation of these mutations could be the consequence of intra-host viral evolution due to prolonged infection in immunocompromised hosts. In this study, we document the microevolution of SARS-CoV-2 recovered from sequential tracheal aspirates from an immunosuppressed patient on tacrolimus, steroids and convalescent plasma therapy, and identify the emergence of multiple NTD and RBD mutations associated with reduced antibody neutralization as early as three weeks after infection. SARS-CoV-2 genomes from the first swab (Day 0) and three tracheal aspirates (Day 7, 21 and 27) were compared at the sequence level. We identified five different S protein mutations at the NTD or RBD regions from the second tracheal aspirate sample (21 Day). The S:Q493R substitution and S:243-244LA deletion had ~70% frequency, while ORF1a:A138T, S:141-144LGVY deletion, S:E484K and S:Q493K substitutions demonstrated ~30%, ~30%, ~20% and ~10% mutation frequency, respectively. However, the third tracheal aspirate sample collected one week later (Day 27) was predominated by the haplotype of ORF1a:A138T, S:141-144LGVY deletion and S:E484K (> 95% mutation frequency). Notably, S protein deletions (141-144LGVY and 243-244LA deletions in NTD region) and substitutions (Q493K/R and E484K in the RBD region) previously showed reduced susceptibly to monoclonal antibody or convalescent plasma. The observation supports the hypothesis that VOCs can independently arise and that immunocompromised patients on convalescent plasma therapy are potential breeding grounds for immune-escape mutants.

A Novel Diagnostic Test to Screen SARS-CoV-2 Variants Containing E484K and N501Y Mutations (preprint)

Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility. While the concerning variants are fast spreading in various geographical areas, identification and monitoring of these variants is lagging far behind, due in large part to the slow speed and insufficient capacity of viral sequencing. In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report. Using this tool, we screened a total of 435 clinical NS samples collected from COVID patients at 8 hospitals within the Hackensack Meridian Health network in New Jersey. While B.1.351 and P.1 variants were absent from the current study, our data revealed a dramatic increase in the frequency of E484K over time, underscoring the need for continuous epidemiological monitoring.