Investigation of the Host Kinome Response to Coronavirus Infection Reveals PI3K/mTOR Inhibitors as Betacoronavirus Antivirals.

Host kinases play essential roles in the host cell cycle, innate immune signaling, the stress response to viral infection, and inflammation. Previous work has demonstrated that coronaviruses specifically target kinase cascades to subvert host cell responses to infection and rely upon host kinase activity to phosphorylate viral proteins to enhance replication. Given the number of kinase inhibitors that are already FDA approved to treat cancers, fibrosis, and other human disease, they represent an attractive class of compounds to repurpose for host-targeted therapies against emerging coronavirus infections. To further understand the host kinome response to betacoronavirus infection, we employed multiplex inhibitory bead mass spectrometry (MIB-MS) following MERS-CoV and SARS-CoV-2 infection of human lung epithelial cell lines. Our MIB-MS analyses revealed activation of mTOR and MAPK signaling following MERS-CoV and SARS-CoV-2 infection, respectively. SARS-CoV-2 host kinome responses were further characterized using paired phosphoproteomics, which identified activation of MAPK, PI3K, and mTOR signaling. Through chemogenomic screening, we found that clinically relevant PI3K/mTOR inhibitors were able to inhibit coronavirus replication at nanomolar concentrations similar to direct-acting antivirals. This study lays the groundwork for identifying broad-acting, host-targeted therapies to reduce betacoronavirus replication that can be rapidly repurposed during future outbreaks and epidemics. The proteomics, phosphoproteomics, and MIB-MS datasets generated in this study are available in the Proteomics Identification Database (PRIDE) repository under project identifiers PXD040897 and PXD040901.

Neurological and neuropsychological sequelae of Zika virus infection in children in León, Nicaragua.

Objectives: To describe the presence and persistence of neurological and neuropsychological sequelae among children with acquired Zika virus infection and assess whether those sequelae were more common in children infected with Zika virus compared to uninfected children. Methods: We conducted a prospective cohort study of children with and without Zika virus infection in León, Nicaragua, using a standard clinical assessment tool and questionnaire to collect data on symptoms at three visits, about 6 months apart, and a battery of standardized instruments to evaluate neurocognitive function, behavior, depression, and anxiety at the last two visits. Results: Sixty-two children were enrolled, with no significant differences in demographics by infection group. Children infected with Zika virus had a range of neurological symptoms, some of which persisted for 6 to 12 months; however, no consistent pattern of symptoms was observed. At baseline a small percentage of children infected with Zika virus had an abnormal finger-to-nose test (13%), cold touch response (13%), and vibration response (15%) versus 0% in the uninfected group. Neurocognitive deficits and behavioral problems were common in both groups, with no significant differences between the groups. Children infected with Zika virus had lower cognitive efficiency scores at the 6-month visit. Anxiety and depression were infrequent in both groups. Conclusions: Larger studies are needed to definitively investigate the relationship between Zika virus infection and neurological symptoms and neurocognitive problems, with adjustment for factors affecting cognition and behavior, including mood and sleep disorders, home learning environment, history of neuroinvasive infections, and detailed family history of neuropsychological problems.

Neurological and neuropsychological sequelae of Zika virus infection in children in León, Nicaragua

[ABSTRACT]. Objectives. To describe the presence and persistence of neurological and neuropsychological sequelae among children with acquired Zika virus infection and assess whether those sequelae were more common in children infected with Zika virus compared to uninfected children. Methods. We conducted a prospective cohort study of children with and without Zika virus infection in León, Nicaragua, using a standard clinical assessment tool and questionnaire to collect data on symptoms at three visits, about 6 months apart, and a battery of standardized instruments to evaluate neurocognitive function, behavior, depression, and anxiety at the last two visits. Results. Sixty-two children were enrolled, with no significant differences in demographics by infection group. Children infected with Zika virus had a range of neurological symptoms, some of which persisted for 6 to 12 months; however, no consistent pattern of symptoms was observed. At baseline a small percentage of children infected with Zika virus had an abnormal finger-to-nose test (13%), cold touch response (13%), and vibration response (15%) versus 0% in the uninfected group. Neurocognitive deficits and behavioral problems were common in both groups, with no significant differences between the groups. Children infected with Zika virus had lower cognitive efficiency scores at the 6-month visit. Anxiety and depression were infrequent in both groups. Conclusions. Larger studies are needed to definitively investigate the relationship between Zika virus infec- tion and neurological symptoms and neurocognitive problems, with adjustment for factors affecting cognition and behavior, including mood and sleep disorders, home learning environment, history of neuroinvasive infec- tions, and detailed family history of neuropsychological problems.

[RESUMEN]. Objetivos. Describir la presencia y persistencia de secuelas neurológicas y neuropsicológicas en pacientes pediátricos que contrajeron la infección por el virus del Zika y evaluar si dichas secuelas fueron más comunes en los infectados con el virus del Zika en comparación con los no infectados. Métodos. Se realizó un estudio de cohorte prospectivo en pacientes pediátricos con y sin infección por el virus del Zika en León (Nicaragua), con una herramienta de evaluación clínica estándar y un cuestionario para recopilar datos sobre los síntomas en tres visitas, con aproximadamente seis meses de diferencia, y un con- junto de instrumentos estandarizados para evaluar la función neurocognitiva, el comportamiento, la depresión y la ansiedad en las últimas dos visitas. Resultados. Participaron 62 niños y niñas sin diferencias significativas en la demografía por grupo de infección. Los participantes infectados con el virus del Zika mostraron una variedad de síntomas neurológi- cos, algunos de los cuales persistieron entre 6 y 12 meses; no obstante, no se observó un patrón sistemático en los síntomas. Al inicio del estudio, un pequeño porcentaje de participantes infectados con el virus del Zika mostró resultados anormales a las pruebas dedo-nariz (13%), respuesta al tacto (frío) (13%) y respuesta a la vibración (15%), frente a un 0% en el grupo no infectado. Los déficits neurocognitivos y los problemas de comportamiento fueron comunes en ambos grupos, sin diferencias significativas entre los grupos. Los partic- ipantes infectados con el virus del Zika mostraron puntuaciones de eficiencia cognitiva más bajas en la visita a los 6 meses. La ansiedad y la depresión fueron poco frecuentes en ambos grupos. Conclusiones. Son necesarios estudios más amplios para investigar definitivamente la relación entre la infec- ción por el virus del Zika y los síntomas neurológicos y los problemas neurocognitivos, haciendo ajustes para los factores relacionados con la cognición y el comportamiento, incluidos los trastornos del estado de ánimo y el sueño, el entorno de aprendizaje en el hogar, los antecedentes de infecciones neuroinvasivas y los antecedentes familiares detallados de problemas neuropsicológicos.

[RESUMO]. Objetivos. Descrever a presença e a persistência de sequelas neurológicas e neuropsicológicas em crianças com infecção pelo vírus zika e avaliar se essas sequelas foram mais comuns em crianças infectadas pelo vírus zika em comparação com crianças não infectadas. Métodos. Realizamos um estudo de coorte prospectivo em crianças com e sem infecção pelo vírus zika em León, Nicarágua, usando uma ferramenta de avaliação clínica padrão e um questionário para coletar dados de sintomas em três consultas, com cerca de 6 meses de intervalo, além de um conjunto de ferramentas padronizadas para avaliar função neurocognitiva, comportamento, depressão e ansiedade nas duas últimas consultas. Resultados. Foram incluídas 62 crianças, sem diferenças significativas nas características demográficas por grupo de infecção. As crianças infectadas pelo vírus zika tinham uma gama de sintomas neurológicos, alguns dos quais persistiram por 6 a 12 meses. Entretanto, não se observou nenhum padrão consistente de sintomas. No início do estudo, uma pequena porcentagem de crianças infectadas com o vírus zika apresen- tou resultado anormal na prova índex-nariz (13%), resposta ao toque frio (13%) e sensibilidade vibratória (15%), em comparação a 0% no grupo não infectado. Déficits neurocognitivos e problemas comportamentais foram frequentes em ambos os grupos, mas sem diferenças significativas entre eles. As crianças infectadas com o vírus zika tiveram resultados mais baixos de eficiência cognitiva na consulta de 6 meses. Ansiedade e depressão não foram observadas com frequência em ambos os grupos. Conclusões. São necessários estudos mais amplos para investigar a relação exata entre a infecção pelo vírus zika e sintomas neurológicos e problemas neurocognitivos, com ajuste para fatores que afetam a cog- nição e o comportamento, incluindo distúrbios do humor e do sono, ambiente de aprendizagem em casa, história de infecções neuroinvasivas e história familiar detalhada de problemas neuropsicológicos.

Outcomes of convalescent plasma with defined high- versus lower-neutralizing antibody titers against SARS-CoV-2 among hospitalized patients: CoronaVirus Inactivating Plasma (CoVIP), double-blind phase 2 study.

BackgroundCOVID-19 Convalescent Plasma (CCP) was an early and widely adopted putative therapy for severe COVID-19. Results from randomized control trials and observational studies have failed to demonstrate a clear therapeutic role for CCP for severe SARS-CoV-2 infection. Underlying these inconclusive findings is a broad heterogeneity in the concentrations of neutralizing antibodies (nAb) between different CCP donors. The present study was designed to evaluate nAb titer threshold for clinically effective CCP. MethodsWe conducted a double-blind, phase 2 study to evaluate the safety and effectiveness of nAb titer-defined CCP in adults admitted to an academic referral hospital. Patients positive on a SARS-CoV-2 nucleic acid amplification test and with symptoms for < 10 days were eligible. Participants received either CCP with nAb titers [≥]1:160-1:640 (standard titer group) or >1:640 (high titer group) in addition to standard of care treatments. Adverse events were contrasted by CCP titer. The primary clinical outcome was time to hospital discharge, with mortality and respiratory support evaluated as secondary outcomes. FindingsBetween August 28 and December 4, 2020, 316 participants were screened, 55 received CCP, with 41 and 14 receiving standard versus high titer CCP, respectively. Participants were a median of 61 years of age (IQR 52-67), 36% women, 25% Black and 33% Hispanic. Severe adverse events (SAE) ([≥] grade 3) occurred in 4 (29%) and 23 (56%) of participants in the high versus standard titer groups, respectively by day 28 (Risk Difference -0.28 [95% CI -0.56, 0.01]). There were no observed treatment-related AEs. By day 55, time to hospital discharge was shorter among participants receiving high versus standard titer, accounting for death as a competing event (hazard ratio 1.94 [95% CI 1.05, 3.58], Grays p=0.02). InterpretationIn this phase 2 trial in a high-risk population of patients admitted for Covid-19, we found earlier time to hospital discharge and lower occurrences of life-threatening SAEs among participants receiving CCP with nAb titers >1:640 compared with participants receiving CCP with lower nAb titer CCP. Though limited by a small study size these findings support further study of high-nAb titer CCP defined as >1:640 in the treatment of COVID-19. FundingThis clinical study was supported by the UNC Health Foundation and the North Carolina Policy Collaboratory at the University of North Carolina at Chapel Hill with funding from the North Carolina Coronavirus Relief Fund established and appropriated by the North Carolina General Assembly. The laboratory assays for neutralizing antibody titers and SARS-CoV-2 specific antibody-binding assays were partially supported by The NIH NCI/NIAID SeroNet Serocenter of Excellence Award U54 CA260543. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSCOVID-19 Convalescent Plasma (CCP) has emergency use authorization from the FDA for early treatment of COVID-19 in either outpatient or inpatient settings. Evidence supporting the use of CCP for severe COVID-19 is mixed and still emerging. One major limitation in interpreting published clinical trials and the clinical role of CCP is incomplete understanding of necessary neutralizing antibody (nAb) titer for clinically effective CCP. Observational studies suggest that higher antibody-content CCP is more effective than lower antibody-content CCP, or that very low antibody-content CCP is harmful. We searched PubMed articles published between February 1, 2020, and April 15, 2022, using the terms "COVID-19", "convalescent plasma", "SARS-CoV-2", and "CCP" alone and in combination. Our search yielded 6,468 results which we filtered to 280 and 162 by selecting Clinical Trial and Randomized Controlled Trial article types, respectively. Among these, we identified 25 open-label or blinded efficacy or effectiveness studies in hospitalized patients that were relevant to our study. Preliminary reports show wide variability in the antibody content of CCP used in clinical trials, the assays used to define CCP antibody content, and the estimates of clinical outcomes following CCP therapy for hospitalized patients. Only one study deliberately infused CCP with nAb > 1:640. Post-hoc analyses of potent monoclonal antibody therapy in hospitalized patients in the UK showed survival benefit when monoclonal antibody was infused to patients who had not yet seroconverted by spike antibody ELISA, suggesting that if dosed appropriately, antibody-based therapies may have a role in improving outcomes of severe COVID-19. Added value of this studyThis phase 2 study showed that CCP with high nAb titer (>1:640) provided more rapid recovery to hospital discharge and fewer COVID-19 attributable AEs than CCP with nAb titer between the FDA-recommended minimum standard and 4-fold higher ([≥]1:160-1:640). The hazard ratio of time to hospital discharge from baseline through day 55, accounting for death as a competing event, contrasting patients receiving high versus standard CCP titer was 1.94 (95% CI 1.05-3.58). Adjusted hazard ratios of high versus standard titer CCP receipt for time to hospital discharge were consistent with the primary unadjusted findings. Mortality through 55 days was lower in the high titer group, but with a wide confidence interval that did not reach statistical significance. Implications of all available evidenceOur data that CCP with nAb >1:640 expedites recovery of patients admitted with COVID-19 compared with CCP with nAb [≥]1:160-1:640 suggests that a threshhold of nAb [≥]1:160 may be too low to define CCP as high titer. Analyses in larger CCP trials should consider full reporting of nAb in CCP units administered at individual study participant level, and specifically whether CCP contained nAb >1:640. Further investigation of CCP with nAb >1:640 is warranted given that raising the threshhold of nAb, or a correlative specific anti-spike antibody assay, used to qualify high titer CCP in clinical trials could inform policy guidance and clinical use of CCP.

Immunological memory to Common Cold Coronaviruses assessed longitudinally over a three-year period

Understanding immune memory to Common Cold Coronaviruses (CCCs) is relevant for assessing its potential impact on the outcomes of SARS-CoV-2 infection, and for the prospects of pan-corona vaccines development. We performed a longitudinal analysis, of pre-pandemic samples collected from 2016-2019. CD4+ T cells and antibody responses specific for CCC and to other respiratory viruses, and chronic or ubiquitous pathogens were assessed. CCC-specific memory CD4+ T cells were detected in most subjects, and their frequencies were comparable to those for other common antigens. Notably, responses to CCC and other antigens such as influenza and Tetanus Toxoid (TT) were sustained over time. CCC-specific CD4+ T cell responses were also associated with low numbers of HLA-DR+CD38+ cells and their magnitude did not correlate with yearly changes in the prevalence of CCC infections. Similarly, spike RBD-specific IgG responses for CCC were stable throughout the sampling period. Finally, high CD4+ T cell reactivity to CCC, but not antibody responses, was associated with high pre-existing SARS-CoV-2 immunity. Overall, these results suggest that the steady and sustained CCC responses observed in the study cohort are likely due to a relatively stable pool of CCC-specific memory CD4+ T cells instead of fast decaying responses and frequent reinfections.

The Serological Sciences Network (SeroNet) for COVID-19: Depth and Breadth of Serology Assays and Plans for Assay Harmonization

BackgroundIn October 2020, the National Cancer Institute (NCI) Serological Sciences Network (SeroNet) was established to study the immune response to COVID-19, and "to develop, validate, improve, and implement serological testing and associated technologies." SeroNet is comprised of 25 participating research institutions partnering with the Frederick National Laboratory for Cancer Research (FNLCR) and the SeroNet Coordinating Center. Since its inception, SeroNet has supported collaborative development and sharing of COVID-19 serological assay procedures and has set forth plans for assay harmonization. MethodsTo facilitate collaboration and procedure sharing, a detailed survey was sent to collate comprehensive assay details and performance metrics on COVID-19 serological assays within SeroNet. In addition, FNLCR established a protocol to calibrate SeroNet serological assays to reference standards, such as the U.S. SARS-CoV-2 serology standard reference material and First WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin (20/136), to facilitate harmonization of assay reporting units and cross-comparison of study data. ResultsSeroNet institutions reported development of a total of 27 ELISA methods, 13 multiplex assays, 9 neutralization assays, and use of 12 different commercial serological methods. FNLCR developed a standardized protocol for SeroNet institutions to calibrate these diverse serological assays to reference standards. ConclusionsSeroNet institutions have established a diverse array of COVID-19 serological assays to study the immune response to SARS-CoV-2 virus and vaccines. Calibration of SeroNet serological assays to harmonize results reporting will facilitate future pooled data analyses and study cross-comparisons.

Neurological and neuropsychological sequelae of Zika virus infection in children in León, Nicaragua / Secuelas neurológicas y neuropsicológicas de la infección por el virus del Zika en niños y niñas en León, Nicaragua / Sequelas neurológicas e neuropsicológicas da infecção pelo vírus zika em crianças em León, Nicarágua

ABSTRACT Objectives. To describe the presence and persistence of neurological and neuropsychological sequelae among children with acquired Zika virus infection and assess whether those sequelae were more common in children infected with Zika virus compared to uninfected children. Methods. We conducted a prospective cohort study of children with and without Zika virus infection in León, Nicaragua, using a standard clinical assessment tool and questionnaire to collect data on symptoms at three visits, about 6 months apart, and a battery of standardized instruments to evaluate neurocognitive function, behavior, depression, and anxiety at the last two visits. Results. Sixty-two children were enrolled, with no significant differences in demographics by infection group. Children infected with Zika virus had a range of neurological symptoms, some of which persisted for 6 to 12 months; however, no consistent pattern of symptoms was observed. At baseline a small percentage of children infected with Zika virus had an abnormal finger-to-nose test (13%), cold touch response (13%), and vibration response (15%) versus 0% in the uninfected group. Neurocognitive deficits and behavioral problems were common in both groups, with no significant differences between the groups. Children infected with Zika virus had lower cognitive efficiency scores at the 6-month visit. Anxiety and depression were infrequent in both groups. Conclusions. Larger studies are needed to definitively investigate the relationship between Zika virus infection and neurological symptoms and neurocognitive problems, with adjustment for factors affecting cognition and behavior, including mood and sleep disorders, home learning environment, history of neuroinvasive infections, and detailed family history of neuropsychological problems.

RESUMEN Objetivos. Describir la presencia y persistencia de secuelas neurológicas y neuropsicológicas en pacientes pediátricos que contrajeron la infección por el virus del Zika y evaluar si dichas secuelas fueron más comunes en los infectados con el virus del Zika en comparación con los no infectados. Métodos. Se realizó un estudio de cohorte prospectivo en pacientes pediátricos con y sin infección por el virus del Zika en León (Nicaragua), con una herramienta de evaluación clínica estándar y un cuestionario para recopilar datos sobre los síntomas en tres visitas, con aproximadamente seis meses de diferencia, y un conjunto de instrumentos estandarizados para evaluar la función neurocognitiva, el comportamiento, la depresión y la ansiedad en las últimas dos visitas. Resultados. Participaron 62 niños y niñas sin diferencias significativas en la demografía por grupo de infección. Los participantes infectados con el virus del Zika mostraron una variedad de síntomas neurológicos, algunos de los cuales persistieron entre 6 y 12 meses; no obstante, no se observó un patrón sistemático en los síntomas. Al inicio del estudio, un pequeño porcentaje de participantes infectados con el virus del Zika mostró resultados anormales a las pruebas dedo-nariz (13%), respuesta al tacto (frío) (13%) y respuesta a la vibración (15%), frente a un 0% en el grupo no infectado. Los déficits neurocognitivos y los problemas de comportamiento fueron comunes en ambos grupos, sin diferencias significativas entre los grupos. Los participantes infectados con el virus del Zika mostraron puntuaciones de eficiencia cognitiva más bajas en la visita a los 6 meses. La ansiedad y la depresión fueron poco frecuentes en ambos grupos. Conclusiones. Son necesarios estudios más amplios para investigar definitivamente la relación entre la infección por el virus del Zika y los síntomas neurológicos y los problemas neurocognitivos, haciendo ajustes para los factores relacionados con la cognición y el comportamiento, incluidos los trastornos del estado de ánimo y el sueño, el entorno de aprendizaje en el hogar, los antecedentes de infecciones neuroinvasivas y los antecedentes familiares detallados de problemas neuropsicológicos.

RESUMO Objetivos. Descrever a presença e a persistência de sequelas neurológicas e neuropsicológicas em crianças com infecção pelo vírus zika e avaliar se essas sequelas foram mais comuns em crianças infectadas pelo vírus zika em comparação com crianças não infectadas. Métodos. Realizamos um estudo de coorte prospectivo em crianças com e sem infecção pelo vírus zika em León, Nicarágua, usando uma ferramenta de avaliação clínica padrão e um questionário para coletar dados de sintomas em três consultas, com cerca de 6 meses de intervalo, além de um conjunto de ferramentas padronizadas para avaliar função neurocognitiva, comportamento, depressão e ansiedade nas duas últimas consultas. Resultados. Foram incluídas 62 crianças, sem diferenças significativas nas características demográficas por grupo de infecção. As crianças infectadas pelo vírus zika tinham uma gama de sintomas neurológicos, alguns dos quais persistiram por 6 a 12 meses. Entretanto, não se observou nenhum padrão consistente de sintomas. No início do estudo, uma pequena porcentagem de crianças infectadas com o vírus zika apresentou resultado anormal na prova índex-nariz (13%), resposta ao toque frio (13%) e sensibilidade vibratória (15%), em comparação a 0% no grupo não infectado. Déficits neurocognitivos e problemas comportamentais foram frequentes em ambos os grupos, mas sem diferenças significativas entre eles. As crianças infectadas com o vírus zika tiveram resultados mais baixos de eficiência cognitiva na consulta de 6 meses. Ansiedade e depressão não foram observadas com frequência em ambos os grupos. Conclusões. São necessários estudos mais amplos para investigar a relação exata entre a infecção pelo vírus zika e sintomas neurológicos e problemas neurocognitivos, com ajuste para fatores que afetam a cognição e o comportamento, incluindo distúrbios do humor e do sono, ambiente de aprendizagem em casa, história de infecções neuroinvasivas e história familiar detalhada de problemas neuropsicológicos.

Vandetanib Reduces Inflammatory Cytokines and Ameliorates COVID-19 in Infected Mice

The portfolio of SARS-CoV-2 small molecule drugs is currently limited to a handful that are either approved (remdesivir), emergency approved (dexamethasone, baricitinib) or in advanced clinical trials. We have tested 45 FDA-approved kinase inhibitors in vitro against murine hepatitis virus (MHV) as a model of SARS-CoV-2 replication and identified 12 showing inhibition in the delayed brain tumor (DBT) cell line. Vandetanib, which targets the vascular endothelial growth factor receptor (VEGFR), the epidermal growth factor receptor (EGFR), and the RET-tyrosine kinase showed the most promising results on inhibition versus toxic effect on SARS-CoV-2-infected Caco-2 and A549-hACE2 cells (IC50 0.79 M) while also showing a reduction of > 3 log TCID50/mL for HCoV-229E. The in vivo efficacy of vandetanib was assessed in a mouse model of SARS-CoV-2 infection and statistically significantly reduced the levels of IL-6, IL-10, TNF-, and mitigated inflammatory cell infiltrates in the lungs of infected animals but did not reduce viral load. Vandetanib rescued the decreased IFN-1{beta} caused by SARS-CoV-2 infection in mice to levels similar to that in uninfected animals. Our results indicate that the FDA-approved vandetanib is a potential therapeutic candidate for COVID-19 positioned for follow up in clinical trials either alone or in combination with other drugs to address the cytokine storm associated with this viral infection.

A prospective study of asymptomatic SARS-CoV-2 infection among individuals involved in academic research under limited operations during the COVID-19 pandemic

BackgroundEarly in the pandemic, transmission risk from asymptomatic infection was unclear making it imperative to monitor infection in workplace settings. Further, data on SARS-CoV-2 seroprevalence within university populations has been limited. MethodsWe performed a longitudinal study of University research employees on campus July-December 2020. We conducted questionnaires on COVID-19 risk factors, RT-PCR testing, and SARS-CoV-2 serology using an in-house spike RBD assay, laboratory-based Spike NTD assay, and standard nucleocapsid platform assay. We estimated prevalence and cumulative incidence of seroconversion with 95% confidence intervals using the inverse of the Kaplan-Meier estimator. Results910 individuals were included in this analysis. At baseline, 6.2% (95% CI 4.29-8.19) were seropositive using the spike RBD assay; four (0.4%) were seropositive using the nucleocapsid assay, and 44 (4.8%) using the Spike NTD assay. Cumulative incidence was 3.61% (95% CI: 2.04-5.16). Six asymptomatic individuals had positive RT-PCR results. ConclusionsPrevalence and incidence of SARS-CoV-2 infections was low; however differences in target antigens of serological tests provided different estimates. Future research on appropriate methods of serological testing in unvaccinated and vaccinated populations is needed. Frequent RT-PCR testing of asymptomatic individuals is required to detect acute infections, and repeated serosurveys are beneficial for monitoring subclinical infection.

Machine Learning Models Identify Inhibitors of SARS-CoV-2.

With the rapidly evolving SARS-CoV-2 variants of concern, there is an urgent need for the discovery of further treatments for the coronavirus disease (COVID-19). Drug repurposing is one of the most rapid strategies for addressing this need, and numerous compounds have already been selected for in vitro testing by several groups. These have led to a growing database of molecules with in vitro activity against the virus. Machine learning models can assist drug discovery through prediction of the best compounds based on previously published data. Herein, we have implemented several machine learning methods to develop predictive models from recent SARS-CoV-2 in vitro inhibition data and used them to prioritize additional FDA-approved compounds for in vitro testing selected from our in-house compound library. From the compounds predicted with a Bayesian machine learning model, lumefantrine, an antimalarial was selected for testing and showed limited antiviral activity in cell-based assays while demonstrating binding (Kd 259 nM) to the spike protein using microscale thermophoresis. Several other compounds which we prioritized have since been tested by others and were also found to be active in vitro. This combined machine learning and in vitro testing approach can be expanded to virtually screen available molecules with predicted activity against SARS-CoV-2 reference WIV04 strain and circulating variants of concern. In the process of this work, we have created multiple iterations of machine learning models that can be used as a prioritization tool for SARS-CoV-2 antiviral drug discovery programs. The very latest model for SARS-CoV-2 with over 500 compounds is now freely available at www.assaycentral.org.

Clinical and Epidemiological Features of Acute Zika Virus Infections in León, Nicaragua.

The American Zika virus (ZIKV) epidemic has highlighted the need to gain a better understanding of this emerging virus. The goal of this study was to describe the clinical symptoms, laboratory findings, and risk factors for symptomatic ZIKV infection in an area with ongoing transmission of other arboviral infections. We recruited patients at least 2 years of age seeking care at public health centers in León, Nicaragua, between January 2016 and August 2017, for fever, maculopapular rash, and/or nonsuppurative conjunctivitis with a duration of less than 1 week. A laboratory diagnosis of ZIKV was established using a combination of molecular and serological tests. Clinical and laboratory findings and potential risk factors were compared between participants with and without acute ZIKV infection. Fifty-eight (26%) of the 225 participants included in the analysis were found to have acute ZIKV infection. Pregnancy and reports of previous arboviral infection were associated with a higher risk of ZIKV infection. Rash, conjunctivitis, sore throat, and lower absolute neutrophil counts were associated with acute ZIKV infection. The clinical characteristics and risk factors identified were consistent with those identified by previous studies; however, we found sore throat to be a feature of ZIKV infection. We also found that neutrophil counts were lower in ZIKV-infected subjects. These clinical symptoms and laboratory data may help clinicians suspect ZIKV infection during future outbreaks.

SARS-CoV-2 mRNA Vaccine Induces Robust Specific and Cross-reactive IgG and Unequal Strain-specific Neutralizing Antibodies in Naïve and Previously Infected Recipients

With the advance of SARS-CoV-2 vaccines, the outlook for overcoming the global COVID-19 pandemic has improved. However, understanding of immunity and protection offered by the SARS-CoV-2 vaccines against circulating variants of concern (VOC) is rapidly evolving. We investigated the mRNA vaccine-induced antibody responses against the referent WIV04 (Wuhan) strain, circulating variants, and human endemic coronaviruses in 168 naive and previously infected people at three-time points. Samples were collected prior to vaccination, after the first and after the second doses of one of the two available mRNA-based vaccines. After full vaccination, both naive and previously infected participants developed comparable robust SARS-CoV-2 specific spike IgG levels, modest IgM and IgA binding antibodies, and varying degrees of HCoV cross-reactive antibodies. However, the strength and frequency of neutralizing antibodies produced in naive people were significantly lower than in the previously infected group. We also found that 1/3rd of previously infected people had undetectable neutralizing antibodies after the first vaccine dose; 40% of this group developed neutralizing antibodies after the second dose. In all subjects neutralizing antibodies produced against the B.1.351 and P.1 variants were weaker than those produced against the reference and B.1.1.7 strains. Our findings provide support for future booster vaccinations modified to be active against the circulating variants.

SARS-CoV-2 infectious virus, viral RNA in nasopharyngeal swabs, and serostatus of symptomatic COVID-19 outpatients in the United States

BackgroundWhile SARS-CoV-2 infectious virus isolation in outpatients with COVID-19 has been associated with viral RNA levels and symptom duration, little is known about the host, disease and viral determinants of infectious virus detection. MethodsCOVID-19 adult outpatients were enrolled within 7 days of symptom onset. Clinical symptoms were recorded via patient diary. Nasopharyngeal swabs were collected to quantitate SARS-CoV-2 RNA by reverse transcriptase polymerase chain reaction and for infectious virus isolation in Vero E6-cells. SARS-CoV-2 antibodies were measured in serum using a validated ELISA assay. ResultsAmong 204 participants with mild-to-moderate symptomatic COVID19, the median nasopharyngeal viral RNA was 6.5 (IQR 4.7-7.6 log10 copies/mL), and 26% had detectable SARS-CoV-2 antibodies (IgA, IgM, IgG, and/or total Ig) at baseline. Infectious virus was recovered in 7% of participants with SARS-CoV-2 antibodies compared to 58% of participants without antibodies (probability ratio (PR)=0.12, 95% CI: 0.04, 0.36; p=0.00016). Infectious virus isolation was also associated with higher levels of viral RNA (mean RNA difference +2.6 log10, 95% CI: 2.2, 3.0; p<0.0001) and fewer days since symptom onset (PR=0.79, 95% CI: 0.71, 0.88 per day; p<0.0001). ConclusionsThe presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus isolation. Seropositivity and viral RNA levels are likely more reliable markers of infectious virus clearance than subjective measure of COVID-19 symptom duration. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion. ClinicalTrials.gov IdentifierNCT04405570 Key Points (Summary)Among COVID-19 outpatients within 7 days of symptom onset, the presence of SARS-CoV-2-specific antibodies was strongly associated with clearance of infectious virus. Seropositivity appears to be more reliable marker of infectious virus clearance than subjective measure of COVID-19 symptoms.

Antibody response to SARS-CoV-2 infection over six months among Nicaraguan outpatients

New information is emerging about SARS-CoV-2 epidemiology and immunity, but little of this information comes from low- and middle-income countries or from patients receiving care in the outpatient setting. The current study investigated the SARS-CoV-2 infection status and antibody responses in 157 patients seeking care for a respiratory disease suggestive of COVID-19 in private healthcare clinics during the first wave (June-October 2020) of infections in Nicaragua. We examined nasal swabs for the presence of viral RNA via RT-PCR and longitudinally collected sera for the changes in SARS-CoV-2 Spike antibody levels over six months. Among patients with confirmed SARS-CoV-2 infections, we evaluated if clinical symptoms were associated with age, hematological parameters and co-morbidities. The combination of PCR and paired serology identified 60 (38%) of the 157 outpatients as acute COVID-19. While both PCR and serology identified the majority (n = 38, 64%) of the acute infections, a notable number of outpatients were identified by RT-qPCR (n = 13, 22%) or by serology (n = 9, 14%) only. During the longitudinal study, we identified 6 new infections by serology among the 97 non-COVID-19 subjects. In conclusion, this study report that more than one third of the outpatients seeking care for acute respiratory disease during the first epidemic wave of SARS-CoV-2 in Nicaragua had an acute mild COVID-19 infection that correlate with prolonged humoral response. This immune response to the RBD antigen, more likely IgG dependent, significantly increased between the acute to convalescent and decay in the late convalescent but still remained seropositive.

Disparities in SARS-CoV-2 seroprevalence among individuals presenting for care in central North Carolina over a six-month period

BackgroundRobust community-level SARS-CoV-2 prevalence estimates have been difficult to obtain in the American South and outside of major metropolitan areas. Furthermore, though some previous studies have investigated the association of demographic factors such as race with SARS-CoV-2 exposure risk, fewer have correlated exposure risk to surrogates for socioeconomic status such as health insurance coverage. MethodsWe used a highly specific serological assay utilizing the receptor binding domain of the SARS-CoV-2 spike-protein to identify SARS-CoV-2 antibodies in remnant blood samples collected by the University of North Carolina Health system. We estimated the prevalence of SARS-CoV-2 in this cohort with Bayesian regression, as well as the association of critical demographic factors with higher prevalence odds. FindingsBetween April 21st and October 3rd of 2020, a total of 9,624 unique samples were collected from clinical sites in central NC and we observed a seroprevalence increase from 2{middle dot}9 (1{middle dot}7, 4{middle dot}3) to 9{middle dot}1 (7{middle dot}2, 11{middle dot}1) over the study period. Individuals who identified as Latinx were associated with the highest odds ratio of SARS-CoV-2 exposure at 7{middle dot}77 overall (5{middle dot}20, 12{middle dot}10). Increased odds were also observed among Black individuals and individuals without public or private health insurance. InterpretationOur data suggests that for this care-accessing cohort, SARS-CoV-2 seroprevalence was significantly higher than cumulative total cases reported for the study geographical area six months into the COVID-19 pandemic in North Carolina. The increased odds of seropositivity by ethnoracial grouping as well as health insurance highlights the urgent and ongoing need to address underlying health and social disparities in these populations. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for studies published through March 21st, 2021. We used search terms that included "COVID-19", "SARS-CoV-2", "prevalence" and "seroprevalence". Our search resulted in 399 papers, from which we identified 58 relevant studies describing SARS-CoV-2 seroprevalence at sites around the United States from March 1 to December 9, 2020, 12 of which utilized remnant clinical samples and three of which overlapped with our study area. Most notably, one study of 4,422 asymptomatic inpatients and outpatients in central NC from April 28-June 19, 2020 found an estimated seroprevalence of 0{middle dot}7 -0{middle dot}8%, and another study of 177,919 inpatients and outpatients (3,817 from NC) from July 27-September 24, 2020 found an estimated seroprevalence of 2{middle dot}5 -6{middle dot}8%. Added value of this studyThis is the largest SARS-CoV-2 seroprevalence cohort published to date in NC. Importantly, we used a Bayesian framework to account for uncertainty in antibody assay sensitivity and specificity and investigated seropositivity by important demographic variables that have not yet been studied in this context in NC. This study corroborates other reports that specific demographic factors including race, ethnicity and the lack of public or private insurance are associated with elevated risk of SARS-CoV-2 infection. Furthermore, in a subset of serum samples, we identify other SARS-CoV-2 antibodies elicited by these individuals, including functionally neutralizing antibodies. Implications of all the available evidenceIt is difficult to say the exact seroprevalence in the central North Carolina area, but a greater proportion of the population accessing healthcare has been infected by SARS-CoV-2 than is reflected by infection cases confirmed by molecular testing. Furthermore, local governments need to prioritize addressing the many forms of systemic racism and socioeconomic disadvantage that drive SARS-CoV-2 exposure risk, such as residential and occupational risk, and an urgent need to provide access to SARS-CoV-2 testing and vaccination to these groups.

High household transmission of SARS-CoV-2 in the United States: living density, viral load, and disproportionate impact on communities of color

BackgroundFew prospective studies of SARS-CoV-2 transmission within households have been reported from the United States, where COVID-19 cases are the highest in the world and the pandemic has had disproportionate impact on communities of color. Methods and FindingsThis is a prospective observational study. Between April-October 2020, the UNC CO-HOST study enrolled 102 COVID-positive persons and 213 of their household members across the Piedmont region of North Carolina, including 45% who identified as Hispanic/Latinx or non-white. Households were enrolled a median of 6 days from onset of symptoms in the index case. Secondary cases within the household were detected either by PCR of a nasopharyngeal (NP) swab on study day 1 and weekly nasal swabs (days 7, 14, 21) thereafter, or based on seroconversion by day 28. After excluding household contacts exposed at the same time as the index case, the secondary attack rate (SAR) among susceptible household contacts was 60% (106/176, 95% CI 53%-67%). The majority of secondary cases were already infected at study enrollment (73/106), while 33 were observed during study follow-up. Despite the potential for continuous exposure and sequential transmission over time, 93% (84/90, 95% CI 86%-97%) of PCR-positive secondary cases were detected within 14 days of symptom onset in the index case, while 83% were detected within 10 days. Index cases with high NP viral load (>10^6 viral copies/ul) at enrollment were more likely to transmit virus to household contacts during the study (OR 4.9, 95% CI 1.3-18 p=0.02). Furthermore, NP viral load was correlated within families (ICC=0.44, 95% CI 0.26-0.60), meaning persons in the same household were more likely to have similar viral loads, suggesting an inoculum effect. High household living density was associated with a higher risk of secondary household transmission (OR 5.8, 95% CI 1.3-55) for households with >3 persons occupying <6 rooms (SAR=91%, 95% CI 71-98%). Index cases who self-identified as Hispanic/Latinx or non-white were more likely to experience a high living density and transmit virus to a household member, translating into an SAR in minority households of 70%, versus 52% in white households (p=0.05). ConclusionsSARS-CoV-2 transmits early and often among household members. Risk for spread and subsequent disease is elevated in high-inoculum households with limited living space. Very high infection rates due to household crowding likely contribute to the increased incidence of SARS-CoV-2 infection and morbidity observed among racial and ethnic minorities in the US. Quarantine for 14 days from symptom onset of the first case in the household is appropriate to prevent onward transmission from the household. Ultimately, primary prevention through equitable distribution of effective vaccines is of paramount importance. AUTHORS SUMMARYO_ST_ABSWhy was this study done?C_ST_ABSO_LIUnderstanding the secondary attack rate and the timing of transmission of SARS-CoV-2 within households is important to determine the role of household transmission in the larger pandemic and to guide public health policies about quarantine. C_LIO_LIProspective studies looking at the determinants of household transmission are sparse, particularly studies including substantial racial and ethnic minorities in the United States and studies with adequate follow-up to detect sequential transmission events. C_LIO_LIIdentifying individuals at high risk of transmitting and acquiring SARS-CoV-2 will inform strategies for reducing transmission in the household, or reducing disease in those exposed. C_LI What did the researchers do and find?O_LIBetween April-November 2020, the UNC CO-HOST study enrolled 102 households across the Piedmont region of North Carolina, including 45% with an index case who identified as racial or ethnic minorities. C_LIO_LIOverall secondary attack rate was 60% with two-thirds of cases already infected at study enrollment. C_LIO_LIDespite the potential for sequential transmission in the household, the majority of secondary cases were detected within 10 days of symptom onset of the index case. C_LIO_LIViral loads were correlated within families, suggesting an inoculum effect. C_LIO_LIHigh viral load in the index case was associated with a greater likelihood of household transmission. C_LIO_LISpouses/partners of the COVID-positive index case and household members with obesity were at higher risk of becoming infected. C_LIO_LIHigh household living density contributed to an increased risk of household transmission. C_LIO_LIRacial/ethnic minorities had an increased risk of acquiring SARS-CoV-2 in their households in comparison to members of the majority (white) racial group. C_LI What do these findings mean?O_LIHousehold transmission often occurs quickly after a household member is infected. C_LIO_LIHigh viral load increases the risk of transmission. C_LIO_LIHigh viral load cases cluster within households - suggesting high viral inoculum in the index case may put the whole household at risk for more severe disease. C_LIO_LIIncreased household density may promote transmission within racial and ethnic minority households. C_LIO_LIEarly at-home point-of-care testing, and ultimately vaccination, is necessary to effectively decrease household transmission. C_LI

Seroepidemiology of SARS-CoV-2 infections in an urban Nicaraguan population

In a Nicaraguan population-based cohort, SARS-CoV-2 seroprevalence was 34%, with higher prevalence in children compared to adults. Having a seropositive household member was associated with a two-fold probability of individual seropositivity, suggesting a role for household transmission. Co-morbidities and preventive behaviors were not associated with SARS-CoV-2 seroprevalence.

Sex disparities and neutralizing antibody durability to SARS-CoV-2 infection in convalescent individuals

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has now caused over 2 million deaths worldwide and continues to expand. Currently, much is unknown about functionally neutralizing human antibody responses and durability to SARS-CoV-2. Using convalescent sera collected from 101 COVID-19 recovered individuals 21-212 days after symptom onset with forty-eight additional longitudinal samples, we measured functionality and durability of serum antibodies. We also evaluated associations between individual demographic and clinical parameters with functional neutralizing antibody responses to COVID-19. We found robust antibody durability out to six months, as well as significant positive associations with the magnitude of the neutralizing antibody response and male sex. We also show that SARS-CoV-2 convalescent neutralizing antibodies are higher in individuals with cardio-metabolic comorbidities. SignificanceIn this study we found that neutralizing antibody responses in COVID-19 convalescent individuals vary in magnitude but are durable and correlate well with RBD Ig binding antibody levels compared to other SARS-CoV-2 antigen responses. In our cohort, higher neutralizing antibody titers are independently and significantly associated with male sex compared to female sex. We also show for the first time, that higher convalescent antibody titers in male donors are associated with increased age and symptom grade. Furthermore, cardio-metabolic co-morbidities are associated with higher antibody titers independently of sex. Here, we present an in-depth evaluation of serologic, demographic, and clinical correlates of functional antibody responses and durability to SARS-CoV-2.

Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine and Pyronaridine: In vitro Activity Against SARS-CoV-2 and Potential Mechanisms

SARS-CoV-2 is a newly identified virus that has resulted in over 1.3 M deaths globally and over 59 M cases globally to date. Small molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola virus and demonstrated activity against SARS-CoV-2 in vivo. Most notably the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small molecule drugs that are active against Ebola virus would seem a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg virus in vitro in HeLa cells and of mouse adapted Ebola virus in mouse in vivo. We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7 and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC50 values of 180 nM and IC50 198 nM, respectively. We have also tested them in a pseudovirus assay and used microscale thermophoresis to test the binding of these molecules to the spike protein. They bind to spike RBD protein with Kd values of 339 nM and 647 nM, respectively. Human Cmax for pyronaridine and quinacrine is greater than the IC50 hence justifying in vivo evaluation. We also provide novel insights into their mechanism which is likely lysosomotropic.

The RBD Of The Spike Protein Of SARS-Group Coronaviruses Is A Highly Specific Target Of SARS-CoV-2 Antibodies But Not Other Pathogenic Human and Animal Coronavirus Antibodies

A new Severe Acute Respiratory Syndrome Coronavirus variant (SARS-CoV-2) that first emerged in late 2019 is responsible for a pandemic of severe respiratory illness. People infected with this highly contagious virus present with clinically inapparent, mild or severe disease. Currently, the presence of the virus in individual patients and at the population level is being monitored by testing symptomatic cases by PCR for the presence of viral RNA. There is an urgent need for SARS-CoV-2 serologic tests to identify all infected individuals, irrespective of clinical symptoms, to conduct surveillance and implement strategies to contain spread. As the receptor binding domain (RBD) of the viral spike (S) protein is poorly conserved between SARS-CoVs and other pathogenic human coronaviruses, the RBD represents a promising antigen for detecting CoV specific antibodies in people. Here we use a large panel of human sera (70 SARS-CoV-2 patients and 71 control subjects) and hyperimmune sera from animals exposed to zoonotic CoVs to evaluate the performance of the RBD as an antigen for accurate detection of SARS-CoV-2-specific antibodies. By day 9 after the onset of symptoms, the recombinant SARS-CoV-2 RBD antigen was highly sensitive (98%) and specific (100%) to antibodies induced by SARS-CoVs. We observed a robust correlation between levels of RBD binding antibodies and SARS-CoV-2 neutralizing antibodies in patients. Our results, which reveal the early kinetics of SARS-CoV-2 antibody responses, strongly support the use of RBD-based antibody assays for population-level surveillance and as a correlate of neutralizing antibody levels in people who have recovered from SARS-CoV-2 infections.