CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses.

Coronaviruses have threatened humans repeatedly, especially COVID-19 caused by SARS-CoV-2, which has posed a substantial threat to global public health. SARS-CoV-2 continuously evolves through random mutation, resulting in a significant decrease in the efficacy of existing vaccines and neutralizing antibody drugs. It is critical to assess immune escape caused by viral mutations and develop broad-spectrum vaccines and neutralizing antibodies targeting conserved epitopes. Thus, we constructed CovEpiAb, a comprehensive database and analysis resource of human coronavirus (HCoVs) immune epitopes and antibodies. CovEpiAb contains information on over 60 000 experimentally validated epitopes and over 12 000 antibodies for HCoVs and SARS-CoV-2 variants. The database is unique in (1) classifying and annotating cross-reactive epitopes from different viruses and variants; (2) providing molecular and experimental interaction profiles of antibodies, including structure-based binding sites and around 70 000 data on binding affinity and neutralizing activity; (3) providing virological characteristics of current and past circulating SARS-CoV-2 variants and in vitro activity of various therapeutics; and (4) offering site-level annotations of key functional features, including antibody binding, immunological epitopes, SARS-CoV-2 mutations and conservation across HCoVs. In addition, we developed an integrated pipeline for epitope prediction named COVEP, which is available from the webpage of CovEpiAb. CovEpiAb is freely accessible at https://pgx.zju.edu.cn/covepiab/.

Vacunas frente a la COVID-19: perfil de seguridad tras un año de seguimiento / COVID-19 vaccines: safety profile after one year of follow-up

Introducción: Tras declararse la pandemia mundial por el coronavirus COVID-19, se instauraron medidas para com-batirlo, destacando la existencia de vacunas frente a la COVID-19: dos de ARN mensajero [ARNm] y dos de vector viral no replicante [VVNR]. Nuestro objetivo fue contribuir a la ampliación del perfil de seguridad de dichas vacunas mediante la detección y notificación de reacciones adversas (RAs) en un área sanitaria con 174.398 tarjetas sanitarias durante el año 2021.Método: Estudio observacional descriptivo retrospectivo realizado en un hospital de segundo nivel. Las fuentes de detección de las RAs fueron: Sistema de Codificación del Centro al Alta del Paciente Ingresado [SIAC] y notificación espontánea. Los datos empleados fueron extraídos de la historia clínica electrónica y recogidos en un documento de Microsoft Excell. Resultados: De las 654 RAs detectadas, 36 pertenecieron a vacunas frente a la COVID-19, detectándose el 72 % mediante notificación espontánea y siendo el 91,67 % graves. Se produjeron en 29 pacientes (mediana de edad: 61 años; 51,72 % mujeres), dos de ellos con infección previa por COVID-19. El 50 % de las RAs sucedieron tras la segun-da dosis. Destacaron: trombosis venosa profunda (TVP), tromboembolismo pulmonar (TEP) y miopericarditis con vacunas de ARNm; y vasculitis y miocarditis en VVNR. Conclusiones: Aunque la bibliografía disponible señala que la frecuencia de RAs graves con dichas vacunas suele ser rara, resulta importante su seguimiento. El alto porcentaje de RAs detectadas por notificación espontánea refle-ja la implicación de los profesionales sanitarios en la ampliación del perfil de seguridad. (AU)

Introduction: After declaring the global pandemic due to the coronavirus COVID-19, measures were established to combat it, highlighting the existence of COVID-19 vaccines: two messenger RNA [mRNA] and two non-replicating viral vector [VVNR].Our objective was to contribute to expanding the safety profile of these vaccines through the detection and notifica-tion of adverse reactions (ARs) in a health area with 174,398 health cards during the year 2021.Method: Retrospective descriptive observational study carried out in a second level hospital. The sources of detec-tion of the ADRs were: Coding System of the Center at the Discharge of the Admitted Patient [SIAC] and spontaneous notification. The data used were extracted from the electronic medical record and collected in a Microsoft Excell document.Results: Of the 654 ARs detected, 36 belonged to COVID-19 vaccines, 72 % being detected by spontaneous noti-fication and 91.67 % being serious. They occurred in 29 patients (median age: 61 years; 51.72 % women), two of them with previous COVID-19 infection. 50 % of the ARs occurred after the second dose. They highlighted: deep vein thrombosis (DVT), pulmonary thromboembolism (PTE) and myopericarditis with mRNA vaccines; and vasculitis and myocarditis in VVNR.Conclusions: Although the available bibliography indicates that the frequency of serious ARs with these vaccines is usually rare, their follow-up is important. The high percentage of ADRs detected by spontaneous notification reflects the involvement of healthcare professionals to expanding the safety profile. (AU)

Seroprevalence of four endemic human coronaviruses and, reactivity and neutralization capability against SARS-CoV-2 among children in the Philippines.

Four endemic human coronaviruses (HCoV), HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43, are closely related to SARS-CoV-2. These coronaviruses are known to infect humans living in temperate areas, including children under 5 years old; however, the seroprevalence of four HCoVs among children in tropical areas, including the Philippines, remains unclear. This study aimed to assess the prevalence of antibodies against four HCoVs and to determine the reactivity and neutralization of these antibodies against SARS-CoV-2 among children in the Philippines. A total of 315 serum samples collected from 2015 to 2018, before the emergence of SARS-CoV-2, in Biliran island, Philippines, were tested for the presence of antibodies against four HCoVs and SARS-CoV-2 using recombinant spike ectodomain proteins by IgG-enzyme-linked immunosorbent assay (ELISA). Reactivity to and neutralization of SARS-CoV-2 were also investigated. The seroprevalence of the four HCoVs was 63.8% for HCoV-229E, 71.4% for HCoV-NL63, 76.5% for HCoV-HKU1, and 83.5% for HCoV-OC43 by ELISA. Age group analysis indicated that seropositivity to all HCoVs reached 80% by 2-3 years of age. While 69/315 (21.9%) of the samples showed reactive to SARS-CoV-2, almost no neutralization against SARS-CoV-2 was detected using neutralization assay. Reactivity of antibodies against SARS-CoV-2 spike protein obtained by ELISA may not correlate with neutralization capability.

Impacto de la pandemia por COVID-19 en la implantación de una guía de buenas prácticas sobre las lesiones por presión / Impact of the COVID-19 pandemic on the implementation of best practice guidelines on pressure injuries

Objetivo: Evaluar el impacto de la COVID-19 en la implantaciónde la Guía de Buenas Prácticas clínicas de la Registered Nurses’Association of Ontario, de valoración del riesgo y prevención de laslesiones por presión sobre los indicadores de calidad asistencial enla Unidad de Medicina Interna del Hospital Universitari GermansTrias i Pujol. Metodología: Estudio observacional, analítico, de 2cohortes retrospectivas, que compara los indicadores de calidad pre ypostimplementación de 2017 con los del año 2021. Explotación dedatos de forma retrospectiva y pseudoanonimizada. Análisis descriptivounivariante, así como inferencial para el contraste de hipótesis deestudio. En todos los casos se utilizaron aproximaciones bilaterales,siendo el nivel de significación del 5% (α = 0,05). Resultados: Seincluyeron 946 sujetos, de los que el 49,9% fueron hombres y el50,1% mujeres. La media de edad fue de 75 años. La incidencia delesiones por presión fue del 8,1% en 2017 y del 8,9% en 2021, sinexistir evidencias estadísticamente significativas (p = 0,8). Respectoa la proporción de lesiones por presión de origen nosocomial,también se observó un considerable aumento, que fue del 27,5% en2017 y del 60% en 2021, aunque tampoco se hallaron diferenciasestadísticamente significativas (p = 0,094). Sin embargo, en cuantoal riesgo de presentar lesiones por presión y de su aparición, sí que seobservaron diferencias estadísticamente significativas en ambos años (p< 0,001 en 2017, y p = 0,011 en 2021). Conclusiones: La pandemiaobligó a detener el proceso de implantación de las guías de buenasprácticas, repercutiendo en los indicadores de calidad asistencial. (AU)

Objective: To assess the impact of COVID-19 on theimplementation of the Risk Assessment and Prevention ofPressure Ulcers Best Practice Guideline (BPG) of the RegisteredNurses’ Association of Ontario, in quality indicators in thegeneral internal medicine unit of the Hospital UniversitariGermans Trias i Pujol. Methodology: Observational studyof 2 retrospective cohorts, comparing the pre- and postimplementation quality indicators of 2017 with those ofthe year 2021. A pseudonymized data exploitation wasconducted for subsequent univariate descriptive analysis, aswell as inferential analysis and hypothesis contrasting. Bilateralapproaches were used in all cases, with a significance level of 5%(α = 0.05). Results: A total of 946 individuals were included, ofwhich 49.9% were men and 50.1% were women. The mean agewas 75 years. The incidence of PI was 8.1% in 2017 and 8.9%in 2021, with no statistically significant difference (p = 0.8).Regarding the proportion of hospital-acquired PI, a considerableincrease was also observed, being 27.5% in 2017 and 60% in2021, although no statistically significant differences were foundeither (p = 0.094). However, regarding the risk of presentingPI and their incidence, statistically significant differences wereobserved in both years (p < 0.001 in 2017, and p = 0.011 in2021). Conclusions: The pandemic made it necessary to stopthe BPG implementation process, impacting negatively on thequality of care indicators. (AU)

Abordaje multidisciplinarde un paciente con una úlceraperianal asociada a pomadaantihemorroidal / Multidisciplinary approach to a patient with a perianal ulcer associated with hemorrhoidal ointment

Introducción: Hasta la fecha, la manifestación de una úlcera perianalprovocada por una pomada antihemorroidal no se ha descrito confrecuencia. Sin embargo, se ha objetivado un incremento de loscasos durante la pandemia de COVID-19. Caso clínico: Varónde 82 años independiente, que presentó una úlcera perianal de35,8 cm² sin ninguna patología ni enfermedad concomitante queexplicara su causa. La aplicación de criterios de exclusión exhaustivos,incluida una biopsia para rechazar el pioderma gangrenoso,identificó una pomada rectal hemorroidal como la causa de la úlcera.Plan de actuación: La herida curó tras aplicar una intervenciónmultidisciplinaria y una terapia con factores de crecimientoautólogos. Discusión y conclusiones: Este caso ha sido escasamentereportado en la literatura, aunque esta pomada hemorroidal secomercializa desde hace más de 40 años. Se recomienda evaluaciónmédica antes de la prescripción. (AU)

Introduction: Perianal ulcers resulting from the use of hemorrhoidalointments have been rarely reported to date. Nevertheless, therehas been a surge in the number of cases reported during theCOVID-19 pandemic. Case report: An independent 82-year-oldmale experienced a 35,80 cm² perianal ulcer, with no underlyingcondition or concomitant disease that could explain the cause ofthe ulcer. The application of thorough exclusion criteria, including abiopsy to rule out pyoderma gangrenosum, led to the identificationof a hemorrhoidal rectal ointment as the cause. Action plan: Theulcer healed completely when a multidisciplinary intervention and anautologous growth factors advanced therapy were applied. Discussionand conclusions: This case has been scarcely reported in the literature,although this hemorrhoidal ointment has been on the market for over40 years. Medical assessment before prescription and patients’ followup is recommended. (AU)

Limited Recognition of Highly Conserved Regions of SARS-CoV-2.

Understanding the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) is critical to overcome the current coronavirus disease (COVID-19) pandemic. Efforts are being made to understand the potential cross-protective immunity of memory T cells, induced by prior encounters with seasonal coronaviruses, in providing protection against severe COVID-19. In this study we assessed T-cell responses directed against highly conserved regions of SARS-CoV-2. Epitope mapping revealed 16 CD8+ T-cell epitopes across the nucleocapsid (N), spike (S), and open reading frame (ORF)3a proteins of SARS-CoV-2 and five CD8+ T-cell epitopes encoded within the highly conserved regions of the ORF1ab polyprotein of SARS-CoV-2. Comparative sequence analysis showed high conservation of SARS-CoV-2 ORF1ab T-cell epitopes in seasonal coronaviruses. Paradoxically, the immune responses directed against the conserved ORF1ab epitopes were infrequent and subdominant in both convalescent and unexposed participants. This subdominant immune response was consistent with a low abundance of ORF1ab encoded proteins in SARS-CoV-2 infected cells. Overall, these observations suggest that while cross-reactive CD8+ T cells likely exist in unexposed individuals, they are not common and therefore are unlikely to play a significant role in providing broad preexisting immunity in the community. IMPORTANCE T cells play a critical role in protection against SARS-CoV-2. Despite being highly topical, the protective role of preexisting memory CD8+ T cells, induced by prior exposure to circulating common coronavirus strains, remains less clear. In this study, we established a robust approach to specifically assess T cell responses to highly conserved regions within SARS-CoV-2. Consistent with recent observations we demonstrate that recognition of these highly conserved regions is associated with an increased likelihood of milder disease. However, extending these observations we observed that recognition of these conserved regions is rare in both exposed and unexposed volunteers, which we believe is associated with the low abundance of these proteins in SARS-CoV-2 infected cells. These observations have important implications for the likely role preexisting immunity plays in controlling severe disease, further emphasizing the importance of vaccination to generate the immunodominant T cells required for immune protection.

Cross-reactive memory T cells associate with protection against SARS-CoV-2 infection in COVID-19 contacts.

Cross-reactive immune responses to SARS-CoV-2 have been observed in pre-pandemic cohorts and proposed to contribute to host protection. Here we assess 52 COVID-19 household contacts to capture immune responses at the earliest timepoints after SARS-CoV-2 exposure. Using a dual cytokine FLISpot assay on peripheral blood mononuclear cells, we enumerate the frequency of T cells specific for spike, nucleocapsid, membrane, envelope and ORF1 SARS-CoV-2 epitopes that cross-react with human endemic coronaviruses. We observe higher frequencies of cross-reactive (p = 0.0139), and nucleocapsid-specific (p = 0.0355) IL-2-secreting memory T cells in contacts who remained PCR-negative despite exposure (n = 26), when compared with those who convert to PCR-positive (n = 26); no significant difference in the frequency of responses to spike is observed, hinting at a limited protective function of spike-cross-reactive T cells. Our results are thus consistent with pre-existing non-spike cross-reactive memory T cells protecting SARS-CoV-2-naïve contacts from infection, thereby supporting the inclusion of non-spike antigens in second-generation vaccines.

Selection and T-cell antigenicity of synthetic long peptides derived from SARS-CoV-2.

The pandemic caused by SARS-CoV-2 has led to the successful development of effective vaccines however the prospect of variants of SARS-CoV-2 and future coronavirus outbreaks necessitates the investigation of other vaccine strategies capable of broadening vaccine mediated T-cell responses and potentially providing cross-immunity. In this study the SARS-CoV-2 proteome was assessed for clusters of immunogenic epitopes restricted to diverse human leucocyte antigen. These regions were then assessed for their conservation amongst other coronaviruses representative of different alpha and beta coronavirus genera. Sixteen highly conserved peptides containing numerous HLA class I and II restricted epitopes were synthesized from these regions and assessed in vitro for their antigenicity against T-cells from individuals with previous SARS-CoV-2 infection. Monocyte derived dendritic cells were generated from these peripheral blood mononuclear cells (PBMC), loaded with SARS-CoV-2 peptides, and used to induce autologous CD4+ and CD8+ T cell activation. The SARS-CoV-2 peptides demonstrated antigenicity against the T-cells from individuals with previous SARS-CoV-2 infection indicating that this approach holds promise as a method to activate anti-SAR-CoV-2 T-cell responses from conserved regions of the virus which are not included in vaccines utilising the Spike protein.

SARS-CoV-2 mRNA vaccine induces robust specific and cross-reactive IgG and unequal neutralizing antibodies in naive and previously infected people.

Understanding vaccine-mediated protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical to overcoming the global coronavirus disease 2019 (COVID-19) pandemic. We investigate mRNA-vaccine-induced antibody responses against the reference strain, seven variants, and seasonal coronaviruses in 168 healthy individuals at three time points: before vaccination, after the first dose, and after the second dose. Following complete vaccination, both naive and previously infected individuals developed comparably robust SARS-CoV-2 spike antibodies and variable levels of cross-reactive antibodies to seasonal coronaviruses. However, the strength and frequency of SARS-CoV-2 neutralizing antibodies in naive individuals were lower than in previously infected individuals. After the first vaccine dose, one-third of previously infected individuals lacked neutralizing antibodies; this was improved to one-fifth after the second dose. In all individuals, neutralizing antibody responses against the Alpha and Delta variants were weaker than against the reference strain. Our findings support future tailored vaccination strategies against emerging SARS-CoV-2 variants as mRNA-vaccine-induced neutralizing antibodies are highly variable among individuals.

Review: A systematic review of virus-like particles of coronavirus: Assembly, generation, chimerism and their application in basic research and in the clinic.

Virus-like particles (VLPs) are nano-scale particles that are morphologically similar to a live virus but which lack a genetic component. Since the pandemic spread of COVID-19, much focus has been placed on coronavirus (CoV)-related VLPs. CoVs contain four structural proteins, though the minimum requirement for VLP formation differs among virus species. CoV VLPs are commonly produced in mammalian and insect cell systems, sometimes in the form of chimeric VLPs that enable surface display of CoV epitopes. VLPs are an ideal model for virological research and have been applied as vaccines and diagnostic reagents to aid in clinical disease control. This review summarizes and updates the research progress on the characteristics of VLPs from different known CoVs, mainly focusing on assembly, in vitro expression systems for VLP generation, VLP chimerism, protein-based nanoparticles and their applications in basic research and clinical settings, which may aid in development of novel VLP vaccines against emerging coronavirus diseases such as SARS-CoV-2.

The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2.

Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC.

Interferon Control of Human Coronavirus Infection and Viral Evasion: Mechanistic Insights and Implications for Antiviral Drug and Vaccine Development.

Recognition of viral infections by various pattern recognition receptors (PRRs) activates an inflammatory cytokine response that inhibits viral replication and orchestrates the activation of adaptive immune responses to control the viral infection. The broadly active innate immune response puts a strong selective pressure on viruses and drives the selection of variants with increased capabilities to subvert the induction and function of antiviral cytokines. This revolutionary process dynamically shapes the host ranges, cell tropism and pathogenesis of viruses. Recent studies on the innate immune responses to the infection of human coronaviruses (HCoV), particularly SARS-CoV-2, revealed that HCoV infections can be sensed by endosomal toll-like receptors and/or cytoplasmic RIG-I-like receptors in various cell types. However, the profiles of inflammatory cytokines and transcriptome response induced by a specific HCoV are usually cell type specific and determined by the virus-specific mechanisms of subverting the induction and function of interferons and inflammatory cytokines as well as the genetic trait of the host genes of innate immune pathways. We review herein the recent literatures on the innate immune responses and their roles in the pathogenesis of HCoV infections with emphasis on the pathobiological roles and therapeutic effects of type I interferons in HCoV infections and their antiviral mechanisms. The knowledge on the mechanism of innate immune control of HCoV infections and viral evasions should facilitate the development of therapeutics for induction of immune resolution of HCoV infections and vaccines for efficient control of COVID-19 pandemics and other HCoV infections.

Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies.

Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. Sequence-based clonal clustering can identify antibodies with similar epitope complementarity, however, antibodies from markedly different lineages but with similar structures can engage the same epitope. We describe a novel computational method for epitope profiling based on structural modelling and clustering. Using the method, we demonstrate that sequence dissimilar but functionally similar antibodies can be found across the Coronavirus Antibody Database, with high accuracy (92% of antibodies in multiple-occupancy structural clusters bind to consistent domains). Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than is suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis.

Evidence for increased SARS-CoV-2 susceptibility and COVID-19 severity related to pre-existing immunity to seasonal coronaviruses.

The importance of pre-existing immune responses to seasonal endemic coronaviruses (HCoVs) for the susceptibility to SARS-CoV-2 infection and the course of COVID-19 is the subject of an ongoing scientific debate. Recent studies postulate that immune responses to previous HCoV infections can either have a slightly protective or no effect on SARS-CoV-2 pathogenesis and, consequently, be neglected for COVID-19 risk stratification. Challenging this notion, we provide evidence that pre-existing, anti-nucleocapsid antibodies against endemic α-coronaviruses and S2 domain-specific anti-spike antibodies against ß-coronavirus HCoV-OC43 are elevated in patients with COVID-19 compared to pre-pandemic donors. This finding is particularly pronounced in males and in critically ill patients. Longitudinal evaluation reveals that antibody cross-reactivity or polyclonal stimulation by SARS-CoV-2 infection are unlikely to be confounders. Thus, specific pre-existing immunity to seasonal coronaviruses may increase susceptibility to SARS-CoV-2 and predispose individuals to an adverse COVID-19 outcome, guiding risk management and supporting the development of universal coronavirus vaccines.

Pre-Existing Cross-Reactive Antibody Responses Do Not Significantly Impact Inactivated COVID-19 Vaccine-Induced Neutralization.

Recent exposure to seasonal coronaviruses (sCoVs) may stimulate cross-reactive antibody responses against severe acute respiratory syndrome CoV 2 (SARS-CoV-2). However, previous studies have produced divergent results regarding protective or damaging immunity induced by prior sCoV exposure. It remains unknown whether pre-existing humoral immunity plays a role in vaccine-induced neutralization and antibody responses. In this study, we collected 36 paired sera samples from 36 healthy volunteers before and after immunization with inactivated whole-virion SARS-CoV-2 vaccines for COVID-19, and analyzed the distribution and intensity of pre-existing antibody responses at the epitope level pre-vaccination as well as the relationship between pre-existing sCoV immunity and vaccine-induced neutralization. We observed large amounts of pre-existing cross-reactive antibodies in the conserved regions among sCoVs, especially the S2 subunit. Excep t for a few peptides, the IgG and IgM fluorescence intensities against S, M and N peptides did not differ significantly between pre-vaccination and post-vaccination sera of vaccinees who developed a neutralization inhibition rate (%inhibition) <40 and %inhibition ≥40 after two doses of the COVID-19 vaccine. Participants with strong and weak pre-existing cross-reactive antibodies (strong pre-CRA; weak pre-CRA) had similar %inhibition pre-vaccination (10.9% ± 2.9% vs. 12.0% ± 2.2%, P=0.990) and post-vaccination (43.8% ± 25.1% vs. 44.6% ± 21.5%, P=0.997). Overall, the strong pre-CRA group did not show a significantly greater increase in antibody responses to the S protein linear peptides post-vaccination compared with the weak pre-CRA group. Therefore, we found no evidence for a significant impact of pre-existing antibody responses on inactivated vaccine-induced neutralization and antibody responses. Our research provides an important basis for inactivated SARS-CoV-2 vaccine use in the context of high sCoV seroprevalence.

Cross-reactive antibodies after SARS-CoV-2 infection and vaccination.

Current SARS-CoV-2 vaccines are losing efficacy against emerging variants and may not protect against future novel coronavirus outbreaks, emphasizing the need for more broadly protective vaccines. To inform the development of a pan-coronavirus vaccine, we investigated the presence and specificity of cross-reactive antibodies against the spike (S) proteins of human coronaviruses (hCoV) after SARS-CoV-2 infection and vaccination. We found an 11- to 123-fold increase in antibodies binding to SARS-CoV and MERS-CoV as well as a 2- to 4-fold difference in antibodies binding to seasonal hCoVs in COVID-19 convalescent sera compared to pre-pandemic healthy donors, with the S2 subdomain of the S protein being the main target for cross-reactivity. In addition, we detected cross-reactive antibodies to all hCoV S proteins after SARS-CoV-2 vaccination in macaques and humans, with higher responses for hCoV more closely related to SARS-CoV-2. These findings support the feasibility of and provide guidance for development of a pan-coronavirus vaccine.

Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses.

Initial exposure to a pathogen elicits an adaptive immune response to control and eradicate the threat. Interrogating the abundance and specificity of the naive B cell repertoire drives understanding of how to mount protective responses. Here, we isolated naive B cells from eight seronegative human donors targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD). Single-cell B cell receptor (BCR) sequencing identified diverse gene usage and no restriction on complementarity determining region length. A subset of recombinant antibodies produced by naive B cell precursors bound to SARS-CoV-2 RBD and engaged circulating variants including B.1.1.7, B.1.351, and B.1.617.2, as well as preemergent bat-derived coronaviruses RaTG13, SHC104, and WIV1. By structural characterization of a naive antibody in complex with SARS-CoV-2 spike, we identified a conserved mode of recognition shared with infection-induced antibodies. We found that representative naive antibodies could signal in a B cell activation assay, and by using directed evolution, we could select for a higher-affinity RBD interaction, conferred by a single amino acid change. The minimally mutated, affinity-matured antibodies also potently neutralized SARS-CoV-2. Understanding the SARS-CoV-2 RBD­specific naive repertoire may inform potential responses capable of recognizing future SARS-CoV-2 variants or emerging coronaviruses, enabling the development of pan-coronavirus vaccines aimed at engaging protective germline responses.

Biology of COVID-19 and related viruses: Epidemiology, signs, symptoms, diagnosis, and treatment.

Coronaviruses belong to the family Coronaviridae order Nidovirales and are known causes of respiratory and intestinal disease in various mammalian and avian species. Species of coronaviruses known to infect humans are referred to as human coronaviruses (HCoVs). While traditionally, HCoVs have been a significant cause of the common cold, more recently, emergent viruses, including severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused a global pandemic. Here, we discuss coronavirus disease (COVID-19) biology, pathology, epidemiology, signs and symptoms, diagnosis, treatment, and recent clinical trials involving promising treatments.