Genomic evidence for reinfection with SARS-CoV-2: a case study

Two-Step In Vitro Model to Evaluate the Cellular Immune Response to SARS-CoV-2

The cellular immune response plays an important role in COVID-19, caused by SARS-CoV-2. This feature makes use of in vitro models' useful tools to evaluate vaccines and biopharmaceutical effects. Here, we developed a two-step model to evaluate the cellular immune response after SARS-CoV-2 infection-induced or spike protein stimulation in peripheral blood mononuclear cells (PBMC) from both unexposed and COVID-19 (primo-infected) individuals (Step1). Moreover, the supernatants of these cultures were used to evaluate its effects on lung cell lines (A549) (Step2). When PBMC from the unexposed were infected by SARS-CoV-2, cytotoxic natural killer and nonclassical monocytes expressing inflammatory cytokines genes were raised. The supernatant of these cells can induce apoptosis of A549 cells (mock vs. Step2 [mean]: 6.4% × 17.7%). Meanwhile, PBMCs from primo-infected presented their memory CD4+ T cells activated with a high production of IFNG and antiviral genes. Supernatant from past COVID-19 subjects contributed to reduce apoptosis (mock vs. Step2 [ratio]: 7.2 × 1.4) and to elevate the antiviral activity (iNOS) of A549 cells (mock vs. Step2 [mean]: 31.5% × 55.7%). Our findings showed features of immune primary cells and lung cell lines response after SARS-CoV-2 or spike protein stimulation that can be used as an in vitro model to study the immunity effects after SARS-CoV-2 antigen exposure.

Mental health of older people in social isolation: the role of physical activity at home during the COVID-19 pandemic

The COVID-19 pandemic involves a new coronavirus characterized by a respiratory disease resulting from an infection with severe acute respiratory syndrome by coronavirus 2 (SARS-CoV-2). The severity and fatality of COVID-19 are directly related to age and immunocompromised states, with older adults making up the vast majority of cases. The elderly with a higher risk of serious complications due to COVID-19 and deaths are also the group most susceptible to the damage of social isolation, impacting on mental health, resulting in a more sedentary lifestyle, and health problems due to several causes, implying need for greater attention, care and protection. Physical activity has shown excellent results for mental health, being used in different treatments and populations, when considering the elderly, one of the ways to mitigate this impact on mental health is the practice of physical activity. Here, we discuss the impacts of social isolation on mental health and the role of physical activity and exercise in the homes of the elderly as a way to protect the spread of other diseases from all causes during the COVID-19 pandemic period. To this end, we discuss some possibilities that can be used by the elderly in the period of social isolation, to the point of remaining active within their homes.

SARS-CoV-2 infection in general practice in Ireland: a seroprevalence study

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody testing in community settings may help us better understand the immune response to this virus and, therefore, help guide public health efforts.

Aim

To conduct a seroprevalence study of immunoglobulin G (IgG) antibodies in Irish GP clinics.

Design & setting

Participants were 172 staff and 799 patients from 15 general practices in the Midwest region of Ireland.

Method

This seroprevalence study utilised two manufacturers’ point-of-care (POC) SARS-CoV-2 immunoglobulin M (IgM)—IgG combined antibody tests, which were offered to patients and staff in general practice from 15 June to 10 July 2020.

Results

IgG seroprevalence was 12.6% in patients attending general practice and 11.1% in staff working in general practice, with administrative staff having the lowest seroprevalence at 2.5% and nursing staff having the highest at 17.6%. Previous symptoms suggestive of COVID-19 and history of a polymerase chain reaction (PCR) test were associated with higher seroprevalence. IgG antibodies were detected in approximately 80% of participants who had a previous PCR-confirmed infection. Average length of time between participants’ positive PCR test and positive IgG antibody test was 83 days.

Conclusion

Patients and healthcare staff in general practice in Ireland had relatively high rates of IgG to SARS-CoV-2 compared with the national average between 15 June and 10 July 2020 (1.7%). Four-fifths of participants with a history of confirmed COVID-19 disease still had detectable antibodies an average of 12 weeks post-infection. While not proof of immunity, SARS-CoV-2 POC testing can be used to estimate IgG seroprevalence in general practice settings.

Update on geographical variation and distribution of SARS-nCoV-2: A systematic review

Knowledge of a new mutant strain of SARS-coronavirus (CoV-2) is enormously essential to identify a targeted drug and for the development of the vaccine. In this article, we systematically reviewed the different mutation strains (variant of concern [VOC] and variant of interest [VOI]) which were found in different countries such as the UK, Singapore, China, Germany, Vietnam, Western Africa, Dublin, Ireland, Brazil, Iran, Italy, France, America, and Philippines. We searched four literature databases (PubMed, EMBASE, NATURE, and Willey online library) with suitable keywords and the time filter was November 2019 to June 16, 2021. To understand the worldwide spread of variants of SARS-CoV-2, we included a total of 27 articles of case reports, clinical and observational studies in the systematic review. However, these variants mostly spread because of their ability to increase transmission, virulence, and escape immunity. So, in this paper is we found mutated strains of SARS-CoV-2 like VOCs that are found in different regions across the globe are ALPHA strain in the U.K, BETA strain in South Africa, GAMMA strain in Brazil, Gamma and Beta strains in European Countries, and some VOIs like Theta variant in the Philippines.

Development and Evaluation of a Set of Spike and Receptor Binding Domain-Based Enzyme-Linked Immunosorbent Assays for SARS-CoV-2 Serological Testing

The implementation and validation of anti-SARS-CoV-2 IgG serological assays are reported in this paper. S1 and RBD proteins were used to coat ELISA plates, and several secondary antibodies served as reporters. The assays were initially validated with 50 RT-PCR positive COVID-19 sera, which showed high IgG titers of mainly IgG1 isotype, followed by IgG3. Low or no IgG2 and IgG4 titers were detected. Then, the RBD/IgG assay was further validated with 887 serum samples from RT-PCR positive COVID-19 individuals collected at different times, including 7, 14, 21, and 40 days after the onset of symptoms. Most of the sera were IgG positive at day 40, with seroconversion happening after 14–21 days. A third party conducted an additional performance test of the RBD/IgG assay with 406 sera, including 149 RT-PCR positive COVID-19 samples, 229 RT-PCR negative COVID-19 individuals, and 28 sera from individuals with other viral infections not related to SARS-CoV-2. The sensitivity of the assay was 99.33%, with a specificity of 97.82%. All the sera collected from individuals with infectious diseases other than COVID-19 were negative. Given the robustness of this RBD/IgG assay, it received approval from the sanitary authority in Mexico (COFEPRIS) for production and commercialization under the name UDISTEST-V2G^®.

Anti-SARS-CoV-2 Antibody Levels Measured by the AdviseDx SARS-CoV-2 Assay Are Concordant with Previously Available Serologic Assays but Are Not Fully Predictive of Sterilizing Immunity

With the availability of widespread SARS-CoV-2 vaccination, high-throughput quantitative anti-spike protein serological testing will likely become increasingly important. Here, we investigated the performance characteristics of the recently FDA-authorized semiquantitative anti-spike protein AdviseDx SARS-CoV-2 IgG II assay compared to the FDA-authorized anti-nucleocapsid protein Abbott Architect SARS-CoV-2 IgG, Roche Elecsys anti-SARS-CoV-2-S, EuroImmun anti-SARS-CoV-2 enzyme-linked immunosorbent assay (ELISA), and GenScript surrogate virus neutralization assays and examined the humoral response associated with vaccination, natural protection, and vaccine breakthrough infection. The AdviseDx assay had a clinical sensitivity at 14 days after symptom onset or 10 days after PCR detection of 95.6% (65/68; 95% confidence interval [CI], 87.8 to 98.8%), with two discrepant individuals seroconverting shortly thereafter. The AdviseDx assay demonstrated 100% positive percent agreement with the four other assays examined using the same symptom onset or PCR detection cutoffs. Using a recently available WHO international standard for anti-SARS-CoV-2 antibody, we provide assay unit conversion factors to international units for each of the assays examined. We performed a longitudinal survey of healthy vaccinated individuals, finding that median AdviseDx immunoglobulin levels peaked 7 weeks after first vaccine dose at approximately 4,000 IU/ml. Intriguingly, among the five assays examined, there was no significant difference in antigen binding level or neutralizing activity between two seropositive patients protected against SARS-CoV-2 infection in a previously described fishing vessel outbreak and five health care workers who experienced vaccine breakthrough of SARS-CoV-2 infection, all with variants of concern. These findings suggest that protection against SARS-CoV-2 infection cannot currently be predicted exclusively using in vitro antibody assays against wild-type SARS-CoV-2 spike. Further work is required to establish protective correlates for SARS-CoV-2 infection.

Immune response to SARS-CoV-2 in children: A review of the current knowledge

Host immune responses to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), especially in children, are still under investigation. Children with coronavirus disease 2019 (COVID‐19) constitute a significant study group of immune responses as they rarely present with severe clinical manifestations, require hospitalization, or develop complications such as multisystem inflammatory syndrome in children (MIS‐C) associated with SARS‐CoV‐2 infection. The deciphering of children’s immune responses during COVID‐19 infection will provide information about the protective mechanisms, while new potential targets for future therapies are likely to be revealed. Despite the limited immunological studies in children with COVID‐19, this review compares data between adults and children in terms of innate and adaptive immunity to SARS‐CoV‐2, discusses the possible reasons why children are mostly asymptomatic, and highlights unanswered or unclear immunological issues. Current evidence suggests that the activity of innate immunity seems to be crucial to the early phases of SARS‐CoV‐2 infection and adaptive memory immunity is vital to prevent reinfection.

Despite the limited immunological studies from children with COVID‐19, this review compares data between adults and children in terms of innate and adaptive immunity to SARS‐CoV‐2, discusses the possible reasons why children are mostly asymptomatic, and highlights unanswered or unclear immunological issues.

Safety and humoral responses to BNT162b2 mRNA vaccination of SARS-CoV-2 previously infected and naive populations

Since COVID-19 risk of reinfection is of great concern, the safety and efficacy of the mRNA-based vaccines in previously infected populations should be assessed. We studied 78 individuals previously infected with SARS-CoV-19, who received a single dose of BNT162b2 mRNA COVID-19 vaccine, and 1:2 ratio matched infection-naïve cohort who received two injections. The evaluation procedure included symptom monitoring, and serological tests. Among the post-infected population, the median IgG-S response after the first vaccine dose was 3.35 AU, compared to 2.38 AU after the second vaccine injection in the infection naive group. A strong correlation was demonstrated between IgG-S level before vaccination, and the corresponding responses after a single vaccine dose (r = 0.8, p < 0.001) in the post infected population. Short-term severe symptoms that required medical attention were found in 6.8% among the post-infected individuals, while none were found in the infection naïve population. Our data suggest that a single vaccine dose is sufficient to induce an intense immune response in post-infected population regardless of seropositivity. Although some short-term safety issues were observed compared to the infection naïve population, a single dose regimen can be considered safe in post-infected populations.

COVID-19 Research: Lessons from Non-Human Primate Models

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19). It emerged from China in December 2019 and rapidly spread across the globe, causing a pandemic with unprecedented impacts on public health and economy. Therefore, there is an urgent need for the development of curative treatments and vaccines. In humans, COVID-19 pathogenesis shows a wide range of symptoms, from asymptomatic to severe pneumonia. Identifying animal models of SARS-CoV-2 infection that reflect the clinical symptoms of COVID-19 is of critical importance. Nonhuman primates (NHPss) correspond to relevant models to assess vaccine and antiviral effectiveness. This review discusses the use of NHPs as models for COVID-19 research, with focus on the pathogenesis of SARS-CoV-2 infection, drug discovery and pre-clinical evaluation of vaccine candidates.

Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection Cases Corroborated by Sequencing

Evaluating cases of reinfection may offer some insight into areas for further investigation regarding durability of immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sixty cases of reinfection with viral sequencing were identified in PubMed, Embase, Web of Science, and medRxiv before May 1, 2021.Episodes of infection were separated by a median of 116 days. Severity of illness was greater among individuals reinfected within 90 days of initial infection, no asymptomatic initial cases developed severe reinfection, nearly half of cases had suspected escape variants, and nearly all individuals tested following reinfection were found to have detectable levels of anti-SARS-CoV-2 antibodies. This analysis is limited by the heterogeneous methods used among reports. Reinfection continues to be relatively rare. As the case rate presumably increases over time, this review will inform measurements to determine the natural history and causal determinants of reinfection in more rigorous observational cohort studies and other standardized surveillance approaches.

Laboratory-confirmed SARS-CoV-2 reinfection in the population treated at social security

The scientific community has questioned whether reinfection with SARS-CoV-2 is possible. Gradually, cases of reinfection have been documented. In Mexico, people with SARS-CoV-2 reinfection have not been officially identified. To allow a retrospective investigation of patients with PCR-confirmed SARS-CoV-2 and to identify how reinfected with this virus occurs in a population that requires medical attention. A retrospective search of the epidemiological surveillance system was performed to identify people who met the clinical criteria based on laboratory diagnosis of SARS-CoV-2 and temporality to identify cases of reinfection. Clinical information was collected from clinical records. Seven people with two separate COVID-19 events were identified in medical units in Quintana Roo, Mexico between April and December 2020. The overall median interval between the two events was 156 days (61-191 days). Six people were health workers, and one was a member of the general population. This is one of the first reports of reinfection in health personnel in Mexico, revealing that the frequency of reinfection is low among positive cases and that the interval between infection episodes was three months. There are several scenarios in the natural history of the disease that must be considered based on adequate anamnesis with a clinical-epidemiological approach to determine the correct diagnostic category.

Antibody Attributes that Predict the Neutralization and Effector Function of Polyclonal Responses to SARS-CoV-2.. [PMID: 34401890 PMCID: PMC8366811 DOI: 10.1101/2021.08.06.21261710]

While antibodies provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. In this study, we employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These predictive models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.

Science's Response to CoVID-19

CoVID-19 is a multi-symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we do not discuss herein, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID-19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID-19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.

Impaired immune response mediated by prostaglandin E2 promotes severe COVID-19 disease

The SARS-CoV-2 coronavirus has led to a pandemic with millions of people affected. The present study finds that risk-factors for severe COVID-19 disease courses, i.e. male sex, older age and sedentary life style are associated with higher prostaglandin E2 (PGE2) serum levels in blood samples from unaffected subjects. In COVID-19 patients, PGE2 blood levels are markedly elevated and correlate positively with disease severity. SARS-CoV-2 induces PGE2 generation and secretion in infected lung epithelial cells by upregulating cyclo-oxygenase (COX)-2 and reducing the PG-degrading enzyme 15-hydroxyprostaglandin-dehydrogenase. Also living human precision cut lung slices (PCLS) infected with SARS-CoV-2 display upregulated COX-2. Regular exercise in aged individuals lowers PGE2 serum levels, which leads to increased Paired-Box-Protein-Pax-5 (PAX5) expression, a master regulator of B-cell survival, proliferation and differentiation also towards long lived memory B-cells, in human pre-B-cell lines. Moreover, PGE2 levels in serum of COVID-19 patients lowers the expression of PAX5 in human pre-B-cell lines. The PGE2 inhibitor Taxifolin reduces SARS-CoV-2-induced PGE2 production. In conclusion, SARS-CoV-2, male sex, old age, and sedentary life style increase PGE2 levels, which may reduce the early anti-viral defense as well as the development of immunity promoting severe disease courses and multiple infections. Regular exercise and Taxifolin treatment may reduce these risks and prevent severe disease courses.

Home alone? Effect of weather-induced behaviour on spread of SARS-CoV-2 in Germany

In early 2020 the world was struck by the epidemic of novel SARS-CoV-2 virus. Like many others, German government has introduced severe contact restrictions to limit the spread of infection. This paper analyses effects of weather on the spread of the disease under the described circumstances. We demonstrate that regions reported lower growth rates of the number of the infection cases after days with higher temperatures, no rain and low humidity. We argue that this effect is channelled through human behaviour. The evidence suggests that "good" weather attracts individuals to outdoor (safer) environments, thus, deterring people from indoor (less safe) environments. Understanding this relationship is important for improving the measures aiming at combating the spread of the virus.

Persistence of immunity to SARS-CoV-2 over time in the ski resort Ischgl

Background In early March 2020, a SARS-CoV-2 outbreak in the ski resort Ischgl in Austria triggered the spread of SARS-CoV-2 throughout Austria and Northern Europe. In a previous study, we found that the seroprevalence in the adult population of Ischgl had reached 45% by the end of April, representing an exceptionally high level of local seropositivity in Europe. We performed a follow-up study in Ischgl, which is the first to show persistence of immunity and protection against SARS-CoV-2 and some of its variants at a community level. Methods Of the 1259 adults that participated in the baseline study, 801 have been included in the follow-up in November 2020. The study involved the analysis of binding and neutralizing antibodies and T cell responses. In addition, the incidence of SARS-CoV-2 and its variants in Ischgl was compared to the incidence in similar municipalities in Tyrol until April 2021. Findings For the 801 individuals that participated in both studies, the seroprevalence declined from 51.4% (95% confidence interval (CI) 47.9-54.9) to 45.4% (95% CI 42.0-49.0). Median antibody concentrations dropped considerably (5.345, 95% CI 4.833 - 6.123 to 2.298, 95% CI 2.141 - 2.527) but antibody avidity increased (17.02, 95% CI 16.49 - 17.94 to 42.46, 95% CI 41.06 - 46.26). Only one person had lost detectable antibodies and T cell responses. In parallel to this persistent immunity, we observed that Ischgl was relatively spared, compared to similar municipalities, from the prominent second COVID-19 wave that hit Austria in November 2020. In addition, we used sequencing data to show that the local immunity acquired from wild-type infections also helped to curb infections from variants of SARS-CoV-2 which spread in Austria since January 2021. Interpretation The relatively high level of seroprevalence (40-45%) in Ischgl persisted and might have been associated with the observed protection of Ischgl residents against virus infection during the second COVID-19 wave as well as against variant spread in 2021. Funding Funding was provided by the government of Tyrol and the FWF Austrian Science Fund.

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study

BACKGROUND

A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia.

METHODS

In this observational, genomic epidemiological study, we did genomic sequencing of all laboratory-confirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK.

FINDINGS

Between Jan 25, 2020, and Jan 31, 2021, there were 20 451 laboratory-confirmed cases of COVID-19 in Victoria, Australia, of which 15 431 were submitted for sequencing, and 11 711 met all quality control metrics and were included in our analysis. We identified 595 genomic clusters, with a median of five cases per cluster (IQR 2-11). Overall, samples from 11 503 (98·2%) of 11 711 cases clustered with another sample in Victoria, either within a genomic cluster or transmission network. Genomic analysis revealed that 10 426 cases, including 10 416 (98·4%) of 10 584 locally acquired cases, diagnosed during the second wave (between June and October, 2020) were derived from a single incursion from hotel quarantine, with the outbreak lineage (transmission network G, lineage D.2) rapidly detected in other Australian states and territories. Phylodynamic analyses indicated that the epidemic growth rate of the outbreak lineage in Victoria during the initial growth phase (samples collected between June 4 and July 9, 2020; 47·4 putative transmission events, per branch, per year [1/years; 95% credible interval 26·0-85·0]), was similar to that of other reported variants, such as B.1.1.7 in the UK (mean approximately 71·5 1/years). Strict interventions were implemented, and the outbreak lineage has not been detected in Australia since Oct 29, 2020. Subsequent cases represented independent international or interstate introductions, with limited local spread.

INTERPRETATION

Our study highlights how rapid escalation of clonal outbreaks can occur from a single incursion. However, strict quarantine measures and decisive public health responses to emergent cases are effective, even with high epidemic growth rates. Real-time genomic surveillance can alter the way in which public health agencies view and respond to COVID-19 outbreaks.

FUNDING

The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.

Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors

Arrival of the novel SARS-CoV-2 has launched a worldwide effort to identify both pre-approved and novel therapeutics targeting the viral proteome, highlighting the urgent need for efficient drug discovery strategies. Even with effective vaccines, infection is possible, and at-risk populations would benefit from effective drug compounds that reduce the lethality and lasting damage of COVID-19 infection. The CoV-2 MacroD-like macrodomain (Mac1) is implicated in viral pathogenicity by disrupting host innate immunity through its mono (ADP-ribosyl) hydrolase activity, making it a prime target for antiviral therapy. We therefore solved the structure of CoV-2 Mac1 from non-structural protein 3 (Nsp3) and applied structural and sequence-based genetic tracing, including newly determined A. pompejana MacroD2 and GDAP2 amino acid sequences, to compare and contrast CoV-2 Mac1 with the functionally related human DNA-damage signaling factor poly (ADP-ribose) glycohydrolase (PARG). Previously, identified targetable features of the PARG active site allowed us to develop a pharmacologically useful PARG inhibitor (PARGi). Here, we developed a focused chemical library and determined 6 novel PARGi X-ray crystal structures for comparative analysis. We applied this knowledge to discovery of CoV-2 Mac1 inhibitors by combining computation and structural analysis to identify PARGi fragments with potential to bind the distal-ribose and adenosyl pockets of the CoV-2 Mac1 active site. Scaffold development of these PARGi fragments has yielded two novel compounds, PARG-345 and PARG-329, that crystallize within the Mac1 active site, providing critical structure-activity data and a pathway for inhibitor optimization. The reported structural findings demonstrate ways to harness our PARGi synthesis and characterization pipeline to develop CoV-2 Mac1 inhibitors targeting the ADP-ribose active site. Together, these structural and computational analyses reveal a path for accelerating development of antiviral therapeutics from pre-existing drug optimization pipelines.

COVID-19 Reinfection in a Young Medical Doctor: A Case Report

There is hardly any report of reinfection due to coronavirus disease 2019 (COVID-19) in medical professionals from Nepal. We report a case of a 32-year-old doctor with COVID-19 reinfection. Symptoms during the first infection were mild. After one month, he was reinfected and developed diarrhea as well as a continuous high fever. His d-dimer and ferritin were much increased. Computed tomography chest showed bilateral lymph nodes, minimal pleural effusion, and scattered linear fibrosis. After discharge, his depression and myalgia persisted for one month. During reinfection, his symptoms were more severe and cost of treatment was almost eight times his monthly salary and he could not work for six weeks. Possible reasons for severe reinfection and differential diagnoses like cytokine storm, multisystem inflammatory syndrome, reactivation of COVID-19, and infection due to new variants were discussed. Whether infected or vaccinated or not, all should take recommended vaccination and primary-preventive as well as health-promotive measures.

Modeling neutral viral mutations in the spread of SARS-CoV-2 epidemics

Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks in which viruses are explicitly represented by finite chains of nucleotides that can mutate inside the host. Under the hypothesis of neutral evolution we compute analytically the average pairwise genetic distance between all infecting viruses over time. We also derive a mean-field version of this equation that can be added directly to compartmental models such as SIR or SEIR to estimate the genetic evolution. We compare our results with the inferred genetic evolution of SARS-CoV-2 at the beginning of the epidemic in China and found good agreement with the analytical solution of our model. Finally, using genetic distance as a proxy for different strains, we use numerical simulations to show that the lower the connectivity between communities, e.g., cities, the higher the probability of reinfection.

COVID-19 false dichotomies and a comprehensive review of the evidence regarding public health, COVID-19 symptomatology, SARS-CoV-2 transmission, mask wearing, and reinfection

Scientists across disciplines, policymakers, and journalists have voiced frustration at the unprecedented polarization and misinformation around coronavirus disease 2019 (COVID-19) pandemic. Several false dichotomies have been used to polarize debates while oversimplifying complex issues. In this comprehensive narrative review, we deconstruct six common COVID-19 false dichotomies, address the evidence on these topics, identify insights relevant to effective pandemic responses, and highlight knowledge gaps and uncertainties. The topics of this review are: 1) Health and lives vs. economy and livelihoods, 2) Indefinite lockdown vs. unlimited reopening, 3) Symptomatic vs. asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, 4) Droplet vs. aerosol transmission of SARS-CoV-2, 5) Masks for all vs. no masking, and 6) SARS-CoV-2 reinfection vs. no reinfection. We discuss the importance of multidisciplinary integration (health, social, and physical sciences), multilayered approaches to reducing risk ("Emmentaler cheese model"), harm reduction, smart masking, relaxation of interventions, and context-sensitive policymaking for COVID-19 response plans. We also address the challenges in understanding the broad clinical presentation of COVID-19, SARS-CoV-2 transmission, and SARS-CoV-2 reinfection. These key issues of science and public health policy have been presented as false dichotomies during the pandemic. However, they are hardly binary, simple, or uniform, and therefore should not be framed as polar extremes. We urge a nuanced understanding of the science and caution against black-or-white messaging, all-or-nothing guidance, and one-size-fits-all approaches. There is a need for meaningful public health communication and science-informed policies that recognize shades of gray, uncertainties, local context, and social determinants of health.

Decline in neutralising antibody responses, but sustained T-cell immunity, in COVID-19 patients at 7 months post-infection

Objectives

This study aimed to explore the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific humoral responses and T-cell responses in patients who have recovered from coronavirus disease 2019 (COVID-19) to understand the natural protective immune responses and to facilitate the development of vaccines.

Methods

We conducted a combined assessment of the changes in neutralising antibody levels and SARS-CoV-2-specific T-cell responses over time in 27 patients up to 7 months after infection.

Results

The neutralising antibody remained detectable in 96.3% of the patients at their second visit at about 7 months post-onset of symptoms. However, their humoral responses, including titres of the spike receptor-binding domain IgG and neutralising antibody, decreased significantly compared with those at first clinic visit. By contrast, the proportions of spike-specific CD4⁺ T cells, but not CD8⁺ T cells, in COVID-19 patients after recovery were persistently higher than those in healthy controls. No significant change was observed in the proportion of spike-specific CD4⁺ T cells in patients who had recovered from COVID-19 within 7 months.

Conclusion

The SARS-CoV-2-specific T-cell immune responses persisted, while the neutralising antibodies decayed. Further studies are needed to extend the longevity of neutralising antibodies and to evaluate whether these T cells are sufficient to protect patients from reinfection.

Recurrent and persistent infection with SARS-CoV-2 - epidemiological data and case reports from Western Sweden, 2020

BACKGROUND

Reinfections with SARS-CoV-2 have been reported and most cases were classified as mild. Reports of persistent infection with SARS-CoV-2 are rare.

AIM

To investigate the frequency of recurrent and persistent infection with SARS-CoV-2.

METHODS

Possible cases of reinfection and persistent infection were retrospectively identified in a database of 59,998 patients. Deep sequencing of SARS-CoV-2 genomes was performed.

RESULTS

We report the first case of COVID-19 reinfection in Sweden and three cases of infection with persistence over several months. The rate of sequencing-verified reinfection was 0.02% (one patient out of 6014 patients testing positive during the period).

CONCLUSIONS

The reinfected patient had mild symptoms during the second episode, which might reflect partial immunity. The frequency of reinfection during the first wave of the pandemic in western Sweden was very low. Our results indicate that elderly with a putative reinfection more likely have persistent COVID-19.

Severe reinfection with severe acute respiratory syndrome coronavirus 2 in a nursing home resident: a case report

BACKGROUND

The topic of natural immunity related to severe acute respiratory syndrome coronavirus 2 remains controversial. Although evidence suggests postinfection immunity can be achieved, there have been reported cases of reinfection with similar or milder symptoms. Information on severe disease manifestation during reinfection is not known. We present a case of reinfection with a more severe presentation as compared with the initial infection.

CASE REPORT

We describe a white male patient from a nursing home who was reinfected with severe acute respiratory syndrome coronavirus 2 with severe disease manifesting as dyspnea, fevers, and encephalopathy with hypoxemic respiratory failure requiring intubation, elevated inflammatory markers, and lung infiltrates on imaging, after initially testing positive with mild symptoms 2 months prior to presentation. Notably, severe acute respiratory syndrome coronavirus 2 antibodies were detected, which indicated this was a coronavirus disease 2019 reinfection. After treatment with remdesivir, dexamethasone, and convalescent plasma, he was subsequently extubated and discharged home after 2 weeks.

CONCLUSION

It is not clear whether an initial infection with severe acute respiratory syndrome coronavirus 2 and recovery provides prolonged immunity beyond 2 months. Furthermore, even if antibodies are present, it does not guarantee an attenuated course during reinfection. Therefore, vaccination plays an important role in prevention. Long-term cohort studies will be needed to study the factors behind reinfection.

Dynamics of SARS-CoV-2 with waning immunity in the UK population

The dynamics of immunity are crucial to understanding the long-term patterns of the SARS-CoV-2 pandemic. Several cases of reinfection with SARS-CoV-2 have been documented 48-142 days after the initial infection and immunity to seasonal circulating coronaviruses is estimated to be shorter than 1 year. Using an age-structured, deterministic model, we explore potential immunity dynamics using contact data from the UK population. In the scenario where immunity to SARS-CoV-2 lasts an average of three months for non-hospitalized individuals, a year for hospitalized individuals, and the effective reproduction number after lockdown ends is 1.2 (our worst-case scenario), we find that the secondary peak occurs in winter 2020 with a daily maximum of 387 000 infectious individuals and 125 000 daily new cases; threefold greater than in a scenario with permanent immunity. Our models suggest that longitudinal serological surveys to determine if immunity in the population is waning will be most informative when sampling takes place from the end of the lockdown in June until autumn 2020. After this period, the proportion of the population with antibodies to SARS-CoV-2 is expected to increase due to the secondary wave. Overall, our analysis presents considerations for policy makers on the longer-term dynamics of SARS-CoV-2 in the UK and suggests that strategies designed to achieve herd immunity may lead to repeated waves of infection as immunity to reinfection is not permanent. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.

SARS-CoV-2 antibody dynamics and transmission from community-wide serological testing in the Italian municipality of Vo'

In February and March 2020, two mass swab testing campaigns were conducted in Vo', Italy. In May 2020, we tested 86% of the Vo' population with three immuno-assays detecting antibodies against the spike and nucleocapsid antigens, a neutralisation assay and Polymerase Chain Reaction (PCR). Subjects testing positive to PCR in February/March or a serological assay in May were tested again in November. Here we report on the results of the analysis of the May and November surveys. We estimate a seroprevalence of 3.5% (95% Credible Interval (CrI): 2.8-4.3%) in May. In November, 98.8% (95% Confidence Interval (CI): 93.7-100.0%) of sera which tested positive in May still reacted against at least one antigen; 18.6% (95% CI: 11.0-28.5%) showed an increase of antibody or neutralisation reactivity from May. Analysis of the serostatus of the members of 1,118 households indicates a 26.0% (95% CrI: 17.2-36.9%) Susceptible-Infectious Transmission Probability. Contact tracing had limited impact on epidemic suppression.

Beyond the new normal: Assessing the feasibility of vaccine-based suppression of SARS-CoV-2

As the COVID-19 pandemic drags into its second year, there is hope on the horizon, in the form of SARS-CoV-2 vaccines which promise disease suppression and a return to pre-pandemic normalcy. In this study we critically examine the basis for that hope, using an epidemiological modeling framework to establish the link between vaccine characteristics and effectiveness in bringing an end to this unprecedented public health crisis. Our findings suggest that a return to pre-pandemic social and economic conditions without fully suppressing SARS-CoV-2 will lead to extensive viral spread, resulting in a high disease burden even in the presence of vaccines that reduce risk of infection and mortality. Our modeling points to the feasibility of complete SARS-CoV-2 suppression with high population-level compliance and vaccines that are highly effective at reducing SARS-CoV-2 infection. Notably, vaccine-mediated reduction of transmission is critical for viral suppression, and in order for partially-effective vaccines to play a positive role in SARS-CoV-2 suppression, complementary biomedical interventions and public health measures must be deployed simultaneously.

Is increased mortality by multiple exposures to COVID-19 an overseen factor when aiming for herd immunity?

BACKGROUND

Governments across the globe responded with different strategies to the COVID-19 pandemic. While some countries adopted measures, which have been perceived controversial, others pursued a strategy aiming for herd immunity. The latter is even more controversial and has been called unethical by the WHO Director-General. Inevitably, without proper control measures, viral diversity increases and multiple infectious exposures become common, when the pandemic reaches its maximum. This harbors not only a potential threat overseen by simplified theoretical arguments in support of herd immunity, but also deserves attention when assessing response measures to increasing numbers of infection.

METHODS AND FINDINGS

We extend the simulation model underlying the pandemic preparedness web interface CovidSim 1.1 (http://covidsim.eu/) to study the hypothetical effect of increased morbidity and mortality due to 'multi-infections', either acquired at by successive infective contacts during the course of one infection or by a single infective contact with a multi-infected individual. The simulations are adjusted to reflect roughly the situation in the USA. We assume a phase of general contact reduction ("lockdown") at the beginning of the epidemic and additional case-isolation measures. We study the hypothetical effects of varying enhancements in morbidity and mortality, different likelihoods of multi-infected individuals to spread multi-infections and different susceptibility to multi-infections in different disease phases. It is demonstrated that multi-infections lead to a slight reduction in the number of infections, as these are more likely to get isolated due to their higher morbidity. However, the latter substantially increases the number of deaths. Furthermore, simulations indicate that a potential second lockdown can substantially decrease the epidemic peak, the number of multi-infections and deaths.

CONCLUSIONS

Enhanced morbidity and mortality due to multiple disease exposure is a potential threat in the COVID-19 pandemic that deserves more attention. Particularly it underlines another facet questioning disease management strategies aiming for herd immunity.

Genome-Wide Variation in Betacoronaviruses

The Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 originated in bats and adapted to infect humans. Several SARS-CoV-2 strains have been identified. Genetic variation is fundamental to virus evolution and, in response to selection pressure, is manifested as the emergence of new strains and species adapted to different hosts or with novel pathogenicity. The combination of variation and selection forms a genetic footprint on the genome, consisting of the preferential accumulation of mutations in particular areas. Properties of betacoronaviruses contributing to variation and the emergence of new strains and species are beginning to be elucidated. To better understand their variation, we profiled the accumulation of mutations in all species in the genus Betacoronavirus, including SARS-CoV-2 and two other species that infect humans: SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Variation profiles identified both genetically stable and variable areas at homologous locations across species within the genus Betacoronavirus. The S glycoprotein is the most variable part of the genome and is structurally disordered. Other variable parts include proteins 3 and 7 and ORF8, which participate in replication and suppression of antiviral defense. In contrast, replication proteins in ORF1b are the least variable. Collectively, our results show that variation and structural disorder in the S glycoprotein is a general feature of all members of the genus Betacoronavirus, including SARS-CoV-2. These findings highlight the potential for the continual emergence of new species and strains with novel biological properties and indicate that the S glycoprotein has a critical role in host adaptation.

IMPORTANCE Natural infection with SARS-CoV-2 and vaccines triggers the formation of antibodies against the S glycoprotein, which are detected by antibody-based diagnostic tests. Our analysis showed that variation in the S glycoprotein is a general feature of all species in the genus Betacoronavirus, including three species that infect humans: SARS-CoV, SARS-CoV-2, and MERS-CoV. The variable nature of the S glycoprotein provides an explanation for the emergence of SARS-CoV-2, the differentiation of SARS-CoV-2 into strains, and the probability of SARS-CoV-2 repeated infections in people. Variation of the S glycoprotein also has important implications for the reliability of SARS-CoV-2 antibody-based diagnostic tests and the design and deployment of vaccines and antiviral drugs. These findings indicate that adjustments to vaccine design and deployment and to antibody-based diagnostic tests are necessary to account for S glycoprotein variation.

Multiple Sclerosis, Disease-Modifying Therapies and COVID-19: A Systematic Review on Immune Response and Vaccination Recommendations

Understanding the risks of COVID-19 in patients with Multiple Sclerosis (MS) receiving disease-modifying therapies (DMTs) and their immune reactions is vital to analyze vaccine response dynamics. A systematic review on COVID-19 course and outcomes in patients receiving different DMTs was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Emerging data on SARS-CoV-2 vaccines was used to elaborate recommendations. Data from 4417 patients suggest that MS per se do not portend a higher risk of severe COVID-19. As for the general population, advanced age, comorbidities, and higher disability significantly impact COVID-19 outcomes. Most DMTs have a negligible influence on COVID-19 incidence and outcome, while for those causing severe lymphopenia and hypogammaglobulinemia, such as anti-CD20 therapies, there might be a tendency of increased hospitalization, worse outcomes and a higher risk of re-infection. Blunted immune responses have been reported for many DMTs, with vaccination implications. Clinical evidence does not support an increased risk of MS relapse or vaccination failure, but vaccination timing needs to be individually tailored. For cladribine and alemtuzumab, it is recommended to wait 3-6 months after the last cycle until vaccination. For the general anti-CD20 therapies, vaccination must be deferred toward the end of the cycle and the next dose administered at least 4-6 weeks after completing vaccination. Serological status after vaccination is highly encouraged. Growing clinical evidence and continuous surveillance are extremely important to continue guiding future treatment strategies and vaccination protocols.

Estimating infectiousness throughout SARS-CoV-2 infection course

Two elementary parameters for quantifying viral infection and shedding are viral load and whether samples yield a replicating virus isolate in cell culture. We examined 25,381 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Germany, including 6110 from test centers attended by presymptomatic, asymptomatic, and mildly symptomatic (PAMS) subjects, 9519 who were hospitalized, and 1533 B.1.1.7 lineage infections. The viral load of the youngest subjects was lower than that of the older subjects by 0.5 (or fewer) log10 units, and they displayed an estimated ~78% of the peak cell culture replication probability; in part this was due to smaller swab sizes and unlikely to be clinically relevant. Viral loads above 109 copies per swab were found in 8% of subjects, one-third of whom were PAMS, with a mean age of 37.6 years. We estimate 4.3 days from onset of shedding to peak viral load (108.1 RNA copies per swab) and peak cell culture isolation probability (0.75). B.1.1.7 subjects had mean log10 viral load 1.05 higher than that of non-B.1.1.7 subjects, and the estimated cell culture replication probability of B.1.1.7 subjects was higher by a factor of 2.6.

Host- and Species-Dependent Quasispecies Divergence of Severe Acute Respiratory Syndrome Coronavirus-2 in Non-human Primate Models

Recently, newly emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been continuously reported worldwide. However, the precise evaluation of SARS-CoV-2 microevolution in host is very limited because the exact genetic information of infected virus could not be acquired in human researches. In this report, we performed deep sequencing for seed virus and SARS-CoV-2 isolated in eight cynomolgus and rhesus macaques at 3 days postinoculation and evaluated single-nucleotide polymorphisms (SNPs) in SARS-CoV-2 by variant analysis. A total of 69 single-nucleotide variants (SNVs) were present in the 5′-untranslated region (UTR), 3′-UTR, ORF1ab, S, ORF3a, ORF8, and N genes of the seed virus passaged in VERO cells. Between those present on the seed virus and those on each SARS-CoV-2 isolated from the lungs of the macaques, a total of 29 variants was identified in 4 coding proteins (ORF1ab, S, ORF3a, and N) and non-coding regions (5′- and 3′-UTR). Variant number was significantly different according to individuals and ranged from 2 to 11. Moreover, the average major frequency variation was identified in six sites between the cynomolgus monkeys and rhesus macaques. As with diverse SNPs in SARS-CoV-2, the values of viral titers in lungs were significantly different according to individuals and species. Our study first revealed that the genomes of SARS-CoV-2 differ according to individuals and species despite infection of the identical virus in non-human primates (NHPs). These results are important for the interpretation of longitudinal studies evaluating the evolution of the SARS-CoV-2 in human beings and development of new diagnostics, vaccine, and therapeutics targeting SARS-CoV-2.

Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp13 helicase

The coronavirus disease 2019 (COVID-19) pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global public health challenge. While the efficacy of vaccines against emerging and future virus variants remains unclear, there is a need for therapeutics. Repurposing existing drugs represents a promising and potentially rapid opportunity to find novel antivirals against SARS-CoV-2. The virus encodes at least nine enzymatic activities that are potential drug targets. Here, we have expressed, purified and developed enzymatic assays for SARS-CoV-2 nsp13 helicase, a viral replication protein that is essential for the coronavirus life cycle. We screened a custom chemical library of over 5000 previously characterized pharmaceuticals for nsp13 inhibitors using a fluorescence resonance energy transfer-based high-throughput screening approach. From this, we have identified FPA-124 and several suramin-related compounds as novel inhibitors of nsp13 helicase activity in vitro. We describe the efficacy of these drugs using assays we developed to monitor SARS-CoV-2 growth in Vero E6 cells.

Incidence of SARS-CoV-2 infection in health care workers from Northern Italy based on antibody status: immune protection from secondary infection- A retrospective observational case-controlled study

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Immunity from natural SARS-CoV-2 infection is protective in healthcare workers

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Secondary infection is associated with low or absent serum neutralizing titer

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Anti-Spike IgG were not significantly lower in subjects with secondary infections

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Secondary infection is usually asymptomatic or mildly symptomatic

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Vaccination of SARS-CoV-2-seronegative subjects might be prioritized

Objective

The protection from SARS-CoV-2 infection induced by SARS-CoV-2 anti-S1 and anti-S2 IgG antibody positivity resulting from natural infection was evaluated.

Methods

The frequency of SARS-CoV-2 infection (as determined by virus RNA detection) was evaluated in a group of 1,460 seropositive and a control group of 8,150 seronegative healthcare workers in three Centres of Northern Italy in the period June-November 2020. Neutralizing serum titers were analyzed in seropositive subjects with or without secondary SARS-CoV-2 infection.

Results

During the 6-month survey, 1.78% seropositive subjects developed secondary SARS-CoV-2 infection while 6.63% seronegative controls developed primary infection (odds ratio: 0.26; 95% confidence interval: 0.17-0.38). Secondary infection was associated with low or absent serum neutralizing titer (p<0.01) and was mildly symptomatic in 45.8% cases vs 71.4% symptomatic primary infections (odds ratio: 0.34; 95% confidence interval: 0.16-0.78).

Conclusions

Immunity from natural infection appears protective from secondary infection; therefore, vaccination of seronegative subjects might be prioritized.

Early detection of SARS-CoV-2 P.1 variant in Southern Brazil and reinfection of the same patient by P.2

Multiple variants of the Severe Acute Respiratory Syndrome coronavirus 2 virus (SARS-CoV-2) have been constantly reported across the world. The B.1.1.28 lineage has been evolving in Brazil since February 2020 and originated the P.1 variant of concern (VOC), recently named as the Gamma variant by the newly WHO nomenclature proposal, and P.2 as a variant of interest (VOI). Here we describe an early case of P.1 primary infection in Southern Brazil in late November 2020, soon after the emergence of the variant in Manaus, Northern Brazil. The same male patient was reinfected by another B.1.1.28 variant, namely P.2, in March, 2021. The genomic analysis confirmed genetically significant differences between the two viruses recovered in both infections, the P.1 lineage in the first episode and P.2 in the reinfection. Due the very early detection of P.1, we have also investigated the circulation of P.1 in the same region by differential RT-qPCR, showing that this was an isolated case of P.1 at the time of detection, and this variant has disseminated and became prominent from late January to the end of March, 2021. SARS-CoV-2 recent reports of reinfection have raised critical questions on whether and how well a first infection protects against reinfection.

The Impact of Increasing Disease Prevalence, False Omissions, and Diagnostic Uncertainty on Coronavirus Disease 2019 (COVID-19) Test Performance

CONTEXT.—

Coronavirus disease 2019 (COVID-19) test performance depends on predictive values in settings of increasing disease prevalence. Geospatially distributed diagnostics with minimal uncertainty facilitate efficient point-of-need strategies.

OBJECTIVES.—

To use original mathematics to interpret COVID-19 test metrics; assess US Food and Drug Administration Emergency Use Authorizations and Health Canada targets; compare predictive values for multiplex, antigen, polymerase chain reaction kit, point-of-care antibody, and home tests; enhance test performance; and improve decision-making.

DESIGN.—

PubMed/newsprint-generated articles documenting prevalence. Mathematica and open access software helped perform recursive calculations, graph multivariate relationships, and visualize performance by comparing predictive value geometric mean-squared patterns.

RESULTS.—

Tiered sensitivity/specificity comprised: T1, 90%, 95%; T2, 95%, 97.5%; and T3, 100%, ≥99%. Tier 1 false negatives exceeded true negatives at >90.5% prevalence; false positives exceeded true positives at <5.3% prevalence. High-sensitivity/specificity tests reduced false negatives and false positives, yielding superior predictive values. Recursive testing improved predictive values. Visual logistics facilitated test comparisons. Antigen test quality fell off as prevalence increased. Multiplex severe acute respiratory syndrome (SARS)-CoV-2)*influenza A/B*respiratory syncytial virus testing performed reasonably well compared with tier 3. Tier 3 performance with a tier 2 confidence band lower limit will generate excellent performance and reliability.

CONCLUSIONS.—

The overriding principle is to select the best combined performance and reliability pattern for the prevalence bracket. Some public health professionals recommend repetitive testing to compensate for low sensitivity. More logically, improved COVID-19 assays with less uncertainty conserve resources. Multiplex differentiation of COVID-19 from influenza A/B-respiratory syncytial virus represents an effective strategy if seasonal flu surges next year.

Characterization of antibody response in asymptomatic and symptomatic SARS-CoV-2 infection

SARS-CoV-2 pandemic is causing high morbidity and mortality burden worldwide with unprecedented strain on health care systems. To investigate the time course of the antibody response in relation to the outcome we performed a study in hospitalized COVID-19 patients. As comparison we also investigated the time course of the antibody response in SARS-CoV-2 asymptomatic subjects. Study results show that patients produce a strong antibody response to SARS-CoV-2 with high correlation between different viral antigens (spike protein and nucleoprotein) and among antibody classes (IgA, IgG, and IgM and neutralizing antibodies). The antibody peak is reached by 3 weeks from hospital admission followed by a sharp decrease. No difference was observed in any parameter of the antibody classes, including neutralizing antibodies, between subjects who recovered or with fatal outcome. Only few asymptomatic subjects developed antibodies at detectable levels.

SARS-CoV-2 Transmission Risk Among National Basketball Association Players, Staff, and Vendors Exposed to Individuals With Positive Test Results After COVID-19 Recovery During the 2020 Regular and Postseason

IMPORTANCE

Clinical data are lacking regarding the risk of viral transmission from individuals who have positive reverse-transcription-polymerase chain reaction (RT-PCR) SARS-CoV-2 test results after recovery from COVID-19.

OBJECTIVE

To describe case characteristics, including viral dynamics and transmission of infection, for individuals who have clinically recovered from SARS-CoV-2 infection but continued to have positive test results following discontinuation of isolation precautions.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective cohort study used data collected from June 11, 2020, to October 19, 2020, as part of the National Basketball Association (NBA) closed campus occupational health program in Orlando, Florida, which required daily RT-PCR testing and ad hoc serological testing for SARS-CoV-2 IgG antibodies. Nearly 4000 NBA players, staff, and vendors participated in the NBA's regular and postseason occupational health program in Orlando. Persistent positive cases were those who recovered from a documented SARS-CoV-2 infection, satisfied US Centers for Disease Control and Prevention criteria for discontinuation of isolation precautions, and had at least 1 postinfection positive RT-PCR test(s) result.

EXPOSURES

Person-days of participation in indoor, unmasked activities that involved direct exposure between persistent positive cases and noninfected individuals.

MAIN OUTCOMES AND MEASURES

Transmission of SARS-CoV-2 following interaction with persistent positive individuals, as measured by the number of new COVID-19 cases in the Orlando campus program.

RESULTS

Among 3648 individuals who participated, 36 (1%) were persistent positive cases, most of whom were younger than 30 years (24 [67%]) and male (34 [94%]). Antibodies were detected in 33 individuals (91.7%); all remained asymptomatic following the index persistent positive RT-PCR result. Cycle threshold values for persistent positive RT-PCR test results were typically above the Roche cobas SARS-CoV-2 limit of detection. Cases were monitored for up to 100 days (mean [SD], 51 [23.9] days), during which there were at least 1480 person-days of direct exposure activities, with no transmission events or secondary infections of SARS-CoV-2 detected (0 new cases).

CONCLUSIONS AND RELEVANCE

In this retrospective cohort study of the 2020 NBA closed campus occupational health program, recovered individuals who continued to test positive for SARS-CoV-2 following discontinuation of isolation were not infectious to others. These findings support time-based US Centers of Disease Control and Prevention recommendations for ending isolation.

Conundrum of re-positive COVID-19 cases: A systematic review of case reports and case series

BACKGROUND

The systematic review was conducted to summarize and synthesize evidence from all available case series and case reports published on re-positive COVID-19 cases.

METHODS

The systematic review was registered with Prospero (CRD42020210446). PRISMA guidelines were followed for conducting the systematic review. Inclusion criteria for studies included case reports and case series which have documented cases of positive reverse transcriptase polymerase chain reaction (RT-PCR) after a period of clinical improvement or a negative RT-PCR report. Reviews, opinions, and animal studies were excluded. Methodological quality was assessed using the modified Murad scale.

RESULTS

A total of 30 case reports/case series were included in the study, wherein a total of 219 cases were included. In re-positive cases, the age range varied from 10 months to 91 years. The pooled proportion of positive cases after follow-up using random-effects was 12% (95% confidence interval [CI]: 09%-15%). Among the re-positives, a total of 57 cases (26%) had comorbidities. A total of 51 (23.3%) and 17 (7.8%) re-positive cases had been treated with antivirals and corticosteroids, respectively. Only a few studies have confirmed the presence of antibodies after the first episode. Studies that included contact tracing of re-positives did not find any positive cases among close contacts of re-positive cases.

CONCLUSION

The systemic review found that reinfection is a possibility within 123 days of a negative RT-PCR test in a small number of cases of COVID-19. This has wider ramifications in framing clinical, preventive, and public health policy guidelines.

SARS-CoV-2 antibody kinetics eight months from COVID-19 onset: Persistence of spike antibodies but loss of neutralizing antibodies in 24% of convalescent plasma donors

Elucidating the characteristics of human immune response against SARS-CoV-2 is of high priority and relevant for determining vaccine strategies. We report the results of a follow-up evaluation of anti-SARS-CoV-2 antibodies in 148 convalescent plasma donors who participated in a phase 2 study at a median of 8.3 months (range 6.8-10.5 months) post first symptom onset. Monitoring responses over time, we found contraction of antibody responses for all four antigens tested, with Spike antibodies showing higher persistence than Nucleocapsid antibodies. A piecewise linear random-effects multivariate regression analysis showed a bi-phasic antibody decay with a more pronounced decrease during the first 6 months post symptoms onset by analysis of two intervals. Interestingly, antibodies to Spike showed better longevity whereas their neutralization ability contracted faster. As a result, neutralizing antibodies were detected in only 76% of patients at the last time point. In a multivariate analysis, older age and hospitalization were independently associated with higher Spike, Spike-RBD, Nucleocapsid, N-RBD antibodies and neutralizing antibody levels. Results on persistence and neutralizing ability of anti-SARS-CoV-2 antibodies, especially against Spike and Spike-RBD, should be considered in the design of future vaccination strategies.

Critical Presentation of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection: A Case Report

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfections have been reported; however, most cases are milder than the primary infection. We report the first case of a life-threatening critical presentation of a SARS-CoV-2 reinfection.

METHODS

A 62-year-old man from Palamós (Spain) suffered a first mild coronavirus disease 2019 (COVID-19) episode in March 2020, confirmed by 2 independent SARS-CoV-2 nasopharyngeal polymerase chain reaction (PCR) assays and a normal radiograph. He recovered completely and tested negative on 2 consecutive PCRs. In August 2020, the patient developed a second SARS-CoV-2 infection with life-threatening bilateral pneumonia and Acute respiratory distress syndrome criteria, requiring COVID-19-specific treatment (remdesivir + dexamethasone) plus high-flow oxygen therapy. Nasopharyngeal swabs from the second episode were obtained for virus quantification by real-time PCR, for virus outgrowth and sequencing. In addition, plasma and peripheral blood mononuclear cells during the hospitalization period were used to determine SARS-CoV-2-specific humoral and T-cell responses.

RESULTS

Genomic analysis of SARS-CoV-2 showed that the virus had probably originated shortly before symptom onset. When the reinfection occurred, the subject showed a weak immune response, with marginal humoral and specific T-cell responses against SARS-CoV-2. All antibody isotypes tested as well as SARS-CoV-2 neutralizing antibodies increased sharply after day 8 postsymptoms. A slight increase of T-cell responses was observed at day 19 after symptom onset.

CONCLUSIONS

The reinfection was firmly documented and occurred in the absence of robust preexisting humoral and cellular immunity. SARS-CoV-2 immunity in some subjects is unprotective and/or short-lived; therefore, SARS-CoV-2 vaccine schedules inducing long-term immunity will be required to bring the pandemic under control.

ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections

Sequencing the SARS-CoV-2 genome from clinical samples can be challenging, especially in specimens with low viral titer. Here we report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. The protocol was optimized to improve flexibility and the combination of technical replicates was established as the central strategy to achieve accurate analysis of low-titer/suboptimal samples. We demonstrated the utility of the approach by achieving complete genome reconstruction and the identification of false-positive variants in >170 clinical samples, thus avoiding the generation of inaccurate and/or incomplete sequences. Most importantly, ACoRE was crucial to identify the correct viral strain responsible of a relapse case, that would be otherwise mis-classified as a re-infection due to missing or incorrect variant identification by a standard workflow.

COVID-19: immunopathology, pathophysiological mechanisms, and treatment options

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread globally despite the worldwide implementation of preventive measures to combat the disease. Although most COVID-19 cases are characterised by a mild, self-limiting disease course, a considerable subset of patients develop a more severe condition, varying from pneumonia and acute respiratory distress syndrome (ARDS) to multi-organ failure (MOF). Progression of COVID-19 is thought to occur as a result of a complex interplay between multiple pathophysiological mechanisms, all of which may orchestrate SARS-CoV-2 infection and contribute to organ-specific tissue damage. In this respect, dissecting currently available knowledge of COVID-19 immunopathogenesis is crucially important, not only to improve our understanding of its pathophysiology but also to fuel the rationale of both novel and repurposed treatment modalities. Various immune-mediated pathways during SARS-CoV-2 infection are relevant in this context, which relate to innate immunity, adaptive immunity, and autoimmunity. Pathological findings in tissue specimens of patients with COVID-19 provide valuable information with regard to our understanding of pathophysiology as well as the development of evidence-based treatment regimens. This review provides an updated overview of the main pathological changes observed in COVID-19 within the most commonly affected organ systems, with special emphasis on immunopathology. Current management strategies for COVID-19 include supportive care and the use of repurposed or symptomatic drugs, such as dexamethasone, remdesivir, and anticoagulants. Ultimately, prevention is key to combat COVID-19, and this requires appropriate measures to attenuate its spread and, above all, the development and implementation of effective vaccines. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Coronavirus new variants: the mutations cause and the effect on the treatment and vaccination

Background: The world has watched with growing alarm as scientists in the U.K.  Identified a new coronavirus variant that appears to be more contagious than, and genetically distinct from, other established variants. The scientists keep collecting the facts about the new variant and its impact on symptom, severity, mortality, and vaccine efficacy. Objective: This review shed light on the SARS-CoV-2 2020 virus that appeared in Britain and South Africa in December 2020, known as B.1.1.7. Furthermore, it highlights the main differences between the new COVID-19 version (B.1.1.7) and the other strains of the virus. Conclusion: Mutations are still happening in the SARS-CoV-2 virus as the RNA viruses cause many changes in the proteins of the spikes of the virus and other parts. The British variant has 23 mutations, compared with the version that erupted in Wuhan, that renders the virus more contagious; however, these mutations do not change the disease's severity.

Unraveling the Mystery Surrounding Post-Acute Sequelae of COVID-19

More than one year since its emergence, corona virus disease 2019 (COVID-19) is still looming large with a paucity of treatment options. To add to this burden, a sizeable subset of patients who have recovered from acute COVID-19 infection have reported lingering symptoms, leading to significant disability and impairment of their daily life activities. These patients are considered to suffer from what has been termed as “chronic” or “long” COVID-19 or a form of post-acute sequelae of COVID-19, and patients experiencing this syndrome have been termed COVID-19 long-haulers. Despite recovery from infection, the persistence of atypical chronic symptoms, including extreme fatigue, shortness of breath, joint pains, brain fogs, anxiety and depression, that could last for months implies an underlying disease pathology that persist beyond the acute presentation of the disease. As opposed to the direct effects of the virus itself, the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to be largely responsible for the appearance of these lasting symptoms, possibly through facilitating an ongoing inflammatory process. In this review, we hypothesize potential immunological mechanisms underlying these persistent and prolonged effects, and describe the multi-organ long-term manifestations of COVID-19.

Kidney Transplantation in COVID Pandemic-A Review of Guidelines

The paper describes problems with the transplantation process during the COVID-19 pandemic. Transplantation procedures and programs have been impacted by COVID-19. The number of transplants has fallen noticeably. The first part of the paper points out changes in service organization, in particular donor and recipient pre-transplant and peri-transplant management. If the patients during pre-transplant evaluation need to attend face-to-face appointments, such as blood testing or other investigations, the risk of contracting or spreading COVID-19 should be minimized. “Clear green areas”, which are COVID-19-free pathways, are highly recommended in hospitals during transplant procedures. Diagnostic procedures concerning donors, including CT scans and coronavirus testing (nasopharyngeal swab), are necessary before transplant surgery. COVID-19 symptoms and risks of the transplant population are described. Detailed guidelines from transplant societies concerning changes in immunosuppression in infected recipients are discussed. Management of infected or suspected medical staff is mentioned. The paper ends with guidelines concerning vaccination against COVID-19 in transplant recipients.

The demography and characteristics of SARS-CoV-2 seropositive residents and staff of nursing homes for older adults in the Community of Madrid: the SeroSOS study

Background: Nursing homes for older adults have concentrated large numbers of severe cases and deaths for COVID-19.

Methods: Point seroprevalence study of nursing homes to describe the demography and characteristic of SARS-CoV-2 IgG-positive residents and staff.

Results: Clinical information and blood samples were available for 9,332 residents (mean age 86.7 ± 8.1 years, 76.4% women) and 10,614 staff (mean age 45.6 ± 11.5, 86.2% women). Up to 84.4% of residents had frailty, 84.9% co-morbidity and 69.3% cognitive impairment; 65.2% of workers were health-aides.

COVID-19 seroprevalence was 55.4% (95% CI, 54.4–56.4) for older adults and 31.5% (30.6–32.4) for staff. In multivariable analysis frailty of residents was related with seropositivity (OR: 1.19, p = 0.02). In the case of staff, age > 50 years (2.10, p < 0.001), obesity (1.19, p = 0.01), being a health-aide (1.94, p < 0.001), working in a center with high seroprevalence in residents (3.49, p < 0.001), and contact with external cases of COVID-19 (1.52, p < 0.001) were factors associated with seropositivity. Past symptoms of COVID-19 were good predictors of seropositivity for residents (5.41, p < 0.001) and staff (2.52, p < 0.001).

Conclusions: Level of dependency influences risk of COVID-19 among residents. Individual and work factors, and contacts outside the nursing home are associated with COVID-19 exposure in staff members. It is key to strengthen control measures to prevent the introduction of COVID-19 into care facilities from the community.