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

Reinfection in patients with COVID-19: a systematic review

BACKGROUND

With the continuation of the COVID-19 pandemic, some COVID-19 patients have become reinfected with the virus. Viral gene sequencing has found that some of these patients were reinfected by the different and others by same strains. This has raised concerns about the effectiveness of immunity after infection and the reliability of vaccines. To this end, we conducted a systematic review to assess the characteristics of patients with reinfection and possible causes.

METHODS

A systematic search was conducted across eight databases: PubMed, Embase, Web of Science, The Cochrane Library, CNKI, WanFang, VIP and SinoMed from December 1, 2019 to September 1, 2021. The quality of included studies were assessed using JBI critical appraisal tools and Newcastle-Ottawa Scale.

RESULTS

This study included 50 studies from 20 countries. There were 118 cases of reinfection. Twenty-five patients were reported to have at least one complication. The shortest duration between the first infection and reinfection was 19 days and the longest was 293 days. During the first infection and reinfection, cough (51.6% and 43.9%) and fever (50% and 30.3%) were the most common symptoms respectively. Nine patients recovered, seven patients died, and five patients were hospitalized, but 97 patients' prognosis were unknown. B.1 is the most common variant strain at the first infection. B.1.1.7, B.1.128 and B.1.351 were the most common variant strains at reinfection. Thirty-three patients were infected by different strains and 9 patients were reported as being infected with the same strain.

CONCLUSIONS

Our research shows that it is possible for rehabilitated patients to be reinfected by SARS-COV-2. To date, the causes and risk factors of COVID-19 reinfection are not fully understood. For patients with reinfection, the diagnosis and management should be consistent with the treatment of the first infection. The public, including rehabilitated patients, should be fully vaccinated, wear masks in public places, and pay attention to maintaining social distance to avoid reinfection with the virus.

SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes

Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCE The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.

Assessment of COVID-19 vaccine hesitancy among Zimbabweans: A rapid national survey

Background

As a way of minimising the devastating effects of the coronavirus disease 2019 (COVID-19) pandemic, scientists hastily developed a vaccine. However, the scale-up of the vaccine is likely to be hindered by the widespread social media misinformation. We therefore conducted a study to assess the COVID-19 vaccine hesitancy among Zimbabweans.

Methods

We conducted a descriptive online cross-sectional survey using a self-administered questionnaire among adults. The questionnaire assessed willingness to be vaccinated; socio-demographic characteristics, individual attitudes and perceptions, effectiveness and safety of the vaccine. Multivariable logistic regression analysis was utilized to examine the independent factors associated with vaccine uptake.

Results

We analysed data for 1168 participants, age range of 19–89 years with the majority being females (57.5%). Half (49.9%) of the participants reported that they would accept the COVID-19 vaccine. Majority were uncertain about the effectiveness of the vaccine (76.0%) and its safety (55.0%). About half lacked trust in the government’s ability to ensure availability of an effective vaccine and 61.0% mentioned that they would seek advice from a healthcare worker to vaccinate. Chronic disease [vs no chronic disease—Adjusted Odds Ratio (AOR): 1.50, 95% Confidence Interval (CI)I: 1.10–2.03], males [vs females—AOR: 1.83, 95%CI: 1.37–2.44] and being a healthcare worker [vs not being a health worker—AOR: 1.59, 95%CI: 1.18–2.14] were associated with increased likelihood to vaccinate.

Conclusion

We found half of the participants willing to vaccinate against COVID-19. The majority lacked trust in the government and were uncertain about vaccine effectiveness and safety. The policy makers should consider targeting geographical and demographic groups which were unlikely to vaccinate with vaccine information, education and communication to improve uptake.

SARS-CoV-2 vaccine breakthrough reinfection in a health-care worker of Iraq: a case report

The COVID-19 pandemic has severely affected the entire globe since the first isolation of SARS-CoV-2 from patients with severe respiratory illness in Wuhan, China. Although the global vaccination drive is in full swing, many cases of reinfection have also been reported after vaccination. Currently, there is a scarcity of data available on the reinfection and vaccine breakthrough infections in Iraq. In this letter, we have presented a case report on the SARS-CoV-2 vaccine breakthrough reinfection in a health-care worker after completion of the double-dose vaccination. An increased symptom severity was reported on the second infection, which was confirmed to be of Delta variant. Such vaccine breakthrough infection reports have raised important questions regarding the duration of vaccine-mediated immunity and vaccine effectiveness against all circulating variants. These have further emphasized the importance of following non-pharmaceutical interventions by fully vaccinated individuals, especially at health-care settings.

Immunopathogenesis of patients with COVID-19: from the perspective of immune system 'evolution' and 'revolution'

The pandemic caused by severe acute respiratory syndrome coronavirus 2 is sweeping the world, threatening millions of lives and drastically altering our ways of living. According to current studies, failure to either activate or eliminate inflammatory responses timely and properly at certain stages could result in the progression of the disease. In other words, robust immune responses to coronavirus disease 2019 (COVID-19) are critical. However, they do not theoretically present in some special groups of people, including the young, the aged, patients with autoimmunity or cancer. Differences also do occur between men and women. Our immune system evolves to ensure delicate coordination at different stages of life. The innate immune cells mainly consisted of myeloid lineage cells, including neutrophils, basophils, eosinophils, dendritic cells and mast cells; they possess phagocytic capacity to different degrees at different stages of life. They are firstly recruited upon infection and may activate the adaptive immunity when needed. The adaptive immune cells, on the other way, are comprised mainly of lymphoid lineages. As one grows up, the adaptive immunity matures and expands its memory repertoire, accompanied by an adjustment in quantity and quality. In this review, we would summarise and analyse the immunological characteristics of these groups from the perspective of the immune system 'evolution' as well as 'revolution' that has been studied and speculated so far, which would aid the comprehensive understanding of COVID-19 and personalised-treatment strategy.

4’-fluorouridine and its derivatives as potential COVID-19 oral drugs: a review

Background: Although vaccination is underway, antiviral drugs against coronavirus disease 2019 (COVID-19) are lacking. Remdesivir, a nucleoside analog that works by inhibiting the viral RNA-dependent RNA polymerase (RdRp), is the only fully approved antiviral for the treatment of COVID-19. However, it is limited to intravenous use and is usually recommended only for hospitalized patients with severe COVID-19; therefore, oral drugs that can be prescribed even to non-hospitalized patients are required. According to a recent study, 4′-fluoruridine, a nucleoside analog similar to remdesivir, is a promising candidate for COVID-19 oral therapy due to its ability to stall viral RdRp. Methods: We examined the antiviral activity of 4′-fluorouridine and compared it to other drugs currently in development. The current literature on 4′-fluorouridine's antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been compiled and discussed in this review. Results: The 4'-fluorouridine has antiviral activity against the respiratory syncytial virus, hepatitis C virus, lymphocytic choriomeningitis virus, and other RNA viruses, including SARS-CoV-2. In vitro studies have shown that SARS-CoV-2 is susceptible to 4'-fluorouridine, with the half-maximal effective concentration (EC50) of 0.2 to 0.6 M, and that the 4′-fluorouridine derivative, 4′-fluorouridine-5′-triphosphate, inhibited RdRp via a mechanism distinct from that of the already approved COVID-19 oral drug, molnupiravir. In addition, an in vivo study revealed that SARS-CoV-2 is highly susceptible to 4'-fluorouridine and was effective with a single daily dose versus molnupiravir administered twice daily. Conclusions: Concerns about the genetic effects of molnupiravir may be resolved by the use of 4′-fluorouridine and its derivative, which, unlike molnupiravir, do not alter genetics, but inhibit RdRp instead. Although they are currently considered as strong candidates, further studies are required to determine the antiviral activity of 4′-fluorouridine and its derivative against SARS-CoV-2 and their genetic effects on humans.

Comparative studies on the high-performance compression of SARS-CoV-2 genome collections

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is fast mutating worldwide. The mutated strains have been timely sequenced by worldwide labs, accumulating a huge amount of viral genome sequences open to public for biomedicine research such as mRNA vaccine design and drug recommendation. It is inefficient to transmit the millions of genome sequences without compression. In this study, we benchmark the performance of reference-free and reference-based compression algorithms on SARS-CoV-2 genome collections extracted from NCBI. Experimental results show that reference-based two-level compression is the most suitable approach to the compression, achieving the best compression ratio 1019.33-fold for compressing 132 372 genomes and 949.73-fold for compressing 416 238 genomes. This enormous file size reduction and efficient decompression have enabled a 5-min download and decompression of $10^5$ SARS-CoV-2 genomes. As compression on datasets containing such big numbers of genomes has been explored seldom before, our comparative analysis of the state-of-the-art compression algorithms provides practical guidance for the selection of compression tools and their parameters such as reference genomes to compress viral genome databases with similar characteristics. We also suggested a genome clustering approach using multiple references for a better compression. It is anticipated that the increased availability of SARS-CoV-2 genome datasets will make biomedicine research more productive.

A Recombinant Subunit Vaccine Induces a Potent, Broadly Neutralizing, and Durable Antibody Response in Macaques against the SARS-CoV-2 P.1 (Gamma) Variant

FDA-approved and emergency use-authorized vaccines using new mRNA and viral-vector technology are highly effective in preventing moderate to severe disease; however, information on their long-term efficacy and protective breadth against severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) is currently scarce. Here, we describe the durability and broad-spectrum VOC immunity of a prefusion-stabilized spike (S) protein adjuvanted with liquid or lyophilized CoVaccine HT in cynomolgus macaques. This recombinant subunit vaccine is highly immunogenic and induces robust spike-specific and broadly neutralizing antibody responses effective against circulating VOCs (B.1.351 [Beta], P.1 [Gamma], and B.1.617 [Delta]) for at least three months after the final boost. Protective efficacy and postexposure immunity were evaluated using a heterologous P.1 challenge nearly three months after the last immunization. Our results indicate that while immunization with both high and low S doses shorten and reduce viral loads in the upper and lower respiratory tract, a higher antigen dose is required to provide durable protection against disease as vaccine immunity wanes. Histologically, P.1 infection causes similar COVID-19-like lung pathology as seen with early pandemic isolates. Postchallenge IgG concentrations were restored to peak immunity levels, and vaccine-matched and cross-variant neutralizing antibodies were significantly elevated in immunized macaques indicating an efficient anamnestic response. Only low levels of P.1-specific neutralizing antibodies with limited breadth were observed in control (nonvaccinated but challenged) macaques, suggesting that natural infection may not prevent reinfection by other VOCs. Overall, these results demonstrate that a properly dosed and adjuvanted recombinant subunit vaccine can provide protective immunity against circulating VOCs for at least three months.

Clinical manifestations, treatment options, and comorbidities in COVID-19 relapse patients: A systematic review

Introduction

Interest revolving around coronavirus disease 2019 (COVID‐19) reinfection is escalating rapidly. By definition, reinfection denotes severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), PCR redetection, and COVID‐19 recurrence within three months of the initial symptoms. The main aim of the current systematic review was to evaluate the features of COVID‐19 relapse patients.

Materials and methods

For this study, we used a string of terms developed by a skilled librarian and through a systematical search in PubMed, Web of Science, and Embase for eligible studies. Clinical surveys of any type were included from January 2019 to March 2021. Eligible studies consisted of two positive assessments separated by a negative result via RT‐PCR.

Results

Fifty‐four studies included 207 cases of COVID‐19 reinfection. Children were less likely to have COVID‐19 relapse. However, the most patients were in the age group of 20–40 years. Asthenia (66.6%), headache (66.6%), and cough (54.7%) were prevalent symptoms in the first SARS‐CoV‐2 infection. Asthenia (62.9%), myalgia (62.9%), and headache (61.1%) were most frequent in the second one. The most common treatment options used in first COVID‐19 infection were lopinavir/ritonavir (80%), oxygen support (69.2%), and oseltamivir (66.6). However, for the treatment of second infection, mostly antibiotics (100%), dexamethasone (100%), and remdesivir (80%) were used. In addition, obesity (32.5%), kidney failure (30.7%), and hypertension (30.1%) were the most common comorbidities. Unfortunately, approximately 4.5% of patients died.

Conclusion

We found the potency of COVID‐19 recurrence as an outstanding issue. This feature should be regarded in the COVID‐19 management. Furthermore, the first and second COVID‐19 are similar in clinical features. For clinically practical comparison of the symptoms severity between two epochs of infection, uniform data of both are required. We suggest that future studies undertake a homogenous approach to establish the clinical patterns of the reinfection phenomena.

A highly potent and stable pan-coronavirus fusion inhibitor as a candidate prophylactic and therapeutic for COVID-19 and other coronavirus diseases

The development of broad-spectrum antivirals against human coronaviruses (HCoVs) is critical to combat the current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, as well as future outbreaks of emerging CoVs. We have previously identified a polyethylene glycol-conjugated (PEGylated) lipopeptide, EK1C4, with potent pan-CoV fusion inhibitory activity. However, PEG linkers in peptide or protein drugs may reduce stability or induce anti-PEG antibodies in vivo. Therefore, we herein report the design and synthesis of a series of dePEGylated lipopeptide-based pan-CoV fusion inhibitors featuring the replacement of the PEG linker with amino acids in the heptad repeat 2 C-terminal fragment (HR2-CF) of HCoV-OC43. Among these lipopeptides, EKL1C showed the most potent inhibitory activity against infection by SARS-CoV-2 and its spike (S) mutants, as well as other HCoVs and some bat SARS-related coronaviruses (SARSr-CoVs) tested. The dePEGylated lipopeptide EKL1C exhibited significantly stronger resistance to proteolytic enzymes, better metabolic stability in mouse serum, higher thermostability than the PEGylated lipopeptide EK1C4, suggesting that EKL1C could be further developed as a candidate prophylactic and therapeutic for COVID-19 and other coronavirus diseases.

Genomic evidence of SARS-CoV-2 reinfection in the Republic of Korea

As the coronavirus disease 2019 (COVID-19) pandemic continues, reinfection is likely to become increasingly common. However, confirming COVID-19 reinfection is difficult because it requires whole-genome sequencing of both infections to identify the degrees of genetic differences. Since the first reported case of reinfection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the Republic of Korea in April 2020, four additional cases were classified as suspected reinfection cases. We performed whole-genome sequencing of viral RNA extracted from swabs obtained at the initial infection and reinfection stages of these four suspected cases. The interval between initial infection and reinfection of all four suspected cases was more than 3 months. All four patients were young (10-29 years), and they displayed mild symptoms or were asymptomatic during the initial infection and reinfection episodes. The analysis of genome sequences combined with the epidemiological results revealed that only two of the four cases were confirmed as reinfection, and both were reinfected with the Epsilon variant. Due to the prolonged COVID-19 pandemic, the possibility of reinfections with SARS-CoV-2 variants is increasing, as reported in our study. Therefore, continuous monitoring of cases is necessary.

Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology

Background

Cellular immune memory responses post coronavirus disease 2019 (COVID‐19) have been difficult to assess due to the risks of contaminating the immune response readout with memory responses stemming from previous exposure to endemic coronaviruses. The work herein presents a large‐scale long‐term follow‐up study investigating the correlation between symptomology and cellular immune responses four to five months post seroconversion based on a unique severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2)‐specific peptide pool that contains no overlapping peptides with endemic human coronaviruses.

Methods

Peptide stimulated memory T cell responses were assessed with dual interferon‐gamma (IFNγ) and interleukin (IL)‐2 Fluorospot. Serological analyses were performed using a multiplex antigen bead array.

Results

Our work demonstrates that long‐term SARS‐CoV‐2‐specific memory T cell responses feature dual IFNγ and IL‐2 responses, whereas cross‐reactive memory T cell responses primarily generate IFNγ in response to SARS‐CoV‐2 peptide stimulation. T cell responses correlated to long‐term humoral immune responses. Disease severity as well as specific COVID‐19 symptoms correlated with the magnitude of the SARS‐CoV‐2‐specific memory T cell response four to five months post seroconversion.

Conclusion

Using a large cohort and a SARS‐CoV‐2‐specific peptide pool we were able to substantiate that initial disease severity and symptoms correlate with the magnitude of the SARS‐CoV‐2‐specific memory T cell responses.

SARS-CoV-2 transmission in opposition-controlled Northwest Syria: modeling pandemic responses during political conflict

INTRODUCTION

Ten years of conflict has displaced more than half of Northwest Syria's (NWS) population and decimated the health system, water and sanitation, and public health infrastructure vital for infectious disease control. The first NWS COVID-19 case was declared on July 9, 2020, but impact estimations in this region are minimal. With the rollout of vaccination and emergence of the B.1.617.2 (Delta) variant, we aimed to estimate the COVID-19 trajectory in NWS and the potential effects of vaccine coverage and hospital occupancy.

METHODS

We conducted a mixed-method study, primarily including modeling projections of COVID-19 transmission scenarios with vaccination strategies using an age-structured, compartmental susceptible-exposed-infectious-recovered (SEIR) model, supported by data from 20 semi-structured interviews with frontline health workers to help contextualize interpretation of modeling results.

RESULTS

Modeling suggested that existing low stringency non-pharmaceutical interventions (NPIs) minimally affected COVID-19 transmission. Maintaining existing NPIs after the Delta variant introduction is predicted to result in a second COVID-19 wave, overwhelming hospital capacity and resulting in a fourfold increased death toll. Simulations with up to 60% vaccination coverage by June 2022 predict that a second wave is not preventable with current NPIs. However, 60% vaccination coverage by June 2022 combined with 50% coverage of mask-wearing and handwashing should reduce the number of hospital beds and ventilators needed below current capacity levels. In the worst-case scenario of a more transmissible and lethal variant emerging by January 2022, the third wave is predicted.

CONCLUSION

Total COVID-19 attributable deaths are expected to remain relatively low owing largely to a young population. Given the negative socioeconomic consequences of restrictive NPIs, such as border or school closures for an already deeply challenged population and their relative ineffectiveness in this context, policymakers and international partners should instead focus on increasing COVID-19 vaccination coverage as rapidly as possible and encouraging mask-wearing.

Why Controlling the Asymptomatic Infection Is Important: A Modelling Study with Stability and Sensitivity Analysis

The large proportion of asymptomatic patients is the major cause leading to the COVID-19 pandemic which is still a significant threat to the whole world. A six-dimensional ODE system (SEIAQR epidemical model) is established to study the dynamics of COVID-19 spreading considering infection by exposed, infected, and asymptomatic cases. The basic reproduction number derived from the model is more comprehensive including the contribution from the exposed, infected, and asymptomatic patients. For this more complex six-dimensional ODE system, we investigate the global and local stability of disease-free equilibrium, as well as the endemic equilibrium, whereas most studies overlooked asymptomatic infection or some other virus transmission features. In the sensitivity analysis, the parameters related to the asymptomatic play a significant role not only in the basic reproduction number R0. It is also found that the asymptomatic infection greatly affected the endemic equilibrium. Either in completely eradicating the disease or achieving a more realistic goal to reduce the COVID-19 cases in an endemic equilibrium, the importance of controlling the asymptomatic infection should be emphasized. The three-dimensional phase diagrams demonstrate the convergence point of the COVID-19 spreading under different initial conditions. In particular, massive infections will occur as shown in the phase diagram quantitatively in the case R0>1. Moreover, two four-dimensional contour maps of Rt are given varying with different parameters, which can offer better intuitive instructions on the control of the pandemic by adjusting policy-related parameters.

Screening Large Population Health Databases for Potential COVID-19 Therapeutics: A Pharmacopeia-Wide Association Study (PWAS) of Commonly Prescribed Medications

Background

For both the current and future pandemics, there is a need for high-throughput drug screening methods to identify existing drugs with potential preventative and/or therapeutic activity. Epidemiologic studies could complement lab-focused efforts to identify possible therapeutic agents.

Methods

We performed a pharmacopeia-wide association study (PWAS) to identify commonly prescribed medications and medication classes that are associated with the detection of SARS-CoV-2 in older individuals (>65 years) in long-term care homes (LTCH) and the community, between January 15 th, 2020 and December 31 st, 2020, across the province of Ontario, Canada.

Results

26,121 cases and 2,369,020 controls from LTCH and the community were included in this analysis. Many of the drugs and drug classes evaluated did not yield significant associations with SARS-CoV-2 detection. However, some drugs and drug classes appeared significantly associated with reduced SARS-CoV-2 detection, including cardioprotective drug classes such as statins (weighted OR 0.91, standard p-value <0.01, adjusted p-value <0.01) and beta-blockers (weighted OR 0.87, standard p-value <0.01, adjusted p-value 0.01), along with individual agents ranging from levetiracetam (weighted OR 0.70, standard p-value <0.01, adjusted p-value <0.01) to fluoxetine (weighted OR 0.86, standard p-value 0.013, adjusted p-value 0.198) to digoxin (weighted OR 0.89, standard p-value <0.01, adjusted p-value 0.02).

Conclusions

Using this epidemiologic approach which can be applied to current and future pandemics we have identified a variety of target drugs and drug classes that could offer therapeutic benefit in COVID-19 and may warrant further validation. Some of these agents (e.g. fluoxetine) have already been identified for their therapeutic potential.

Recurrence of Asymptomatic COVID-19 after Recovery among Healthcare Workers

We describe five healthcare workers (HCWs) with a recurrence of asymptomatic SARS-CoV-2 infection at Siloam Teaching Hospital, Indonesia. All cases involved nurses, with an average age of 27 years. The RT-PCR assay confirmed the first and second infection episodes. All cases showed negative RT-PCR results in the period between two infection episodes. The median interval time between two infection episodes was 123 days, ranging from 92 to 158 days. The clinical outcomes for all cases were favourable, with no mortality observed among study cases. Further studies will be required to understand the true nature of this phenomenon.

How to Motivate SARS-CoV-2 Convalescents to Receive a Booster Vaccination? Influence on Vaccination Willingness

(1) Background: Booster vaccinations for SARS-CoV-2 convalescents are essential for achieving herd immunity. For the first time, this study examined the influencing factors of vaccination willingness among SARS-CoV-2 infected individuals and identified vaccination-hesitant subgroups. (2) Methods: Individuals with positive SARS-CoV-2 PCR results were recruited by telephone. They completed an online questionnaire during their home isolation in Germany. This questionnaire assessed the vaccination willingness and its influencing factors. (3) Results: 224 home-isolated individuals with acute SARS-CoV-2 infection were included in the study. Vaccination willingness of home-isolated SARS-CoV-2 infected individuals with asymptomatic or moderate course was 54%. The following factors were associated with significantly lower vaccination willingness: younger age, foreign nationality, low income, low trust in vaccination effectiveness, fear of negative vaccination effects, low trust in the governmental pandemic management, low subjective informativeness about SARS-CoV-2, support of conspiracy theories. (4) Conclusions: The vaccination willingness of home-isolated SARS-CoV-2 infected individuals with asymptomatic or moderate symptomatic course was low. Motivational vaccination campaigns should be adapted to individuals with acute SARS-CoV-2 infection and consider the vaccination-hesitant groups. Vaccination education should be demand-driven, low-threshold, begin during the acute infection phase, and be guided for example by the established 5C model ("confidence, complacency, constraints, calculation, collective responsibility").

The Effect of Varying Interval Definitions on the Prevalence of SARS-CoV-2 Reinfections: A Retrospective Cross-Sectional Cohort Study

Background: We assessed the SARS-CoV-2 reinfection rate in a large patient cohort, and evaluated the effect of varying time intervals between two positive tests on assumed reinfection rates using viral load data. Methods: All positive SARS-CoV-2 samples collected between 1 March 2020 and 1 August 2021 from a laboratory in the region Kennemerland, the Netherlands, were included. The reinfection rate was analyzed using different time intervals between two positive tests varying between 2 and 16 weeks. SARS-CoV-2 PCR crossing point (Cp) values were used to estimate viral loads. Results: In total, 679,513 samples were analyzed, of which 53,366 tests (7.9%) were SARS-CoV-2 positive. The number of reinfections varied between 260 (0.52%) for an interval of 2 weeks, 89 (0.19%) for 4 weeks, 52 (0.11%) for 8 weeks, and 37 (0.09%) for a minimum interval of 16 weeks between positive tests. The median Cp-value (IQR) in the second positive samples decreased when a longer interval was chosen, but stabilized from week 8 onwards. Conclusions: Although the calculated reinfection prevalence was relatively low (0.11% for the 8-week time interval), choosing a different minimum interval between two positive tests resulted in major differences in reinfection rates. As reinfection Cp-values stabilized after 8 weeks, we hypothesize this interval to best reflect novel infection rather than persistent shedding.

Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters

The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Delta variant has evolved to become the dominant SARS-CoV-2 lineage with multiple sub-lineages and there are also reports of re-infections caused by this variant. We studied the disease characteristics induced by the Delta AY.1 variant and compared it with the Delta and B.1 variants in Syrian hamsters. We also assessed the potential of re-infection by these variants in Coronavirus disease 2019 recovered hamsters 3 months after initial infection. The variants produced disease characterized by high viral load in the respiratory tract and interstitial pneumonia. The Delta AY.1 variant produced mild disease in the hamster model and did not show any evidence of neutralization resistance due to the presence of the K417N mutation, as speculated. Re-infection with a high virus dose of the Delta and B.1 variants 3 months after B.1 variant infection resulted in reduced virus shedding, disease severity and increased neutralizing antibody levels in the re-infected hamsters. The reduction in viral load and lung disease after re-infection with the Delta AY.1 variant was not marked. Upper respiratory tract viral RNA loads remained similar after re-infection in all the groups. The present findings show that prior infection could not produce sterilizing immunity but that it can broaden the neutralizing response and reduce disease severity in case of reinfection.

Nasal Nanovaccines for SARS-CoV-2 to Address COVID-19

COVID-19 is still prevalent around the globe. Although some SARS-CoV-2 vaccines have been distributed to the population, the shortcomings of vaccines and the continuous emergence of SARS-CoV-2 mutant virus strains are a cause for concern. Thus, it is vital to continue to improve vaccines and vaccine delivery methods. One option is nasal vaccination, which is more convenient than injections and does not require a syringe. Additionally, stronger mucosal immunity is produced under nasal vaccination. The easy accessibility of the intranasal route is more advantageous than injection in the context of the COVID-19 pandemic. Nanoparticles have been proven to be suitable delivery vehicles and adjuvants, and different NPs have different advantages. The shortcomings of the SARS-CoV-2 vaccine may be compensated by selecting or modifying different nanoparticles. It travels along the digestive tract to the intestine, where it is presented by GALT, tissue-resident immune cells, and gastrointestinal lymph nodes. Nasal nanovaccines are easy to use, safe, multifunctional, and can be distributed quickly, demonstrating strong prospects as a vaccination method for SARS-CoV-2, SARS-CoV-2 variants, or SARS-CoV-n.

Durable T-cellular and humoral responses in SARS-CoV-2 hospitalized and community patients

Background

Neutralizing antibodies are important for protection against the pandemic SARS-CoV-2 virus, and long-term memory responses determine the risk of re-infection or boosting after vaccination. T-cellular responses are considered important for partial protection against novel variants of concern.

Methods

A prospective cohort of hospitalized (n = 14) and community (n = 38) patients with rt-PCR confirmed SARS-CoV-2 infection were recruited. Blood samples and clinical data were collected when diagnosed and at 6 months. Serum samples were analyzed for SARS-CoV-2-spike specific antibodies using ELISA (IgG, IgA, IgM), pseudotype neutralization and microneutralization assays. Peripheral blood mononuclear cells were investigated for virus-specific T-cell responses in the interferon-γ and interleukin-2 fluorescent-linked immunosorbent spot (FluroSpot) assay.

Results

We found durable SARS-CoV-2 spike- and internal protein specific T-cellular responses in patients with persistent antibodies at 6 months. Significantly higher IL-2 and IFN-γ secreting T-cell responses as well as SARS-CoV-2 specific IgG and neutralizing antibodies were detected in hospitalized compared to community patients. The immune response was impacted by age, gender, comorbidity and severity of illness, reflecting clinical observations.

Conclusions

SARS-CoV-2 specific T-cellular and antibody responses persisted for 6 months post confirmed infection. In previously infected patients, re-exposure or vaccination will boost long-term immunity, possibly providing protection against re-infection with variant viruses.

Quantifying Neutralizing Antibodies in Patients with COVID-19 by a Two-Variable Generalized Additive Model

Considering the urgent demand for faster methods to quantify neutralizing antibody titers in patients with coronavirus (CoV) disease 2019 (COVID-19), developing an analytical model or method to replace the conventional virus neutralization test (NT) is essential. Moreover, a "COVID-19 immunity passport" is currently being proposed as a certification for people who travel internationally. Therefore, an enzyme-linked immunosorbent assay (ELISA) was designed to detect severe acute respiratory syndrome CoV 2 (SARS-CoV-2)-neutralizing antibodies in serum, which is based on the binding affinity of SARS-CoV-2 viral spike protein 1 (S1) and the viral spike protein receptor-binding domain (RBD) to antibodies. The RBD is considered the major binding region of neutralizing antibodies. Furthermore, S1 covers the RBD and several other regions, which are also important for neutralizing antibody binding. In this study, we assessed 144 clinical specimens, including those from patients with PCR-confirmed SARS-CoV-2 infections and healthy donors, using both the NT and ELISA. The ELISA results analyzed by spline regression and the two-variable generalized additive model precisely reflected the NT value, and the correlation between predicted and actual NT values was as high as 0.917. Therefore, our method serves as a surrogate to quantify neutralizing antibody titer. The analytic method and platform used in this study present a new perspective for serological testing of SARS-CoV-2 infection and have clinical potential to assess vaccine efficacy. IMPORTANCE Herein, we present a new approach for serological testing for SARS-CoV-2 antibodies using innovative laboratory methods that demonstrate a combination of biology and mathematics. The traditional virus neutralization test is the gold standard method; however, it is time-consuming and poses a risk to medical personnel. Thus, there is a demand for methods that rapidly quantify neutralizing antibody titers in patients with COVID-19 or examine vaccine efficacy at a biosafety level 2 containment facility. Therefore, we used a two-variable generalized additive model to analyze the results of the enzyme-linked immunosorbent assay and found the method to serve as a surrogate to quantify neutralizing antibody titers. This methodology has potential for clinical use in assessing vaccine efficacy.

Sequencing SARS-CoV-2 from antigen tests

Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW™ COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media.

Serological Markers of SARS-CoV-2 Reinfection

As public health guidelines throughout the world have relaxed in response to vaccination campaigns against SARS-CoV-2, it is likely that SARS-CoV-2 will remain endemic, fueled by the rise of more infectious SARS-CoV-2 variants. Moreover, in the setting of waning natural and vaccine immunity, reinfections have emerged across the globe, even among previously infected and vaccinated individuals. As such, the ability to detect reexposure to and reinfection by SARS-CoV-2 is a key component for global protection against this virus and, more importantly, against the potential emergence of vaccine escape mutations. Accordingly, there is a strong and continued need for the development and deployment of simple methods to detect emerging hot spots of reinfection to inform targeted pandemic response and containment, including targeted and specific deployment of vaccine booster campaigns. In this study, we identify simple, rapid immune biomarkers of reinfection in rhesus macaques, including IgG3 antibody levels against nucleocapsid and FcγR2A receptor binding activity of anti-RBD antibodies, that are recapitulated in human reinfection cases. As such, this cross-species analysis underscores the potential utility of simple antibody titers and function as price-effective and scalable markers of reinfection to provide increased resolution and resilience against new outbreaks. IMPORTANCE As public health and social distancing guidelines loosen in the setting of waning global natural and vaccine immunity, a deeper understanding of the immunological response to reexposure and reinfection to this highly contagious pathogen is necessary to maintain public health. Viral sequencing analysis provides a robust but unrealistic means to monitor reinfection globally. The identification of scalable pathogen-specific biomarkers of reexposure and reinfection, however, could significantly accelerate our capacity to monitor the spread of the virus through naive and experienced hosts, providing key insights into mechanisms of disease attenuation. Using a nonhuman primate model of controlled SARS-CoV-2 reexposure, we deeply probed the humoral immune response following rechallenge with various doses of viral inocula. We identified virus-specific humoral biomarkers of reinfection, with significant increases in antibody titer and function upon rechallenge across a range of humoral features, including IgG1 to the receptor binding domain of the spike protein of SARS-CoV-2 (RBD), IgG3 to the nucleocapsid protein (N), and FcγR2A receptor binding to anti-RBD antibodies. These features not only differentiated primary infection from reexposure and reinfection in monkeys but also were recapitulated in a sequencing-confirmed reinfection patient and in a cohort of putatively reinfected humans that evolved a PCR-positive test in spite of preexisting seropositivity. As such, this cross-species analysis using a controlled primate model and human cohorts reveals increases in antibody titers as promising cross-validated serological markers of reinfection and reexposure.

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

Background

The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard.

Results

As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories.

Conclusions

Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI’s BioSample database.

Antibody attributes that predict the neutralization and effector function of polyclonal responses to SARS-CoV-2

BACKGROUND

While antibodies can 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.

METHODS

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.

RESULTS

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 models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion.

CONCLUSIONS

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.

Development of SARS-CoV2 humoral response including neutralizing antibodies is not sufficient to protect patients against fatal infection

More than a year after the start of the pandemic, COVID-19 remains a global health emergency. Although the immune response against SARS-CoV-2 has been extensively studied, some points remain controversial. One is the role of antibodies in viral clearance and modulation of disease severity. While passive transfer of neutralizing antibodies protects against SARS-CoV-2 infection in animal models, titers of anti-SARS-CoV-2 antibodies have been reported to be higher in patients suffering from more severe forms of the disease. A second key question for pandemic management and vaccine design is the persistence of the humoral response. Here, we characterized the antibody response in 187 COVID-19 patients, ranging from asymptomatic individuals to patients who died from COVID-19, and including patients who recovered. We developed in-house ELISAs to measure titers of IgG, IgM and IgA directed against the RBD or N regions in patient serum or plasma, and a spike-pseudotyped neutralization assay to analyse seroneutralization. Higher titers of virus-specific antibodies were detected in patients with severe COVID-19, including deceased patients, compared to asymptomatic patients. This demonstrates that fatal infection is not associated with defective humoral response. Finally, most of recovered patients still had anti-SARS-CoV-2 IgG more than 3 months after infection.

Neutralizing Antibodies and Antibody-Dependent Enhancement in COVID-19: A Perspective

Antibody-dependent enhancement (ADE) is an alternative route of viral entry in the susceptible host cell. In this process, antiviral antibodies enhance the entry access of virus in the cells via interaction with the complement or Fc receptors leading to the worsening of infection. SARS-CoV-2 variants pose a general concern for the efficacy of neutralizing antibodies that may fail to neutralize infection, raising the possibility of a more severe form of COVID-19. Data from various studies on respiratory viruses raise the speculation that antibodies elicited against SARS-CoV-2 and during COVID-19 recovery could potentially exacerbate the infection through ADE at sub-neutralizing concentrations; this may contribute to disease pathogenesis. It is, therefore, of utmost importance to study the effectiveness of the anti-SARS-CoV-2 antibodies in COVID-19-infected subjects. Theoretically, ADE remains a general concern for the efficacy of antibodies elicited during infection, most notably in convalescent plasma therapy and in response to vaccines where it could be counterproductive.

Therapeutics for COVID-19 and post COVID-19 complications: An update

Since its inception in late December 2020 in China, novel coronavirus has affected the global socio-economic aspect. Currently, the world is seeking safe and effective treatment measures against COVID-19 to eradicate it. Many established drug molecules are tested against SARS-CoV-2 as a part of drug repurposing where some are proved effective for symptomatic relief while some are ineffective. Drug repurposing is a practical strategy for rapidly developing antiviral agents. Many drugs are presently being repurposed utilizing basic understanding of disease pathogenesis and drug pharmacodynamics, as well as computational methods. In the present situation, drug repurposing could be viewed as a new treatment option for COVID-19. Several new drug molecules and biologics are engineered against SARS-CoV-2 and are under different stages of clinical development. A few biologics drug products are approved by USFDA for emergency use in the covid management. Due to continuous mutation, many of the approved vaccines are not much efficacious to render the individual immune against opportunistic infection of SARS-CoV-2 mutants. Hence, there is a strong need for the cogent therapeutic agent for covid management. In this review, a consolidated summary of the therapeutic developments against SARS-CoV-2 are depicted along with an overview of effective management of post COVID-19 complications.

Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th J'uly 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.

Immunological Biomarkers in Blood to Monitor the Course and Therapeutic Outcomes of COVID-19

BACKGROUND

The COVID-19 pandemic has posed a great challenge to the medical community because little is known about its clinical course, therapeutic options, and laboratory monitoring tools for diagnosis, prognosis, and surveillance. This review focuses on immune biomarkers that can be measured in peripheral blood in a clinical laboratory under routine conditions to monitor the innate immune system response in the acute phase, as well as the adaptive immune response established both after infection and vaccination.

METHODS

A PubMed search was performed covering January 2020 to June 2021 to extract biomarkers suitable for monitoring the immune response and outcome of COVID-19 and therapeutic interventions, including vaccination.

RESULTS

To monitor the innate immune response, cytokines such as interleukin-6 or acute phase reactants such as C-reactive protein or procalcitonin can be measured on autoanalyzers complemented by automated white blood cell differential counts. The adaptive immune response can be followed by commercially available enzyme-linked immune spot assays to assess the specific activation of T cells or by monitoring immunoglobulin A (IgA), IgM, and IgG antibodies in serum to follow B-cell activation. As antigens of the SARS-CoV-2 virus, spike and nucleocapsid proteins are particularly suitable and allow differentiation between the immune response after infection or vaccination.

CONCLUSIONS

Routine immune monitoring of COVID-19 is feasible in clinical laboratories with commercially available instruments and reagents. Strategies such as whether biomarkers reflecting the response of the innate and adaptive immune system can be used to make predictions and assist in individualizing therapeutic interventions or vaccination strategies need to be determined in appropriate clinical trials. Promising preliminary data are already available based on single-center reports and completed or ongoing vaccination trials.

SARS-CoV-2 reinfection prevents acute respiratory disease in Syrian hamsters but not replication in the upper respiratory tract

Human cases of SARS-CoV-2 reinfection have been documented throughout the pandemic, but are likely under-reported. In the current study, we use the Syrian hamster SARS-CoV-2 model to assess reinfection with homologous WA1 and heterologous B.1.1.7 (Alpha) and B.1.351 (Beta) SARS-CoV-2 variants over time. Upon primary infection with SARS-CoV-2 WA1, hamsters rapidly develop a strong and long-lasting humoral immune response. After reinfection with homologous and heterologous SARS-CoV-2 variants, this immune response protects hamsters from clinical disease, virus replication in the lower respiratory tract, and acute lung pathology. However, reinfection leads to SARS-CoV-2 replication in the upper respiratory tract with the potential for virus shedding. Our findings indicate that reinfection results in restricted SARS-CoV-2 replication despite substantial levels of humoral immunity, denoting the potential for transmission through reinfected asymptomatic individuals.

Persistence and viability of SARS-CoV-2 in primary infection and reinfections

Since the beginning of the SARS-CoV-2 epidemic, virus isolation in the infected patient was only possible for a short period of time and it was striking that this occurred constantly and did not provide guidance on the clinical course. This fact led to confusion about the efficacy of some of the drugs initially used, which seemed to have a high efficiency in viral clearance and proved ineffective in modifying the course of the disease. The immune response also did not prove to be definitive in terms of evolution, although most of the patients with very mild disease had a weak or no antibody response, and the opposite was true for the most severe patients. With whatever the antibody response, few cases have been re-infected after a first infection and generally, those that have, have not reproduced a spectrum of disease similar to the first infection. Among those re-infected, a large number have been asymptomatic or with very few symptoms, others have had a moderate picture and very few have had a poor evolution. Despite this dynamic of rapid viral clearance, laboratory tests were still able to generate positive results in the recovery of genomic sequences and this occurred in patients who were already symptom-free, in others who were still ill and in those who were very seriously ill. There was also no good correlate. For this reason and with the perspective of this year and the half of pandemic, we compiled what the literature leaves us in these aspects and anticipating that, as always in biology, there are cases that jump the limits of the general behavior of the dynamics of infection in general.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Sequence Characteristics of Coronavirus Disease 2019 (COVID-19) Persistence and Reinfection

BACKGROUND

Both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection and persistent infection have been reported, but sequence characteristics in these scenarios have not been described. We assessed published cases of SARS-CoV-2 reinfection and persistence, characterizing the hallmarks of reinfecting sequences and the rate of viral evolution in persistent infection.

METHODS

A systematic review of PubMed was conducted to identify cases of SARS-CoV-2 reinfection and persistence with available sequences. Nucleotide and amino acid changes in the reinfecting sequence were compared with both the initial and contemporaneous community variants. Time-measured phylogenetic reconstruction was performed to compare intrahost viral evolution in persistent SARS-CoV-2 to community-driven evolution.

RESULTS

Twenty reinfection and 9 persistent infection cases were identified. Reports of reinfection cases spanned a broad distribution of ages, baseline health status, reinfection severity, and occurred as early as 1.5 months or >8 months after the initial infection. The reinfecting viral sequences had a median of 17.5 nucleotide changes with enrichment in the ORF8 and N genes. The number of changes did not differ by the severity of reinfection and reinfecting variants were similar to the contemporaneous sequences circulating in the community. Patients with persistent coronavirus disease 2019 (COVID-19) demonstrated more rapid accumulation of sequence changes than seen with community-driven evolution with continued evolution during convalescent plasma or monoclonal antibody treatment.

CONCLUSIONS

Reinfecting SARS-CoV-2 viral genomes largely mirror contemporaneous circulating sequences in that geographic region, while persistent COVID-19 has been largely described in immunosuppressed individuals and is associated with accelerated viral evolution.

Reinfection With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Patients Undergoing Serial Laboratory Testing

BACKGROUND

A better understanding of reinfection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has become one of the healthcare priorities in the current pandemic. We determined the rate of reinfection, associated factors, and mortality during follow-up in a cohort of patients with SARS-CoV-2 infection.

METHODS

We analyzed 9119 patients with SARS-CoV-2 infection who received serial tests in total of 62 healthcare facilities in the United States between 1 December 2019 and 13 November 2020. Reinfection was defined by 2 positive tests separated by interval of >90 days and resolution of first infection was confirmed by 2 or more consecutive negative tests. We performed logistic regression analysis to identify demographic and clinical characteristics associated with reinfection.

RESULTS

Reinfection was identified in 0.7% (n = 63, 95% confidence interval [CI]: .5%-.9%) during follow-up of 9119 patients with SARS-CoV-2 infection. The mean period (±standard deviation [SD]) between 2 positive tests was 116 ± 21 days. A logistic regression analysis identified that asthma (odds ratio [OR] 1.9, 95% CI: 1.1-3.2) and nicotine dependence/tobacco use (OR 2.7, 95% CI: 1.6-4.5) were associated with reinfection. There was a significantly lower rate of pneumonia, heart failure, and acute kidney injury observed with reinfection compared with primary infection among the 63 patients with reinfection There were 2 deaths (3.2%) associated with reinfection.

CONCLUSIONS

We identified a low rate of reinfection confirmed by laboratory tests in a large cohort of patients with SARS-CoV-2 infection. Although reinfection appeared to be milder than primary infection, there was associated mortality.

COVID-19 reinfections among naturally infected and vaccinated individuals

The protection against emerging SARS-CoV-2 variants by pre-existing antibodies elicited due to the current vaccination or natural infection is a global concern. We aimed to investigate the rate of SARS-CoV-2 infection and its clinical features among infection-naïve, infected, vaccinated, and post-infection-vaccinated individuals. A cohort was designed among icddr,b staff registered for COVID-19 testing by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). Reinfection cases were confirmed by whole-genome sequencing. From 19 March 2020 to 31 March 2021, 1644 (mean age, 38.4 years and 57% male) participants were enrolled; where 1080 (65.7%) were tested negative and added to the negative cohort. The positive cohort included 750 positive patients (564 from baseline and 186 from negative cohort follow-up), of whom 27.6% were hospitalized and 2.5% died. Among hospitalized patients, 45.9% had severe to critical disease and 42.5% required oxygen support. Hypertension and diabetes mellitus were found significantly higher among the hospitalised patients compared to out-patients; risk ratio 1.3 and 1.6 respectively. The risk of infection among positive cohort was 80.2% lower than negative cohort (95% CI 72.6-85.7%; p < 0.001). Genome sequences showed that genetically distinct SARS-CoV-2 strains were responsible for reinfections. Naturally infected populations were less likely to be reinfected by SARS-CoV-2 than the infection-naïve and vaccinated individuals. Although, reinfected individuals did not suffer severe disease, a remarkable proportion of naturally infected or vaccinated individuals were (re)-infected by the emerging variants.

A 63-Year-Old Man with a Diagnosis of Re-Infection with SARS-CoV-2 Nine Weeks After an Initial Hospital Admission with COVID-19 Pneumonia

BACKGROUND This report describes a 63-year-old Polish man presenting with COVID-19 (Coronavirus Disease 2019) pneumonia in early 2020, before vaccines to prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were available. Nine weeks following recovery from the initial infection, he tested positive again for SARS-CoV-2. CASE REPORT Man, age 63, was admitted to the Military Institute of Medicine on March 12, 2020, with body temperature 40°C, a cough, and breathlessness. On March 12, 2020, SARS-CoV-2 RNA was found in a nasopharynx smear. A chest X-ray (RTG) showed discrete areas of interstitial densities. On June 13, 2020, after 32 days of hospitalization and 2 negative real-time polymerase chain rection (RT-PCR) test results, patient was released home in good general condition. On July 23, 2020 he reported to the emergency room with fever of 39°C and general weakness. A nasopharynx smear confirmed SARS-CoV-2 infection. On admission, the patient was in moderately good condition with auscultatory changes typical for pneumonia on both sides of the chest. On the seventh day of hospitalization, the patient was transported to the Intensive Care Unit (ICU) due to drastic deterioration in respiratory function. Respiratory support with non-invasive high-flow oxygen therapy (Opti-Flow) was used. On August 20, 2020, after negative RT-PCR test results, he was discharged in good general condition. CONCLUSIONS This case of COVID-19 pneumonia presented early in the COVID-19 pandemic of 2020, and the laboratory diagnosis of the initial and subsequent SARS-CoV-2 infection relied on the laboratory methods available at that time. However, several cases of repeat SARS-CoV-2 infection have been described before the development of vaccines in late 2020.

Three waves changes, new variant strains, and vaccination effect against COVID-19 pandemic

It has been more than one year since the first case of the coronaviruses was infected by COVID-19 in China. The world witnessed three waves of the corona virus till now, and more upcoming is expected, whereas several challenges are presented. Empirical data displayed that the features of the virus effects do vary between the three periods. The severity of the disease, differences in symptoms, attitudes of the people have been reported, although the comparative characteristics of the three waves still keep essentially indefinite. In contrast, the sense of danger toward the cries gradually decreases in most countries. This may be due to some factors, including the approved vaccines, introducing alternative plans from politicians to control and deal with the epidemic, and decreasing the mortality rates. However, the alarm voice started to rise again with the appearance of new variant strains with several mutations in the virus. Several more questions began to be asked without sufficient answers. Mutations in COVID-19 have introduced an extreme challenge in preventing and treating SARS-COV-2. The essential feature for mutations is producing new variants known by high tensmibility, disturbing the viral fitness, and enhancing the virus replication. One of the variants that has emerged recently is the Delta variant (B.1.617.2), which was firstly detected in India. In November 2021, a more ferocious mutant appeared in South Africa, also called omicron (B.1.1.529). These mutants grabbed world attention because of their higher transmissibility than the progenitor variants and spread rapidly. Several information about the virus are still confusing and remains secret. There are eight approved vaccines in the market; however, the investigation race about their effect against reinfection and their role against the new variants is still under investigation. Furthermore, this is the first time vaccinating against COVID-19, so the question remains: Will we need an annual dose of the corona vaccines, and the side effects don't been observed till now?

Molecularly imprinted polypyrrole based sensor for the detection of SARS-CoV-2 spike glycoprotein

This study describes the application of a polypyrrole-based sensor for the determination of SARS-CoV-2-S spike glycoprotein. The SARS-CoV-2-S spike glycoprotein is a spike protein of the coronavirus SARS-CoV-2 that recently caused the worldwide spread of COVID-19 disease. This study is dedicated to the development of an electrochemical determination method based on the application of molecularly imprinted polymer technology. The electrochemical sensor was designed by molecular imprinting of polypyrrole (Ppy) with SARS-CoV-2-S spike glycoprotein (MIP-Ppy). The electrochemical sensors with MIP-Ppy and with polypyrrole without imprints (NIP-Ppy) layers were electrochemically deposited on a platinum electrode surface by a sequence of potential pulses. The performance of polymer layers was evaluated by pulsed amperometric detection. According to the obtained results, a sensor based on MIP-Ppy is more sensitive to the SARS-CoV-2-S spike glycoprotein than a sensor based on NIP-Ppy. Also, the results demonstrate that the MIP-Ppy layer is more selectively interacting with SARS-CoV-2-S glycoprotein than with bovine serum albumin. This proves that molecularly imprinted MIP-Ppy-based sensors can be applied for the detection of SARS-CoV-2 virus proteins.

Nine-month course of SARS-CoV-2 antibodies in individuals with COVID-19 infection

Background

The continual course of the pandemic points to the importance of studies on the rate and durability of protective immunity after infection or vaccination.

Aims

In this study, we aimed to monitor anti-nucleocapsid (N) and anti-spike (S) antibodies against SARS-CoV-2 nearly 9 months duration after infection.

Methods

Anti-nucleocapsid (N) (at 11–15-20–29-38 weeks) and anti-spike antibodies (at 11 and 38 weeks) against SARS-CoV-2 were monitored during 38 weeks after the initial symptoms of COVID-19.

Results

Of 37 cases between 18 and 57 years old, 54% were women. The findings showed that anti-N antibodies decreased significantly after the 15th week (between 15 and 20 weeks, p = 0.016; 20–29 weeks, p = 0.0009; and 29–38 weeks, p = 0.049). At the 38th week, mean antibody levels decreased 35% compared to the 11th week, and 8% of the cases turned negative results. Anti-N antibody average level was 56.48 on the 11th week (the cut-off index threshold ≥ 1). It was estimated statistically that it would decrease to an average of 20.48 in weeks 53–62. In females, average antibody levels of all measurements were lower than males (p > 0.05). Anti-S antibody levels 14% increased at 38th week compared to 11th week (quantitative positivity threshold ≥ 0.8 U/ml), and no cases were negative at 38th week.

Conclusions

Patients had ≥ 90% positivity after at least 9 months of symptoms, both anti-N and anti-S antibodies. In all samples, both anti-N and anti-S antibody levels were lower in females. The findings suggest that the quantitative values of anti-S antibodies remained high for at least 9 months and could provide protection.

Reinfection rates among patients previously infected by SARS-CoV-2: systematic review and meta-analysis

BACKGROUND

Asymptomatic or symptomatic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be followed by reinfection. The protection conferred by prior infection among coronavirus disease 2019 (COVID-19) patients is unclear. We assessed the incidence of SARS-CoV-2 reinfection and the protection effect of previous infection against reinfection.

METHODS

We searched PubMed, EMBASE, Cochrane, Scopus, Web of Science, and ClinicalTrials.gov for publications up until the end date of May 1, 2021. The reinfection rate of recovered patients and the protection against reinfection were analyzed using meta-analysis.

RESULTS

Overall, 19 studies of 1096 reinfection patients were included. The pooled reinfection rate was 0.65% (95% confidence interval [CI] 0.39-0.98%). The symptomatic reinfection rate was a bit lower (0.37% [95% CI 0.11-0.78%], I2 = 99%). The reinfection rate was much higher in high-risk populations (1.59% [95% CI 0.30-3.88%], I2 = 90%). The protection against reinfection and symptomatic reinfection was similar (87.02% [95% CI 83.22-89.96%] and 87.17% [95% CI 83.09-90.26%], respectively).

CONCLUSIONS

The rate of reinfection with SARS-CoV-2 is relatively low. The protection against SARS-CoV-2 after natural infection is comparable to that estimated for vaccine efficacy. These data may help guide public health measures and vaccination strategies in response to the COVID-19 pandemic. High-quality clinical studies are needed to establish the relevant risk factors in recovered patients.

A lethal mouse model for evaluating vaccine-associated enhanced respiratory disease during SARS-CoV-2 infection

One safety concern during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine development has been the vaccine-associated enhanced disease, which is characterized by eosinophilic immunopathology and T helper cell type 2 (T_H2)–biased immune responses with insufficient neutralizing antibodies. In this study, we established a lethal animal model using BALB/c mice and a mouse-passaged isolate (QHmusX) from a European lineage of SARS-CoV-2. The QHmusX strain induced acute respiratory illness, associated with diffuse alveolar damage and pulmonary edema, in T_H2-prone adult BALB/c mice, but not in young mice or T_H1-prone C57BL/6 mice. We also showed that immunization of adult BALB/c mice with recombinant spike protein without appropriate adjuvant caused eosinophilic immunopathology with T_H2-shifted immune response and insufficient neutralizing antibodies after QHmusX infection. This lethal mouse model is useful for evaluating vaccine-associated enhanced respiratory disease during SARS-CoV-2 infection and may provide new insights into the disease pathogenesis of SARS-CoV-2.

The chance of COVID-19 infection after vaccination

The outbreak of COVID-19 that began in Wuhan, China, has constituted a new emerging epidemic that has spread around the world. There are some reports on illustrated the patients getting reinfected after recovering from COVID-19. Here we provide an overview of the biphasic cycle of COVID-19, genetic diversity, immune response and chance of reinfection after recovering from COVID-19. The new generation of COVID-19 is highly contagious and pathogenic infection can lead to acute respiratory distress syndrome. Whilst most patients suffer from a mild form of the disease, there is a rising concern that patients who recover from COVID-19 may be at risk of reinfection. The proportion of the infected population, is increasing worldwide; meanwhile, the rate and concern of reinfection by the recovered population are still high. Moreover, there are a few evidence on the chance of COVID-19 infection even after vaccination, which is around one per cent or less. Although the hypothesis of zero reinfections after vaccination has not been clinically proven, further studies should be performed on the recovered class in clusters to study the progression of the exposed with the re-exposed subpopulations to estimate the possibilities of reinfection and, thereby, advocate the use of these antibodies for vaccine creation.

Trajectory of Viral RNA Load Among Persons With Incident SARS-CoV-2 G614 Infection (Wuhan Strain) in Association With COVID-19 Symptom Onset and Severity

IMPORTANCE

The SARS-CoV-2 viral trajectory has not been well characterized in incident infections. These data are needed to inform natural history, prevention practices, and therapeutic development.

OBJECTIVE

To characterize early SARS-CoV-2 viral RNA load (hereafter referred to as viral load) in individuals with incident infections in association with COVID-19 symptom onset and severity.

DESIGN, SETTING, AND PARTICIPANTS

This prospective cohort study was a secondary data analysis of a remotely conducted study that enrolled 829 asymptomatic community-based participants recently exposed (<96 hours) to persons with SARS-CoV-2 from 41 US states from March 31 to August 21, 2020. Two cohorts were studied: (1) participants who were SARS-CoV-2 negative at baseline and tested positive during study follow-up, and (2) participants who had 2 or more positive swabs during follow-up, regardless of the initial (baseline) swab result. Participants collected daily midturbinate swab samples for SARS-CoV-2 RNA detection and maintained symptom diaries for 14 days.

EXPOSURE

Laboratory-confirmed SARS-CoV-2 infection.

MAIN OUTCOMES AND MEASURES

The observed SARS-CoV-2 viral load among incident infections was summarized, and piecewise linear mixed-effects models were used to estimate the characteristics of viral trajectories in association with COVID-19 symptom onset and severity.

RESULTS

A total of 97 participants (55 women [57%]; median age, 37 years [IQR, 27-52 years]) developed incident infections during follow-up. Forty-two participants (43%) had viral shedding for 1 day (median peak viral load cycle threshold [Ct] value, 38.5 [95% CI, 38.3-39.0]), 18 (19%) for 2 to 6 days (median Ct value, 36.7 [95% CI, 30.2-38.1]), and 31 (32%) for 7 days or more (median Ct value, 18.3 [95% CI, 17.4-22.0]). The cycle threshold value has an inverse association with viral load. Six participants (6%) had 1 to 6 days of viral shedding with censored duration. The peak mean (SD) viral load was observed on day 3 of shedding (Ct value, 33.8 [95% CI, 31.9-35.6]). Based on the statistical models fitted to 129 participants (60 men [47%]; median age, 38 years [IQR, 25-54 years]) with 2 or more SARS-CoV-2-positive swab samples, persons reporting moderate or severe symptoms tended to have a higher peak mean viral load than those who were asymptomatic (Ct value, 23.3 [95% CI, 22.6-24.0] vs 30.7 [95% CI, 29.8-31.4]). Mild symptoms generally started within 1 day of peak viral load, and moderate or severe symptoms 2 days after peak viral load. All 535 sequenced samples detected the G614 variant (Wuhan strain).

CONCLUSIONS AND RELEVANCE

This cohort study suggests that having incident SARS-CoV-2 G614 infection was associated with a rapid viral load peak followed by slower decay. COVID-19 symptom onset generally coincided with peak viral load, which correlated positively with symptom severity. This longitudinal evaluation of the SARS-CoV-2 G614 with frequent molecular testing serves as a reference for comparing emergent viral lineages to inform clinical trial designs and public health strategies to contain the spread of the virus.

Durability of Humoral Immune Responses to SARS-CoV-2 in Citizens of Ariano Irpino (Campania, Italy): A Longitudinal Observational Study With an 11.5-Month Follow-Up

As of November 17, 2021, SARS-CoV-2 (Severe Acute Respiratory Syndrome CoronaVirus 2), the causative agent of COVID-19 (COronaVIrus Disease 19), has infected ~250 million people worldwide, causing around five million deaths. Titers of anti-SARS-CoV-2 neutralizing antibodies were relatively stable for at least 9 months in a population-based study conducted in Wuhan, China, both in symptomatic and in asymptomatic individuals. In the mass screening campaign conducted in the town of Ariano Irpino (Avellino, Italy) in May, 2020, 5.7% (95% CI: 5.3-6-1) of the 13,444 asymptomatic citizens screened were positive for anti-nucleocapsid antibodies against SARS-CoV-2. Among these, 422 citizens were re-tested for anti SARS-CoV-2 antibodies in January, 2021 and/or in April, 2021 and enrolled in this longitudinal observational study. Median (interquartile range) age of the study cohort was 46 years (29–59), with 47 (11.1%) participants of minor age, while 217 (51.4%) participants were females. There was no evidence of re-infection in any of the subjects included. Presence of anti-nuclear antibodies antibodies (Elecysis, Roche) was reported in 95.7 and 93.7% of evaluable participants in January and April, 2021. Multiple logistic regression analysis used to explore associations between age, sex and seroprevalence showed that adults vs. minors had significantly lower odds of having anti-S1 antibodies (Biorad) both in January, 2021 and in April, 2021. Our findings showed that antibodies remained detectable at least 11.5 months after infection in >90% of never symptomatic cases. Further investigation is required to establish duration of immunity against SARS-CoV-2.

Persistence of Anti-SARS-CoV-2 Antibodies in Long Term Care Residents Over Seven Months After Two COVID-19 Outbreaks

Background

As part of the public health outbreak investigations, serological surveys were carried out following two COVID-19 outbreaks in April 2020 and October 2020 in one long term care facility (LTCF) in British Columbia, Canada. This study describes the serostatus of the LTCF residents and monitors changes in their humoral response to SARS-CoV-2 and other human coronaviruses (HCoV) over seven months.

Methods

A total of 132 serum samples were collected from all 106 consenting residents (aged 54-102) post-first outbreak (N=87) and post-second outbreak (N=45) in one LTCF; 26/106 participants provided their serum following both COVID-19 outbreaks, permitting longitudinal comparisons between surveys. Health-Canada approved commercial serologic tests and a pan-coronavirus multiplexed immunoassay were used to evaluate antibody levels against the spike protein, nucleocapsid, and receptor binding domain (RBD) of SARS-CoV-2, as well as the spike proteins of HCoV-229E, HCoV-HKU1, HCoV-NL63, and HCoV-OC43. Statistical analyses were performed to describe the humoral response to SARS-CoV-2 among residents longitudinally.

Findings

Survey findings demonstrated that among the 26 individuals that participated in both surveys, all 10 individuals seropositive after the first outbreak continued to be seropositive following the second outbreak, with no reinfections identified among them. SARS-CoV-2 attack rate in the second outbreak was lower (28.6%) than in the first outbreak (40.2%), though not statistically significant (P>0.05). Gradual waning of anti-nucleocapsid antibodies to SARS-CoV-2 was observed on commercial (median Δ=-3.7, P=0.0098) and multiplexed immunoassay (median Δ=-169579, P=0.014) platforms; however, anti-spike and anti-receptor binding domain (RBD) antibodies did not exhibit a statistically significant decline over 7 months. Elevated antibody levels for beta-HCoVs OC43 (P<0.0001) and HKU1 (P=0.0027) were observed among individuals seropositive for SARS-CoV-2 compared to seronegative individuals.

Conclusion

Our study utilized well-validated serological platforms to demonstrate that humoral responses to SARS-CoV-2 persisted for at least 7 months. Elevated OC43 and HKU1 antibodies among SARS-CoV-2 seropositive individuals may be attributed to cross reaction and/or boosting of humoral response.

Immunity to SARS-CoV-2 induced by infection or vaccination

Adaptive immune responses play critical roles in viral clearance and protection against re-infection, and SARS-CoV-2 is no exception. What is exceptional is the rapid characterization of the immune response to the virus performed by researchers during the first 20 months of the pandemic. This has given us a more detailed understanding of SARS-CoV-2 compared to many viruses that have been with us for a long time. Furthermore, effective COVID-19 vaccines were developed in record time, and their rollout worldwide is already making a significant difference, although major challenges remain in terms of equal access. The pandemic has engaged scientists and the public alike, and terms such as seroprevalence, neutralizing antibodies, antibody escape and vaccine certificates have become familiar to a broad community. Here, we review key findings concerning B cell and antibody (Ab) responses to SARS-CoV-2, focusing on non-severe cases and anti-spike (S) Ab responses in particular, the latter being central to protective immunity induced by infection or vaccination. The emergence of viral variants that have acquired mutations in S acutely highlights the need for continued characterization of both emerging variants and Ab responses against these during the evolving pathogen-immune system arms race.

Gut microbiome, Vitamin D, ACE2 interactions are critical factors in immune-senescence and inflammaging: key for vaccine response and severity of COVID-19 infection

BACKGROUND

The SARS-CoV-2 pandemic continues to spread sporadically in the Unites States and worldwide. The severity and mortality excessively affected the frail elderly with co-existing medical diseases. There is growing evidence that cross-talk between the gut microbiome, Vitamin D and RAS/ACE2 system is essential for a balanced functioning of the elderly immune system and in regulating inflammation. In this review, we hypothesize that the state of gut microbiome, prior to infection determines the outcome associated with COVID-19 sepsis and may also be a critical factor in success to vaccination.

METHODS

Articles from PubMed/Medline searches were reviewed using a combination of terms "SARS-CoV-2, COVID-19, Inflammaging, Immune-senescence, Gut microbiome, Vitamin D, RAS/ACE2, Vaccination".

CONCLUSION

Evidence indicates a complex association between gut microbiota, ACE-2 expression and Vitamin D in COVID-19 severity. Status of gut microbiome is highly predictive of the blood molecular signatures and inflammatory markers and host responses to infection. Vitamin D has immunomodulatory function in innate and adaptive immune responses to viral infection. Anti-inflammatory functions of Vit D include regulation of gut microbiome and maintaining microbial diversity. It promotes growth of gut-friendly commensal strains of Bifida and Fermicutus species. In addition, Vitamin D is a negative regulator for expression of renin and interacts with the RAS/ ACE/ACE-2 signaling axis. Collectively, this triad may be the critical, link in determination of outcomes in SARS-CoV-2 infection. The presented data are empirical and informative. Further research using advanced systems biology techniques and artificial intelligence-assisted integration could assist with correlation of the gut microbiome with sepsis and vaccine responses. Modulating these factors may impact in guiding the success of vaccines and clinical outcomes in COVID-19 infections.