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

Comparison of a Prototype SARS-CoV-2 Lateral Flow IMMUNOASSAY with the BinaxNOWTM COVID-19 Antigen CARD

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic. From the onset of the pandemic, rapid antigen tests have quickly proved themselves to be an accurate and accessible diagnostic platform. The initial (and still most commonly used antigen tests) for COVID-19 diagnosis were constructed using monoclonal antibodies (mAbs) specific to severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP). These mAbs are able to bind SARS-CoV-2 NP due to high homology between the two viruses. However, since first being identified in 2019, SARS-CoV-2 has continuously mutated, and a multitude of variants have appeared. These mutations have an elevated risk of leading to possible diagnostic escape when using tests produced with SARS-CoV-derived mAbs. Here, we established a library of 18 mAbs specific to SARS-CoV-2 NP and used two of these mAbs (1CV7 and 1CV14) to generate a prototype antigen-detection lateral flow immunoassay (LFI). A side-by-side analysis of the 1CV7/1CV14 LFI and the commercially available BinaxNOW^TM COVID-19 Antigen CARD was performed. Results indicated the 1CV7/1CV14 LFI outperformed the BinaxNOW^TM test in the detection of BA.2, BA.2.12.1, and BA.5 Omicron sub-variants when testing remnant RT-PCR positive patient nasopharyngeal swabs diluted in viral transport media.

Who Is at Higher Risk of SARS-CoV-2 Reinfection? Results from a Northern Region of Italy

The SARS-CoV-2 pandemic continues to spread worldwide, generating a high impact on healthcare systems. The aim of the study was to examine the epidemiological burden of SARS-CoV-2 reinfections and to identify potential related risk factors. A retrospective observational study was conducted in Liguria Region, combining data from National Vaccines Registry and Regional Chronic Condition Data Warehouse. In the study period (September 2021 to May 2022), 335,117 cases of SARS-CoV-2 infection were recorded in Liguria, of which 15,715 were reinfected once. During the Omicron phase (which predominated from 3 January 2022), the risk of reinfection was 4.89 times higher (p < 0.001) than during the Delta phase. Unvaccinated and vaccinated individuals with at least one dose for more than 120 days were at increased risk of reinfection compared with vaccinated individuals with at least one dose for ≤120 days, respectively (odds ratio (OR) of 1.26, p < 0.001; OR of 1.18, p < 0.001). Healthcare workers were more than twice as likely to be reinfected than non-healthcare workers (OR of 2.38, p < 0.001). Lower ORs were seen among people aged 60 to 79 years. Two doses or more of vaccination were found to be protective against the risk of reinfection rather than a single dose (mRNA vaccines: OR of 0.06, p < 0.0001, and OR of 0.1, p < 0.0001; vector vaccines: OR of 0.05, p < 0.0001). Patients with chronic renal failure, cardiovascular disease, bronchopneumopathy, neuropathy and autoimmune diseases were at increased risk of reinfection (OR of 1.38, p = 0.0003; OR of 1.09, p < 0.0296; OR of 1.14, p = 0.0056; OR of 1.78, p < 0.0001; OR of 1.18, p = 0.0205). Estimating the epidemiological burden of SARS-CoV-2 reinfections and the role played by risk factors in reinfections is relevant for identifying risk-based preventive strategies in a pandemic context characterized by a high circulation of the virus and a high rate of pathogen mutations.

Targeting SARS-CoV-2 nsp13 Helicase and Assessment of Druggability Pockets: Identification of Two Potent Inhibitors by a Multi-Site In Silico Drug Repurposing Approach

The SARS-CoV-2 non-structural protein 13 (nsp13) helicase is an essential enzyme for viral replication and has been identified as an attractive target for the development of new antiviral drugs. In detail, the helicase catalyzes the unwinding of double-stranded DNA or RNA in a 5′ to 3′ direction and acts in concert with the replication–transcription complex (nsp7/nsp8/nsp12). In this work, bioinformatics and computational tools allowed us to perform a detailed conservation analysis of the SARS-CoV-2 helicase genome and to further predict the druggable enzyme’s binding pockets. Thus, a structure-based virtual screening was used to identify valuable compounds that are capable of recognizing multiple nsp13 pockets. Starting from a database of around 4000 drugs already approved by the Food and Drug Administration (FDA), we chose 14 shared compounds capable of recognizing three out of four sites. Finally, by means of visual inspection analysis and based on their commercial availability, five promising compounds were submitted to in vitro assays. Among them, PF-03715455 was able to block both the unwinding and NTPase activities of nsp13 in a micromolar range.

Accurate identification of SARS-CoV-2 variant delta using graphene/CRISPR-dCas9 electrochemical biosensor

Delta (B.1.617.2), a highly infectious variant of SARS-CoV-2, has been sweeping the world, and threatening the safety of human life seriously. It is urgent to develop a highly selective and sensitive assay to accurately identify the SARS-CoV-2 variant Delta. In this work, we constructed a graphene/CRISPR-dCas9 electrochemical biosensor to accurately identify SARS-CoV-2 variant Delta, where the signal was further amplified by embedded electrochemical probe [Ru(phen)₂dppz]BF₄. This detection assay could be finished within 47 min totally, with the detection limit of 1.2 pM and good reproducibility with a C·V.% of 2.48% (n = 5). And the biosensor could selectively identify Delta among SARS-CoV-2 and other variants, including Alpha, Beta, Gamma. This assay was further validated by 26 real clinical samples, showing 100% clinical sensitivity and 100% clinical specificity, which provides a new direction for identifying other SARS-CoV-2 variants in the future.

A retrospective cross-sectional observational study of SARS-CoV-2 reinfection in La Ribera Health Department, Valencia, Spain

Introduction. The possibility of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a widely proven fact and may have clinical implications.

Hypothesis /Gap Statement. It is not known whether there have been cases of reinfection by SARS-CoV-2 in La Ribera Health Department.

Aim. To determine whether there have been cases of reinfection by SARS-CoV-2 in La Ribera Health Department and to identify their characteristics.

Methodology. Retrospective cross-sectional observational study of cases of reinfection by SARS-CoV-2 in the population of La Ribera Department between March 2020 and February 2021. The positive baseline cohort includes all cases positive by RT-PCR for SARS-CoV-2, with reinfection cases being those that, after resolution of the first episode according to the World Health Organization (WHO) criteria, presented a new positive RT-PCR result.

Results. Out of a total of 15 687 cases with positive RT-PCR, 40 were considered to be reinfections, which meant a cumulative incidence of 0.255 % and an incidence density of 5.05 cases per 100 000 person-days. Most of the cases occurred during the highest incidence peaks of the pandemic in the department. Seventy-five per cent of the patients in these cases were older than 40 years, 42.5 % were healthcare professionals or nursing home residents and 12.5 % had an immunosuppressive comorbidity. There were no severe, critical or death cases. In the reinfection episodes, with respect to the first episode, there was a tendency to be milder, they required fewer days of hospitalization, their RT-PCR became negative earlier, they developed a greater humoral response and the sick leave period was shorter. The median period between the RT-PCR in the first episode and the RT-PCR in the second episode was 127.5 days (range: 48–301; IQR: 89.5–256.25)

Conclusions. SARS-CoV-2 reinfection cases are rare, tend to be mild and can occur within a median period of 127.5 days.

Anti-SARS-CoV-2 antibody immunoreactivity profiles during COVID-19 recurrence

BACKGROUND

This study aimed to evaluate IgG and IgM levels in COVID-19 recurrence.

METHODS

The serum antibody levels and clinical data from 73 healthcare workers with SARS-CoV-2 divided into seroconverted (n=51) and non-seroconverted (n=22) groups were assessed. The presence of specific anti-nucleocapsid (anti-N) IgM and IgG for SARS-CoV-2 was evaluated. IgG antibodies to the SARS-CoV-2 spike receptor-binding domain were used to confirm non-seroconversion in all negative anti-N.

RESULTS

Four recurrent cases displayed mild symptoms and were non-seroconverted until the recurrence of symptoms.

CONCLUSIONS

Undetectable anti-nucleocapsid IgM and IgG levels may be correlated with symptomatic COVID-19 recurrence.

Rapid Increase in Suspected SARS-CoV-2 Reinfections, Clark County, Nevada, USA, December 2021

Genetic differences between SARS-CoV-2 variants raise concerns about reinfection. Public health authorities monitored the incidence of suspected reinfection in Clark County, Nevada, USA, during March 2020-March 2022. Suspected reinfections, defined as a second positive PCR test collected >90 days after an initial positive test, were monitored through an electronic disease surveillance system. We calculated the proportion of all new cases per week that were suspected reinfections and rates per 1,000 previously infected persons by demographic groups. The rate of suspected reinfection remained <2.7% until December 2021, then increased to ≈11%, corresponding with local Omicron variant detection. Reinfection rates were higher among adults 18-50 years of age, women, and minority groups, especially persons identifying as American Indian/Alaska Native. Suspected reinfection became more common in Clark County after introduction of the Omicron variant, and some demographic groups are disproportionately affected. Public health surveillance could clarify the SARS-CoV-2 reinfection burden in communities.

Epidemiological assessment of SARS-CoV-2 reinfection

OBJECTIVES

SARS-CoV-2 vaccination has been shown to reduce infection severity; however, the reinfection frequency among unvaccinated, partially vaccinated, and fully vaccinated individuals remains unclear. This study aims to elucidate the rates of and factors associated with such occurrences.

METHODS

This retrospective epidemiological report included 1362 COVID-19 reinfection cases in Bahrain between April 2020 and July 2021. We analyzed differences in disease severity and reinfection characteristics among various vaccination statuses: fully vaccinated, interrupted vaccination, one-dose vaccination, postreinfection vaccination, and unvaccinated.

RESULTS

Reinfection cases increased from zero per month in April-June 2020 to a sharp peak of 579 in May 2021. A significantly larger proportion of reinfected individuals were male (60.3%, P <0.0001). Reinfection episodes were highest among those 30-39 years of age (29.7%). The fewest reinfection episodes occurred at 3-6 months after the first infection (20.6%) and most occurred ≥9 months after the initial infection (46.4%). Most individuals were asymptomatic during both episodes (35.7%). Reinfection disease severity was mild, with vaccinated patients less likely to have symptomatic reinfection (odds ratio 0.71, P = 0.004). Only 6.6% of reinfected patients required hospitalization. One death was recorded; the patient belonged to the unvaccinated group.

CONCLUSION

Vaccine-induced immunity and previous infection with or without vaccination were effective in reducing reinfection disease severity.

Recurrence of COVID-19 infection symptoms in short time; reinfection or reactivation? Three cases of three healthcare workers and a literature review

Background

Since the beginning of the COVID-19 pandemic, many research papers have been published focusing on some recurrence cases of symptoms after a long period of free symptoms with a negative RT-PCR retest. There is no crucial evidence until now of the possibility of recurrence, immune system reactivation, or reinfection.

Methods

Three cases of resident doctors who recovered from COVID-19 but represented symptoms with new positive RT-PCR were discussed. Clinical data, laboratory tests, RT-PCR results, and antibodies titers all were collected. Moreover, many cases from the literature have been reviewed and compared.

Results

The long-term exposure has not succeeded in forming an effective immune response, especially, since they do not have any significant history of chronic illnesses or a diagnosed immune disorder. While the antibody response occurred only in the second patient, it did not prevent new infection, but did it control the severity of the infection or its complications?

Conclusion

Our three patients are health workers and have been in direct contact with COVID-19 patients. The inflammatory response parameters may not be reliable in predicting the activation of the immune response and the formation of the antibodies. We still need to find answers for reactivation and reinfection issues.

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A direct contact with COVID-19 patients failed in forming an effective response.

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The antibodies controlled the severity, complications and inflammatory response.

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The correlation between the severity of symptoms and laboratory markers.

SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis

Immunocompromised patients can experience prolonged SARS-CoV-2 infections in the setting of a lack of protectivity immunity despite vaccination. As circulating SARS-CoV-2 strains become more heterogeneous, concomitant infection with multiple SARS-CoV-2 variants has become an increasing concern. Immunocompromised patient populations represent potential reservoirs for the emergence of novel SARS-CoV-2 variants through mutagenic change or coinfection followed by recombinatory events. Identification of SARS-CoV-2 coinfections is challenging using traditional next generation sequencing pipelines; however, targeted genotyping approaches can facilitate detection. Here we describe five COVID-19 cases caused by coinfection with different SARS-CoV-2 variants (Delta/Omicron BA.1 and Omicron BA.1/BA.2) as identified by multiplex fragment analysis.

Does potential antibody-dependent enhancement occur during SARS-CoV-2 infection after natural infection or vaccination? A meta-analysis

Coronavirus disease 2019 (COVID-19) continues to constitute an international public health emergency. Vaccination is a prospective approach to control this pandemic. However, apprehension about the safety of vaccines is a major obstacle to vaccination. Amongst health professionals, one evident concern is the risk of antibody-dependent enhancement (ADE), which may increase the severity of COVID-19. To explore whether ADE occurs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and increase confidence in the safety of vaccination, we conducted a meta-analysis to investigate the relationship between post-immune infection and disease severity from a population perspective. Databases, including PubMed, EMBASE, Chinese National Knowledge Infrastructure, SinoMed, Scopus, Science Direct, and Cochrane Library, were searched for articles on SARS-CoV-2 reinfection published until 25 October 2021. The papers were reviewed for methodological quality, and a random effects model was used to analyse the results. Heterogeneity was assessed using the I2 statistic. Publication bias was evaluated using a funnel plot and Egger's test. Eleven studies were included in the final meta-analysis. The pooled results indicated that initial infection and vaccination were protective factors against severe COVID-19 during post-immune infection (OR = 0.55, 95%CI = 0.31-0.98). A subgroup (post-immune infection after natural infection or vaccination) analysis showed similar results. Primary SARS-CoV-2 infection and vaccination provide adequate protection against severe clinical symptoms after post-immune infection. This finding demonstrates that SARS-CoV-2 may not trigger ADE at the population level.

NanoCoV19: An analytical pipeline for rapid detection of severe acute respiratory syndrome coronavirus 2

Nanopore sequencing technology (NST) has become a rapid and cost-effective method for the diagnosis and epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic. Compared with short-read sequencing platforms (e.g., Illumina’s), nanopore long-read sequencing platforms effectively shorten the time required to complete the detection process. However, due to the principles and data characteristics of NST, the accuracy of sequencing data has been reduced, thereby limiting monitoring and lineage analysis of SARS-CoV-2. In this study, we developed an analytical pipeline for SARS-CoV-2 rapid detection and lineage identification that integrates phylogenetic-tree and hotspot mutation analysis, which we have named NanoCoV19. This method not only can distinguish and trace the lineages contained in the alpha, beta, delta, gamma, lambda, and omicron variants of SARS-CoV-2 but is also rapid and efficient, completing overall analysis within 1 h. We hope that NanoCoV19 can be used as an auxiliary tool for rapid subtyping and lineage analysis of SARS-CoV-2 and, more importantly, that it can promote further applications of NST in public-health and -safety plans similar to those formulated to address the COVID-19 outbreak.

SARS-CoV-2 reinfections during the first three major COVID-19 waves in Bulgaria

BACKGROUND

The COVID-19 pandemic has had a devastating impact on the world over the past two years (2020-2021). One of the key questions about its future trajectory is the protection from subsequent infections and disease conferred by a previous infection, as the SARS-CoV-2 virus belongs to the coronaviruses, a group of viruses the members of which are known for their ability to reinfect convalescent individuals. Bulgaria, with high rates of previous infections combined with low vaccination rates and an elderly population, presents a somewhat unique context to study this question.

METHODS

We use detailed governmental data on registered COVID-19 cases to evaluate the incidence and outcomes of COVID-19 reinfections in Bulgaria in the period between March 2020 and early December 2021.

RESULTS

For the period analyzed, a total of 4,106 cases of individuals infected more than once were observed, including 31 cases of three infections and one of four infections. The number of reinfections increased dramatically during the Delta variant-driven wave of the pandemic towards the end of 2021. We observe a moderate reduction of severe outcomes (hospitalization and death) in reinfections relative to primary infections, and a more substantial reduction of severe outcomes in breakthrough infections in vaccinated individuals.

CONCLUSIONS

In the available datasets from Bulgaria, prior infection appears to provide some protection from severe outcomes, but to a lower degree than the reduction in severity of breakthrough infections in the vaccinated compared to primary infections in the unvaccinated.

Occurrence of SARS-CoV-2 reinfections at regular intervals in Ecuador

SARS-CoV-2 reinfection is defined as a new infection with a different virus variant in an individual who has already recovered from a previous episode of COVID-19. The first case of reinfection in the world was described in August 2020, since then, reinfections have increased over time and their incidence has fluctuated with specific SARS-CoV-2 variant waves. Initially, reinfections were estimated to represent less than 1% of total COVID-19 infections. With the advent of the Omicron variant, reinfections became more frequent, representing up to 10% of cases (based on data from developed countries). The frequency of reinfections in Latin America has been scarcely reported. The current study shows that in Ecuador, the frequency of reinfections has increased 10-fold following the introduction of Omicron, after 22 months of surveillance in a single center of COVID-19 diagnostics. Suspected reinfections were identified retrospectively from a database of RT-qPCR-positive patients. Cases were confirmed by sequencing viral genomes from the first and second infections using the ONT MinION platform. Monthly surveillance showed that the main incidence peaks of reinfections were reached within four to five months, coinciding with the increase of COVID-19 cases in the country, suggesting that the emergence of reinfections is related to higher exposure to the virus during outbreaks. This study performed the longest monitoring of SARS-CoV-2 reinfections, showing an occurrence at regular intervals of 4-5 months and confirming a greater propensity of Omicron to cause reinfections.

A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan

Severe acute respiratory syndrome (SARS-CoV-2) is responsible for the worldwide pandemic, COVID-19. The original viral whole-genome was sequenced by a high-throughput sequencing approach from the samples obtained from Wuhan, China. Real-time gene sequencing is the main parameter to manage viral outbreaks because it expands our understanding of virus proliferation, spread, and evolution. Whole-genome sequencing is critical for SARS-CoV-2 variant surveillance, the development of new vaccines and boosters, and the representation of epidemiological situations in the country. A significant increase in the number of COVID-19 cases confirmed in August 2021 in Kazakhstan facilitated a need to establish an effective and proficient system for further study of SARS-CoV-2 genetic variants and the development of future Kazakhstan’s genomic surveillance program. The SARS-CoV-2 whole-genome was sequenced according to SARS-CoV-2 ARTIC protocol (EXP-MRT001) by Oxford Nanopore Technologies at the National Laboratory Astana, Kazakhstan to track viral variants circulating in the country. The 500 samples kindly provided by the Republican Diagnostic Center (UMC-NU) and private laboratory KDL “Olymp” were collected from individuals in Nur-Sultan city diagnosed with COVID-19 from August 2021 to May 2022 using real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR). All samples had a cycle threshold (Ct) value below 20 with an average Ct value of 17.03. The overall average value of sequencing depth coverage for samples is 244X. 341 whole-genome sequences that passed quality control were deposited in the Global initiative on sharing all influenza data (GISAID). The BA.1.1 (n = 189), BA.1 (n = 15), BA.2 (n = 3), BA.1.15 (n = 1), BA.1.17.2 (n = 1) omicron lineages, AY.122 (n = 119), B.1.617.2 (n = 8), AY.111 (n = 2), AY.126 (n = 1), AY.4 (n = 1) delta lineages, one sample B.1.1.7 (n = 1) belongs to alpha lineage, and one sample B.1.637 (n = 1) belongs to small sublineage were detected in this study. This is the first study of SARS-CoV-2 whole-genome sequencing by the ONT approach in Kazakhstan, which can be expanded for the investigation of other emerging viral or bacterial infections on the country level.

A comparison between SARS-CoV-1 and SARS-CoV2: an update on current COVID-19 vaccines

Since the outbreak of the novel coronavirus disease 2019 (COVID-19) in Wuhan, China, many health care systems have been heavily engaged in treating and preventing the disease, and the year 2020 may be called as “historic COVID-19 vaccine breakthrough”. Due to the COVID-19 pandemic, many companies have initiated investigations on developing an efficient and safe vaccine against the virus. From Moderna and Pfizer in the United States to PastocoVac in Pasteur Institute of Iran and the University of Oxford in the United Kingdom, different candidates have been introduced to the market. COVID-19 vaccine research has been facilitated based on genome and structural information, bioinformatics predictions, epitope mapping, and data obtained from the previous developments of severe acute respiratory syndrome coronavirus (SARS-CoV or SARS-CoV-1) and middle east respiratory syndrome coronavirus (MERS-CoV) vaccine candidates. SARS-CoV genome sequence is highly homologous to the one in COVID-19 and both viruses use the same receptor, angiotensin-converting enzyme 2 (ACE2). Moreover, the immune system responds to these viruses, partially in the same way. Considering the on-going COVID-19 pandemic and previous attempts to manufacture SARS-CoV vaccines, this paper is going to discuss clinical cases as well as vaccine challenges, including those related to infrastructures, transportation, possible adverse reactions, utilized delivery systems (e.g., nanotechnology and electroporation) and probable vaccine-induced mutations.

Reinfection and reactivation of SARS-CoV-2

As the cases of SARS-CoV-2 infection escalates, the essence of in-depth knowledge around acquired immunity and emergence of reinfection and reactivation have to be captured. While being a rare phenomenon, reinfection occurs as the result of diminishing protection conferred by antibodies, especially IgG. Reactivation is more concerned with the role of various elements including shedding lingering viral RNA for a prolonged time and incomplete resolution of infection along with the insight of dormant viral exosomes’ role. The concept of testing positive after two consecutive negative results requires proper discrimination of reinfection from reactivation. In this review, we summarized the current evidence for possible mechanisms leading to viral reactivation or test re-positivity. We also pointed out risk factors associated with both reinfection and reactivation.

Rapid repeat infection of SARS-CoV-2 by two highly distinct delta-lineage viruses

An instance of sequential infection of an individual with, firstly, the Delta variant and secondly a Delta-sub-lineage has been identified. The individual was found positive for the AY.26 lineage 22 days after being found positive for the Delta [B.1.617.2] variant. The viruses associated with the cases showed dramatic genomic difference, including 31 changes that resulted in deletions or amino acid substitutions. Seven of these differences were observed in the Spike protein. The patient in question was between 30 and 35 years old and had no underlying health conditions. Though singular, this case illustrates the possibility that infection with the Delta variant may not itself be fully protective against a population of SARS-CoV-2 variants that are becoming increasingly diverse.

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.

SARS-CoV-2 Reinfection Rate and Outcomes in Saudi Arabia: A National Retrospective Study

BACKGROUND

The characterization of reinfection with SARS-CoV-2 has been a subject of concern and controversy, especially with the surge of infections with highly transmissible variants worldwide.

METHODS

This retrospective national study used comorbidities, vaccination status, SARS-CoV-2 variants of concern, and demographics data to profile participants who were reinfected with SARS-CoV-2, defined as having two reverse transcriptase-polymerase chain reaction-positive SARS-CoV-2 tests within at least 90 days apart. A multivariate logistic regression model assessed the risk factors associated with reinfection . Two control groups were selected: nonreinfected participants reporting a positive test (control group one) and those reporting a negative test (control group two).

RESULTS

Between March 2020 and December 2021, 4454 reinfected participants were identified in Saudi Arabia (0.8%, 95% confidence interval [CI] 0.7-0.8). The majority (67.3%) were unvaccinated (95% CI 65.9-68.7) and 0.8% (95% CI 0.6-1.1) had severe or fatal SARS-CoV-2 disease. COVID-19 vaccines were 100% effective against mortality in reinfected individuals who received at least one dose, whereas it conferred 61% (odds ratio [OR] 0.4, 95% CI 0.1-1.0) additional protection against severe disease after the first dose and 100% after the second dose. In the risk factor analysis, reinfection was highly associated with comorbidities, such as HIV (OR 2.5, 95% CI 1.3-5.2; P = 0.009), obesity (OR 2.3, 95% CI 1.3-3.9; P = 0.003), pregnancy (OR 3.2, 95% CI 1.4-7.4; P = 0.005), and working in health care facilities (OR 6.1, 95% CI 3.1-12.9; P <0.0001). The delta variant (B.1.617.2) was the most frequent variant of concern among the reinfected cohort.

CONCLUSION

This in-depth study of the reinfection profile identified risk factors and highlighted the associated SARS-CoV-2 variants. Results showed that naturally acquired immunity to SARS-CoV-2 through multiple reinfections together with vaccine-induced immunity provided substantial protection against severe SARS-CoV-2 disease and mortality.

An agent-based model to assess large-scale COVID-19 vaccination campaigns for the Italian territory: The case study of Lombardy region

BACKGROUND

In Italy, the administration of COVID-19 vaccines began in late 2020. In the early stages, the number of available doses was limited. To maximize the effectiveness of the vaccine campaign, the national health agency assigned priority access to at-risk individuals, such as health care workers and the elderly. Current vaccination campaign strategies do not take full advantage of the latest mathematical models, which capture many subtle nuances, allowing different territorial situations to be analyzed aiming to make context-specific decisions.

OBJECTIVES

The main objective is the definition of an agent-based model using open data and scientific literature to assess and optimize the impact of vaccine campaigns for an Italian region. Specifically, the aim is twofold: (i) estimate the reduction in the number of infections and deaths attributable to vaccines, and (ii) assess the performances of alternative vaccine allocation strategies.

METHODS

The COVID-19 Agent-based simulator Covasim has been employed to build an agent-based model by considering the Lombardy region as case study. The model has been tailored by leveraging open data and knowledge from the scientific literature. Dynamic mobility restrictions and the presence of Variant of Concern have been explicitly represented. Free parameters have been calibrated using the grid search methodology.

RESULTS

The model mimics the COVID-19 wave that hit Lombardy from September 2020 to April 2021. It suggests that 168,492 cumulative infections 2,990 cumulative deaths have been avoided due to the vaccination campaign in Lombardy from January 1 to April 30, 2021. Without vaccines, the number of deaths would have been 66% greater in the 80-89 age group and 114% greater for those over 90. The best vaccine allocation strategy depends on the goal. To minimize infections, the best policy is related to dose availability. If at least 1/3 of the population can be covered in 4 months, targeting at-risk individuals and the elderly first is recommended; otherwise, the youngest people should be vaccinated first. To minimize overall deaths, priority is best given to at-risk groups and the elderly in all scenarios.

CONCLUSIONS

This work proposes a methodological approach that leverages open data and scientific literature to build a model of COVID-19 capable of assessing and optimizing the impact of vaccine campaigns. This methodology can help national institutions to design regional mathematical models that can support pandemic-related decision-making processes.

Mechanical dependency of the SARS-CoV-2 virus and the renin-angiotensin-aldosterone (RAAS) axis: a possible new threat

Pathogens in our environment can act as agents capable of inflicting severe human diseases. Among them, the SARS-CoV-2 virus has recently plagued the globe and paralyzed the functioning of ordinary human life. The virus enters the cell through the angiotensin-converting enzyme-2 (ACE-2) receptor, an integral part of the renin-angiotensin system (RAAS). Reports on hypertension and its relation to the modulation of the RAAS are generating interest in the scientific community. This short review focuses on the SARS-CoV-2 infection's direct and indirect effects on our body through modulation of the RAAS axis. A patient having severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection, which causes COVID-19 relates to hypertension as a pre-existing disease or develops it in a post-COVID scenario. Several studies on how SARS-CoV-2 modulates the RAAS axis indicate that it alters our body's physiological balance. This review seeks to establish a hypothesis on the mechanical dependency of SARS-CoV-2 and RAAS modulation in the human body. This study intends to impart ideas on drug development and designing by targeting the modulation of the RAAS axis to inactivate the pathogenicity of the SARS-CoV-2 virus. A systematic hypothesis can severely attenuate the pathogenicity of the dreadful viruses of the future.

Use of wastewater surveillance for early detection of Alpha and Epsilon SARS-CoV-2 variants of concern and estimation of overall COVID-19 infection burden

A decline in diagnostic testing for SARS-CoV-2 is expected to delay the tracking of COVID-19 variants of concern and interest in the United States. We hypothesize that wastewater surveillance programs provide an effective alternative for detecting emerging variants and assessing COVID-19 incidence, particularly when clinical surveillance is limited. Here, we analyzed SARS-CoV-2 RNA in wastewater from eight locations across Southern Nevada between March 2020 and April 2021. Trends in SARS-CoV-2 RNA concentrations (ranging from 4.3 log₁₀ gc/L to 8.7 log₁₀ gc/L) matched trends in confirmed COVID-19 incidence, but wastewater surveillance also highlighted several limitations with the clinical data. Amplicon-based whole genome sequencing (WGS) of 86 wastewater samples identified the B.1.1.7 (Alpha) and B.1.429 (Epsilon) lineages in December 2020, but clinical sequencing failed to identify the variants until January 2021, thereby demonstrating that 'pooled' wastewater samples can sometimes expedite variant detection. Also, by calibrating fecal shedding (11.4 log₁₀ gc/infection) and wastewater surveillance data to reported seroprevalence, we estimate that ~38% of individuals in Southern Nevada had been infected by SARS-CoV-2 as of April 2021, which is significantly higher than the 10% of individuals confirmed through clinical testing. Sewershed-specific ascertainment ratios (i.e., X-fold infection undercounts) ranged from 1.0 to 7.7, potentially due to demographic differences. Our data underscore the growing application of wastewater surveillance in not only the identification and quantification of infectious agents, but also the detection of variants of concern that may be missed when diagnostic testing is limited or unavailable.

Mild reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant: First case report from Indonesia

Background

Reinfection with SARS-CoV-2 has been well documented, yet little is known about the degree of protection a previous infection provides against reinfection, especially against Variants of Concern (VOC).

Case presentation

Here we describe a case of an unvaccinated 49-year-old man who experienced two sequential SARS-CoV-2 infections with two different variants, as evidenced by genomic sequencing. The first episode was caused by the Pango lineage B.1.466.2 and resulted in severe COVID-19 with 5 days in an intensive care unit (ICU). The second episode occurred approximately 6 months later, during the Delta surge in Indonesia. Genomic analysis showed that the second infection was caused by the Delta variant (Pango lineage B.1.617.2) and resulted in mild disease that did not require hospitalization. No SARS-CoV-2 nucleic acid was detected between the two episodes, but both binding and neutralizing antibodies to SARS-CoV-2 were detected prior to the reinfection, with the second infection leading to an increase in the levels of antibody.

Conclusion

We confirmed that the patient experienced a reinfection instead of persistent viral shedding from the first infection based on epidemiological, clinical, serological, and genomic analyses. Our case supports the hypothesis that SARS-CoV-2 reinfection may occur once antibody titers decrease or following the emergence of a new variant. The milder presentation in the patient’s second infection deserves further investigation to provide a clear picture of the role of post-infection immunity in altering the course of subsequent disease.

Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection

Background

Since the COVID-19 outbreak emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. Although intensive research is ongoing worldwide to understand the emergence of SARS-CoV-2 variants, there is a lack of information on what constitutes the expressed RNA variants in critical and non-critical comorbidity-free young patients. The study sought  to characterize the expressed RNA variants from young patients with critical and non-critical forms of SARS-CoV-2 infection.

Methodology

The bulk ribonucleic acid (RNA) sequencing data with the identifier GSE172114 were downloaded from the Gene Expression Omnibus (GEO) database. The study participants were divided into critical, n = 46, and non-critical, n = 23. FastQC version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. Spliced Transcripts Alignment to a Reference (STAR) version 2.7.10a was used to align reads to the human (hg38) reference genome. Genome Analysis Tool Kit (GATK) best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines.

Results

Our research demonstrates that critical and non-critical SARS-CoV-2-infected individuals are characterized by a unique set of expressed RNA variants. The expressed gene variants are enriched on the innate immune response, specifically neutrophil-mediated immune response. On the other hand, the expressed gene variants are involved in both innate and cellular immune responses.

Conclusion

Deeply phenotyped comorbidity-free young patients with critical and non-critical SARS-CoV-2 infection are characterized by a unique set of expressed RNA variants. The findings in this study can inform the patient classification process in health facilities globally when admitting young patients infected with SARS-CoV-2.

Relatively rapid evolution rates of SARS-CoV-2 spike gene at the primary stage of massive vaccination

A series of stringent non-pharmacological and pharmacological interventions were implemented to contain the pandemic but the pandemic continues. Moreover, vaccination breakthrough infection and reinfection in convalescent coronavirus disease 2019 (COVID-19) cases have been reported. Further, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants emerged with mutations in spike (S) gene, the target of most current vaccines. Importantly, the mutations exhibit a trend of immune escape from the vaccination. Herein the scientific question that if the vaccination drives genetic or antigenic drifts of SARS-CoV-2 remains elusive. We performed correlation analyses to uncover the impacts of wide vaccination on epidemiological characteristics of COVID-19. In addition, we investigated the evolutionary dynamics and genetic diversity of SARS-CoV-2 under immune pressure by utilizing the Bayesian phylodynamic inferences and the lineage entropy calculation respectively. We found that vaccination coverage was negatively related to the infections, severe cases, and deaths of COVID-19 respectively. With the increasing vaccination coverage, the lineage diversity of SARS-CoV-2 dampened, but the rapid mutation rates of the S gene were identified, and the vaccination could be one of the explanations for driving mutations in S gene. Moreover, new epidemics resurged in several countries with high vaccination coverage, questioning their current pandemic control strategies. Hence, integrated vaccination and non-pharmacological interventions are critical to control the pandemic. Furthermore, novel vaccine preparation should enhance its capabilities to curb both disease severity and infection possibility.

COVID-19 and plasma cells: Is there long-lived protection?

Infection with SARS-CoV-2, the etiology of the ongoing COVID-19 pandemic, has resulted in over 450 million cases with more than 6 million deaths worldwide, causing global disruptions since early 2020. Memory B cells and durable antibody protection from long-lived plasma cells (LLPC) are the mainstay of most effective vaccines. However, ending the pandemic has been hampered by the lack of long-lived immunity after infection or vaccination. Although immunizations offer protection from severe disease and hospitalization, breakthrough infections still occur, most likely due to new mutant viruses and the overall decline of neutralizing antibodies after 6 months. Here, we review the current knowledge of B cells, from extrafollicular to memory populations, with a focus on distinct plasma cell subsets, such as early-minted blood antibody-secreting cells and the bone marrow LLPC, and how these humoral compartments contribute to protection after SARS-CoV-2 infection and immunization.

Detection of SARS-CoV-2 Genome for over 100 Days after COVID-19 Onset

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, is spreading globally. In general, the viral genome becomes undetectable within a couple of weeks after infection. Herein, we report a case of long-term detection of the SARS-CoV-2 genome from the same individual for 106 days. Whole genome sequencing was performed on specimens taken at the onset of the disease and at 2 months after onset, and the B.1.1.7 lineage was detected in both samples. Comparison of the full-length sequences revealed a single-base difference and no amino acid mutations. This is the first case in Japan where the virus was detected over a long time, and the full-length sequences were compared.

Prospects of Coffee Leaf against SARS-CoV-2 Infection

In the current climate, many countries are in dire need of effective preventive methods to curb the Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) pandemic. The purpose of this research is to screen and explore natural plant extracts that have the potential to against SARS-CoV-2 and provide alternative options for SARS-CoV-2 prevention and hand sanitizer or spray-like disinfectants. We first used Spike-ACE2 ELISA and TMPRSS2 fluorescence resonance energy transfer (FRET) assays to screen extracts from agricultural by-products from Taiwan with the potential to impede SARS-CoV-2 infection. Next, the SARS-CoV-2 pseudo-particles (Vpp) infection assay was tested to validate the effectiveness. We identified an extract from coffee leaf (Coffea Arabica), a natural plant that effectively inhibited wild-type SARS-CoV-2, and five Variants of Concern (Alpha, Beta, Gamma, Delta, and Omicron strain) from entering host cells. In an attempt to apply coffee leaf extract for hand sanitizer or spray-like disinfectants, we designed a skin-like gelatin membrane experiment. We showed that the high concentration of coffee leaf extract on the skin surface could block SARS-CoV-2 into cells more potently than 75% Ethanol, a standard disinfectant to inactivate SARS-CoV-2. Finally, LC-HRMS analysis was used to identify compounds such as caffeine, chlorogenic acid (CGA), quinic acid, and mangiferin that are associated with an anti-SARS-CoV-2 activity. Our results demonstrated that coffee leaf extract, an agricultural by-product effectively inhibits SARS-CoV-2 Vpp infection through an ACE2-dependent mechanism and may be utilized to develop products against SARS-CoV-2 infection.

Nasal Mucosa Exploited by SARS-CoV-2 for Replicating and Shedding during Reinfection

Reinfection risk is a great concern with regard to the COVID-19 pandemic because a large proportion of the population has recovered from an initial infection, and previous reports found that primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques without viral presence and pathological injury; however, a high possibility for reinfection at the current stage of the pandemic has been proven. We found the reinfection of SARS-CoV-2 in Syrian hamsters with continuous viral shedding in the upper respiratory tracts and few injuries in the lung, and nasal mucosa was exploited by SARS-CoV-2 for replication and shedding during reinfection; meanwhile, no viral replication or enhanced damage was observed in the lower respiratory tracts. Consistent with the mild phenotype in the reinfection, increases in mRNA levels in cytokines and chemokines in the nasal mucosa but only slight increases in the lung were found. Notably, the high levels of neutralizing antibodies in serum could not prevent reinfection in hamsters but may play roles in benefitting the lung recovery and symptom relief of COVID-19. In summary, Syrian hamsters could be reinfected by SARS-CoV-2 with mild symptoms but with obvious viral shedding and replication, and both convalescent and vaccinated patients should be wary of the transmission and reinfection of SARS-CoV-2.

Modelling the interplay of SARS-CoV-2 variants in the United Kingdom

Many COVID-19 vaccines are proving to be highly effective to prevent severe disease and to diminish infections. Their uneven geographical distribution favors the appearance of new variants of concern, as the highly transmissible Delta variant, affecting particularly non-vaccinated people. It is important to device reliable models to analyze the spread of the different variants. A key factor is to consider the effects of vaccination as well as other measures used to contain the pandemic like social behaviour. The stochastic geographical model presented here, fulfills these requirements. It is based on an extended compartmental model that includes various strains and vaccination strategies, allowing to study the emergence and dynamics of the new COVID-19 variants. The model conveniently separates the parameters related to the disease from the ones related to social behavior and mobility restrictions. We applied the model to the United Kingdom by using available data to fit the recurrence of the currently prevalent variants. Our computer simulations allow to describe the appearance of periodic waves and the features that determine the prevalence of certain variants. They also provide useful predictions to help planning future vaccination boosters. We stress that the model could be applied to any other country of interest.

Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference

The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of mutations, we found that while some became 'endemic' to the Bronx, other, novel mutations rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.

Immediate reinfection with Omicron variant after clearance of a previous SARS-CoV-2 infection

SARS-CoV-2 Omicron variant is spreading worldwide, causing unprecedented epidemic peaks due to its transmissibility and immune evasion. We searched in the archive of the Regional Microbiology Laboratory (Umbria, Italy) for immediate reinfection (i.e. infection occurring 25–60 days from primary infection) among 454,764 RT-PCR tests from 261,217 individuals. Lineage heterogeneity was assessed by S gene target failure phenomenon or whole genome sequencing. We found that BA.1 Omicron variant may cause immediate reinfection of patients just recovered from Delta infection. Immediate reinfection was not observed for any other combination of variants, including Delta over Alpha variant and BA.2 over BA.1 Omicron lineage.

An Outbreak of SARS-CoV-2 Reinfection in a Long-Term Care Facility in South Korea

We report a cluster of 12 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection in a long-term care facility in South Korea. There were two outbreaks of SARS-CoV-2 infection in the facility at the beginning and end of October 2021, respectively. All residents in the facility were screened for SARS-CoV-2 infection using RT-PCR as part of the investigation of the second outbreak. Twelve residents, who had infection confirmed during the first outbreak, were found to be re-positive for RT-PCR test at the second outbreak. 8 Of 12 RT-PCR re-positive cases were confirmed as reinfections based on investigation through the whole genome sequencing, viral culture, and serological analysis, despite of the short interval between the first and second outbreaks (29–33 days) and a history of full vaccination for 7 of the 12 re-positive cases. This study suggests that decreased immunity and underlying health condition in older adults makes them susceptible to reinfection, highlighting the importance of prevention and control measures regardless of vaccination status in long-term care settings.

PARIS and SPARTA: Finding the Achilles' Heel of SARS-CoV-2

To understand reinfection rates and correlates of protection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we established eight different longitudinal cohorts in 2020 under the umbrella of the PARIS (Protection Associated with Rapid Immunity to SARS-CoV-2)/SPARTA (SARS SeroPrevalence And Respiratory Tract Assessment) studies. Here, we describe the PARIS/SPARTA cohorts, the harmonized assays and analysis that are performed across the cohorts, as well as case definitions for SARS-CoV-2 infection and reinfection that have been established by the team of PARIS/SPARTA investigators. IMPORTANCE Determining reinfection rates and correlates of protection against SARS-CoV-2 infection induced by both natural infection and vaccination is of high significance for the prevention and control of coronavirus disease 2019 (COVID-19). Furthermore, understanding reinfections or infection after vaccination and the role immune escape plays in these scenarios will inform the need for updates of the current SARS-CoV-2 vaccines and help update guidelines suitable for the postpandemic world.

Impact of prior SARS-CoV-2 infection and COVID-19 vaccination on the subsequent incidence of COVID-19: a multicentre prospective cohort study among UK healthcare workers - the SIREN (Sarscov2 Immunity & REinfection EvaluatioN) study protocol

INTRODUCTION

Understanding the effectiveness and durability of protection against SARS-CoV-2 infection conferred by previous infection and COVID-19 is essential to inform ongoing management of the pandemic. This study aims to determine whether prior SARS-CoV-2 infection or COVID-19 vaccination in healthcare workers protects against future infection.

METHODS AND ANALYSIS

This is a prospective cohort study design in staff members working in hospitals in the UK. At enrolment, participants are allocated into cohorts, positive or naïve, dependent on their prior SARS-CoV-2 infection status, as measured by standardised SARS-CoV-2 antibody testing on all baseline serum samples and previous SARS-CoV-2 test results. Participants undergo monthly antibody testing and fortnightly viral RNA testing during follow-up and based on these results may move between cohorts. Any results from testing undertaken for other reasons (eg, symptoms, contact tracing) or prior to study entry will also be captured. Individuals complete enrolment and fortnightly questionnaires on exposures, symptoms and vaccination. Follow-up is 12 months from study entry, with an option to extend follow-up to 24 months.The primary outcome of interest is infection with SARS-CoV-2 after previous SARS-CoV-2 infection or COVID-19 vaccination during the study period. Secondary outcomes include incidence and prevalence (both RNA and antibody) of SARS-CoV-2, viral genomics, viral culture, symptom history and antibody/neutralising antibody titres.

ETHICS AND DISSEMINATION

The study was approved by the Berkshire Research Ethics Committee, Health Research Authority (IRAS ID 284460, REC reference 20/SC/0230) on 22 May 2020; the vaccine amendment was approved on 12 January 2021. Participants gave informed consent before taking part in the study.Regular reports to national and international expert advisory groups and peer-reviewed publications ensure timely dissemination of findings to inform decision making.

TRIAL REGISTRATION NUMBER

ISRCTN11041050.

Epidemiological and clinical characteristics of SARS-CoV-2 reinfections in a Spanish region

Objective:

We aimed to assess the prevalence and clinical characteristics of SARS-CoV-2 reinfections in a Spanish region.

Methods:

This is a retrospective observational study in all patients with SARS-CoV-2 infections in the Lleida health region from 1 March to 30 November 2020. Reinfections were classified as patients with positive SARS-CoV-2 PCR tests separated by at least 90 days plus a negative test result between both infection episodes. Primary and secondary outcomes: The primary outcome was the percentage of SARS-CoV-2 reinfections among all SARS-CoV-2 infections detected during our study period. Secondary outcomes were the clinical and sociodemographic characteristics of patients with SARS-CoV-2 reinfections.

Results:

Of the 27,758 patients diagnosed with SARS-CoV-2 infection in the study period, 14 were identified as coronavirus reinfection (0.050%). Of the reinfected sample, 12 patients (85.7%) were women. The median age was 41.5 years. Two patients died in the second coronavirus episode.

Conclusion:

The reinfection rate of SARS-CoV-2 in the Spanish region Lleida was relatively low during the observational period in 2020 (less than 1%). These data are in line with the notion that previous SARS-CoV-2 infections may offer a significant protection by so called natural immunity.

Re-infection in COVID-19: Do we exaggerate our worries?

BACKGROUND

Protective long-term immunity following coronavirus disease 2019 (COVID-19) is unclear. The study evaluated the relationship between the vaccination status and risk factors in the re-infection of patients with a diagnosis of COVID-19 who reported to the Public Health Management System in a province in south-eastern Turkey.

METHODS

Patients with positive results for the severe acute respiratory syndrome coronavirus 2 by the real-time reverse transcription polymerase chain reaction (RT-PCR) test in respiratory samples were defined as confirmed cases. Reinfection was diagnosed in cases with COVID-19 real-time RT-PCR positivity, with or without COVID-19-like symptoms, in at least 90 days after the first infection/disease.

RESULTS

A total of 58 811 patients with the diagnosis of COVID-19 from March 11, 2020, to August 31, 2021, were included in the study. Re-infection was detected in 421 (0.7%) of all patients. The mean age of the cases was 38.0±16.0 years, and 51% of them were female. Eight (2.0%) of the cases resulted in death due to re-infection. No hospitalization or mortality was observed in fully vaccinated patients. Additionally, none of the mortal cases had completed the vaccination schedule.

CONCLUSIONS

We are concerned that the re-infection rates and mortality may increase due to new variant strains. Vaccination is the greatest weapon against progression to critical illness in re-infections, even with existing mutations. Therefore, it is important for those without a full vaccination schedule to be vaccinated, even if they have been previously infected.

Recurrent SARS-CoV-2 Infection and Impaired Immunologic Response in a Pediatric Oncologic Patient While Treated With Radiochemotherapy

Immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in pediatric patients with malignant disease may be affected by tumor therapy. Here, we report the case of a child with rhabdomyosarcoma and recurrent SARS-CoV-2 infection. Immunologic responses, analyzed by T-cell activity and anti-viral IgG levels, were impaired and not durable as a result of intensive radiochemotherapy.

IgG targeting distinct seasonal coronavirus- conserved SARS-CoV-2 spike subdomains correlates with differential COVID-19 disease outcomes

Despite SARS-CoV-2 being a "novel" virus, early detection of anti-spike IgG in severe COVID-19 patients may be caused by the amplification of humoral memory responses against seasonal coronaviruses. Here, we examine this phenomenon by characterizing anti-spike IgG responses in non-hospitalized convalescent individuals across a spectrum of COVID-19 severity. We observe that disease severity positively correlates with anti-spike IgG levels, IgG cross-reactivity against other betacoronaviruses (β-CoVs), and FcγR activation. Analysis of IgG targeting β-CoV-conserved and non-conserved immunodominant epitopes within the SARS-CoV-2 spike protein revealed epitope-specific relationships: IgG targeting the conserved heptad repeat (HR) 2 region significantly correlates with milder disease, while targeting the conserved S2'FP region correlates with more severe disease. Furthermore, a lower HR2-to-S2'FP IgG-binding ratio correlates with greater disease severity, with ICU-hospitalized COVID-19 patients showing the lowest HR2/S2'FP ratios. These findings suggest that HR2/S2'FP IgG profiles may predict disease severity and offer insight into protective versus deleterious humoral recall responses.

Clinical Characteristics and Outcomes of Patients with SARS-CoV-2 Reinfection

Objective

To examine the clinical characteristics, risk of hospitalization and mortality of patients diagnosed with SARS-CoV-2 reinfection.

Patients and Methods

We retrospectively reviewed all patients with SARS-CoV-2 reinfection all Mayo Clinic sites between May 23, 2020, and June 30, 2021 (the period before emergence of delta variant in United States). The reinfection was defined as positive SARS-CoV-2 test ≥ 90 days after initial infection or 45-89 days after with symptomatic second episode. Vaccination status was classified as fully vaccinated, first dose and unvaccinated. Comparative analysis of baseline characteristics and comorbidities was performed by hospitalization and vaccination status. The survival analysis of hospitalized patients was performed using cox-proportional hazard regression.

Results

Among 554 reinfected patients, 59 (10.6%) were pediatric, and 495 (89.4%) were adults. The median age was 13.9 years (interquartile range [IQR], 8.5-16.5) for pediatric and 50.2 years (IQR, 28.4-65.6) for adult population. Among adult patients, majority were unvaccinated (83.4%, n=413) and duration to reinfection from initial infection was longest in fully vaccinated group (p < .001). 42 (75%) out of 56 patients were seropositive within seven days of reinfection. In hospitalized adult patients, Charlson Comorbidity Index (CCI) was an independent risk factor for mortality (adjusted hazard ratio [aHR], 0.35; 95% CI, 0.19 to 0.51).

Conclusion

In this study, majority of adult patients with SARS-CoV-2 reinfection were unvaccinated. Furthermore, the duration to reinfection was longest in fully vaccinated individuals. Seropositivity was common among adult patients.

Characteristics of 24 SARS-CoV-2-Sequenced Reinfection Cases in a Tertiary Hospital in Spain

Background

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the main concern is whether reinfections are possible, and which are the associated risk factors. This study aims to describe the clinical and molecular characteristics of 24 sequence-confirmed reinfection SARS-CoV-2 cases over 1 year in Barcelona (Catalonia, Spain).

Methods

Patients with > 45 days between two positive PCR tests regardless of symptoms and negative tests between episodes were initially considered as suspected reinfection cases from November 2020 to May 2021. Whole-genome sequencing (WGS) was performed to confirm genetic differences between consensus sequences and for phylogenetic studies based on PANGOLIN nomenclature. Reinfections were confirmed by the number of mutations, change in lineage, or epidemiological criteria.

Results

From 39 reported suspected reinfection cases, complete viral genomes could be sequenced from both episodes of 24 patients, all were confirmed as true reinfections. With a median age of 44 years (interquartile range [IQR] 32–65), 66% were women and 58% were healthcare workers (HCWs). The median days between episodes were 122 (IQR 72–199), occurring one-third within 3 months. Reinfection episodes were frequently asymptomatic and less severe than primary infections. The absence of seroconversion was associated with symptomatic reinfections. Only one case was reinfected with a variant of concern (VOC).

Conclusion

Severe acute respiratory syndrome coronavirus 2 reinfections can occur in a shorter time than previously reported and are mainly found in immunocompetent patients. Surveillance through WGS is useful to identify viral mutations associated with immune evasion.

Protective effect of a first SARS-CoV-2 infection from reinfection: a matched retrospective cohort study using PCR testing data in England

The duration of immunity after first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the extent to which prior immunity prevents reinfection is uncertain and remains an important question within the context of new variants. This is a retrospective population-based matched observational study where we identified the first polymerase chain reaction (PCR) positive of primary SARS-CoV-2 infection case tests between 1 March 2020 and 30 September 2020. Each case was matched by age, sex, upper tier local authority of residence and testing route to one individual testing negative in the same week (controls) by PCR. After a 90-day pre-follow-up period for cases and controls, any subsequent positive tests up to 31 December 2020 and deaths within 28 days of testing positive were identified, this encompassed an essentially vaccine-free period. We used a conditional logistic regression to analyse the results. There were 517 870 individuals in the matched cohort with 2815 reinfection cases and 12 098 first infections. The protective effect of a prior SARS-CoV-2 PCR-positive episode was 78% (odds ratio (OR) 0.22, 0.21-0.23). Protection rose to 82% (OR 0.18, 0.17-0.19) after a sensitivity analysis excluded 933 individuals with a first test between March and May and a subsequent positive test between June and September 2020. Amongst individuals testing positive by PCR during follow-up, reinfection cases had 77% lower odds of symptoms at the second episode (adjusted OR 0.23, 0.20-0.26) and 45% lower odds of dying in the 28 days after reinfection (adjusted OR 0.55, 0.42-0.71). Prior SARS-CoV-2 infection offered protection against reinfection in this population. There was some evidence that reinfections increased with the alpha variant compared to the wild-type SARS-CoV-2 variant highlighting the importance of continued monitoring as new variants emerge.

Risk of COVID-19 re-infection and its predictors (CORES): protocol for a community-based longitudinal cohort study in Vellore, India

INTRODUCTION

The incidence of SARS-CoV-2 re-infection has not been widely evaluated in low-income and middle-income countries. Understanding immune responses elicited by SARS-CoV-2 natural infection and factors that lead to re-infection in a community setting is important for public health policy. We aim to investigate the risk of primary infection and re-infection among those without and with evidence of prior infection as defined by the presence of antibodies to SARS-CoV-2 spike protein.

METHODS AND ANALYSIS

A baseline seroprevalence survey will test for SARS-CoV-2 antibodies among healthy adults in Vellore, India. Based on an expected seropositivity rate of 50% in the general population, with annual attack rates of 12%, 6%, 4.8% and 4% among those unvaccinated and seronegative, vaccinated and seronegative, unvaccinated and seropositive, and vaccinated and seropositive, respectively, we will recruit 1200 adults who will be followed up for a total of 24 months. Weekly self-collected saliva samples will be tested by reverse transcription-PCR (RT-PCR) to detect SARS-CoV-2 infections, for a period of 1 year. For any person testing RT-PCR positive, blood samples will be collected within 2 days of RT-PCR positivity and on days 30 and 90 to assess the kinetics and longevity of the antibody responses, B cell memory and T cell memory post-infection. The data will be analysed to estimate seroprevalence at baseline and over time, the risk factors for infection, rates of primary infection and re-infection, and provide a comparison of the rates across groups based on infection and vaccination status.

ETHICS AND DISSEMINATION

The study has been approved by the Institutional Review Board (IRB No: 13585) of Christian Medical College and Hospital, Vellore. The results of the study will be made available through journal publications and conference presentations.

TRIAL REGISTRATION NUMBER

Central Trial Registry of India: CTRI/2020/11/029438.

An Update on Protective Effectiveness of Immune Responses After Recovery From COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibits variable immunity responses among hosts based on symptom severity. Whether immunity in recovered individuals is effective for avoiding reinfection is poorly understood. Determination of immune memory status against SARS-CoV-2 helps identify reinfection risk and vaccine efficacy. Hence, after recovery from COVID-19, evaluation of protective effectiveness and durable immunity of prior disease could be significant. Recent reports described the dynamics of SARS-CoV-2 -specific humoral and cellular responses for more than six months in convalescent SARS-CoV-2 individuals. Given the current evidence, NK cell subpopulations, especially the memory-like NK cell subset, indicate a significant role in determining COVID-19 severity. Still, the information on the long-term NK cell immunity conferred by SARS-CoV-2 infection is scant. The evidence from vaccine clinical trials and observational studies indicates that hybrid natural/vaccine immunity to SARS-CoV-2 seems to be notably potent protection. We suggested the combination of plasma therapy from recovered donors and vaccination could be effective. This focused review aims to update the current information regarding immune correlates of COVID-19 recovery to understand better the probability of reinfection in COVID-19 infected cases that may serve as guides for ongoing vaccine strategy improvement.

Long-Term, CD4+ Memory T Cell Response to SARS-CoV-2

The first cases of coronavirus disease-19 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were reported by Chinese authorities at the end of 2019. The disease spread quickly and was declared a global pandemic shortly thereafter. To respond effectively to infection and prevent viral spread, it is important to delineate the factors that affect protective immunity. Herein, a cohort of convalescent healthcare workers was recruited and their immune responses were studied over a period of 3 to 9 months following the onset of symptoms. A cross-reactive T cell response to SARS-CoV-2 and endemic coronaviruses, i.e., OC43 and NL63, was demonstrated in the infected, convalescent cohort, as well as a cohort composed of unexposed individuals. The convalescent cohort, however, displayed an increased number of SARS-CoV-2-specific CD4⁺ T cells relative to the unexposed group. Moreover, unlike humoral immunity and quickly decreasing antibody titers, T cell immunity in convalescent individuals was maintained and stable throughout the study period. This study also suggests that, based on the higher CD4 T cell memory response against nucleocapsid antigen, future vaccine designs may include nucleocapsid as an additional antigen along with the spike protein.

Statistical Challenges in Tracking the Evolution of SARS-CoV-2

Genomic surveillance of SARS-CoV-2 has been instrumental in tracking the spread and evolution of the virus during the pandemic. The availability of SARS-CoV-2 molecular sequences isolated from infected individuals, coupled with phylodynamic methods, have provided insights into the origin of the virus, its evolutionary rate, the timing of introductions, the patterns of transmission, and the rise of novel variants that have spread through populations. Despite enormous global efforts of governments, laboratories, and researchers to collect and sequence molecular data, many challenges remain in analyzing and interpreting the data collected. Here, we describe the models and methods currently used to monitor the spread of SARS-CoV-2, discuss long-standing and new statistical challenges, and propose a method for tracking the rise of novel variants during the epidemic.