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

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.

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 (TH2)–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 TH2-prone adult BALB/c mice, but not in young mice or TH1-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 TH2-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.

Antibody response after one and two jabs of the BNT162b2 vaccine in nursing home residents: The CONsort-19 study

Background

The humoral immune response following COVID‐19 vaccination in nursing home residents is poorly known. A longitudinal study compared levels of IgG antibodies against the spike protein (S‐RBD IgG) (S‐RDB protein IgG) after one and two BNT162b2/Pfizer jabs in residents with and without prior COVID‐19.

Methods

In 22 French nursing homes, COVID‐19 was diagnosed with real‐time reverse‐transcriptase polymerase chain reaction (RT‐PCR) for SARS‐CoV‐2. Blood S‐RDB‐protein IgG and nucleocapsid (N) IgG protein (N‐protein IgG) were measured 21–24 days after the first jab (1,004 residents) and 6 weeks after the second (820 residents).

Results

In 735 residents without prior COVID‐19, 41.7% remained seronegative for S‐RDB‐protein IgG after the first jab vs. 2.1% of the 270 RT‐PCR‐positive residents (p < 0.001). After the second jab, 3% of the 586 residents without prior COVID‐19 remained seronegative. However, 26.5% had low S‐RDB‐protein IgG levels (50–1050 UA/ml) vs. 6.4% of the 222 residents with prior COVID‐19. Residents with an older infection (first wave), or with N‐protein IgG at the time of vaccination, had the highest S‐RDB‐protein IgG levels. Residents with a prior COVID‐19 infection had higher S‐RDB‐protein IgG levels after one jab than those without after two jabs.

Interpretation

A single vaccine jab is sufficient to reach a high humoral immune response in residents with prior COVID‐19. Most residents without prior COVID‐19 are seropositive for S‐RDB‐protein IgG after the second jab, but around 30% have low levels. Whether residents with no or low post‐vaccine S‐RDB protein IgG are at higher risk of symptomatic COVID‐19 requires further analysis.

Coronavirus reinfections: An outlook on evidences and effects

After recovery from COVID-19, a person may become infected again due to reactivation of the virus inside the human body or reinfection with a genetically distinct mutant virus owing to reinfection. The COVID-19 reinfection has been recorded all around the world, albeit it is still uncommon. The reinfection with COVID-19 raises several questions about virus characteristics such as mutation, growth, functioning, and transmissibility, level and durability of immunity, diagnosis, therapy, and efficacy of vaccine(s) on genetically modified viruses and their durability and safety. This chapter focuses on various aspects of COVID-19 reinfection, including its severity, frequency, immunopathogenesis, immune responses, effect on vaccine development, Corona waves and herd immunity, management and prevention strategies. COVID-19 reinfections are often asymptomatic or mildly symptomatic, and are milder than first infections, with a few exceptions. The management of reinfection should be the same as the treatment of the first COVID-19 infection. The deep, extensive, rapid and real-time whole-genome sequencing studies, as well as an enhanced vaccination drive, and rigorous adherence to COVID-19 appropriate behavior, would be critical in limiting the severity of transmission and reinfection.

Systematic Genomic and Clinical Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections and Recurrences Involving the Same Strain

Estimates of the burden of severe acute respiratory syndrome coronavirus 2 reinfections are limited by the scarcity of population-level studies incorporating genomic support. We conducted a systematic study of reinfections in Madrid, Spain, supported by genomic viral analysis and host genetic analysis, to cleanse laboratory errors and to discriminate between reinfections and recurrences involving the same strain. Among the 41,195 cases diagnosed (March 2020-March 2021), 93 (0.23%) had 2 positive reverse transcription PCR tests (55-346 days apart). After eliminating cases with specimens not stored, of suboptimal sequence quality, or belonging to different persons, we obtained valid data from 22 cases. Of those, 4 (0.01%) cases were recurrences involving the same strain; case-patients were 39-93 years of age, and 3 were immunosuppressed. Eighteen (0.04%) cases were reinfections; patients were 19-84 years of age, and most had no relevant clinical history. The second episode was more severe in 8 cases.

Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination

The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.

Immune response to SARS-CoV-2 Variants: A focus on severity, susceptibility, and preexisting immunity

The heterogeneous phenotypes among patients with coronavirus disease 2019 (COVID-19) has drawn worldwide attention, especially those with severe symptoms without comorbid conditions. Immune responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative virus of COVID-19, occur mainly by the innate immune response via the interferon (IFN)-mediated pathways, and the adaptive immunity via the T lymphocyte and the antibody mediated pathways. The ability of the original Wuhan SARS-CoV-2 strain, and possibly more so with new emerging variants, to antagonize IFN-mediated antiviral responses can be behind the higher early viral load, higher transmissibility, and milder symptoms compared to SARS-CoV and are part of the continued clinical evolution of COVID-19. Since it first emerged, several variants of SARS-CoV-2 have been circulating worldwide. Variants that have the potential to elude natural or vaccine-mediated immunity are variants of concern. This review focuses on the main host factors that may explain the immune responses to SARS-CoV-2 and its variants in the context of susceptibility, severity, and preexisting immunity.

Reinfection with SARS-CoV-2: An inconvenient truth?

Data show that antibody-related immunity against SARS-CoV-2 may not be long-lasting. We report two cases regarded as cured from COVID-19, which presented again with symptoms and a positive SARS-CoV-2 RT-PCR test. Case one, a 60-year-old male, had a biphasic presentation of symptoms compatible with COVID-19 infection, associated with a positive RT-PCR test. Case two, a 25-year-old female, had a first positive RT-PCR test during hospital screening, and months later a symptomatic presentation of COVID-19, associated with a positive RT-PCR test. All cases were immunocompetent. Anti-IgG-SARS-CoV-2 blood samples were negative in both. Elevation of analytical inflammatory markers suggested new infection in both cases. COVID-19 reinfection may be a differential diagnosis and primary care physicians should acknowledge it. Previously cured patients should be encouraged to comply with health public preventive measures.

Patterns of SARS-CoV-2 Testing Preferences in a National Cohort in the United States: Latent Class Analysis of a Discrete Choice Experiment

BACKGROUND

Inadequate screening and diagnostic testing in the United States throughout the first several months of the COVID-19 pandemic led to undetected cases transmitting disease in the community and an underestimation of cases. Though testing supply has increased, maintaining testing uptake remains a public health priority in the efforts to control community transmission considering the availability of vaccinations and threats from variants.

OBJECTIVE

This study aimed to identify patterns of preferences for SARS-CoV-2 screening and diagnostic testing prior to widespread vaccine availability and uptake.

METHODS

We conducted a discrete choice experiment (DCE) among participants in the national, prospective CHASING COVID (Communities, Households, and SARS-CoV-2 Epidemiology) Cohort Study from July 30 to September 8, 2020. The DCE elicited preferences for SARS-CoV-2 test type, specimen type, testing venue, and result turnaround time. We used latent class multinomial logit to identify distinct patterns of preferences related to testing as measured by attribute-level part-worth utilities and conducted a simulation based on the utility estimates to predict testing uptake if additional testing scenarios were offered.

RESULTS

Of the 5098 invited cohort participants, 4793 (94.0%) completed the DCE. Five distinct patterns of SARS-CoV-2 testing emerged. Noninvasive home testers (n=920, 19.2% of participants) were most influenced by specimen type and favored less invasive specimen collection methods, with saliva being most preferred; this group was the least likely to opt out of testing. Fast-track testers (n=1235, 25.8%) were most influenced by result turnaround time and favored immediate and same-day turnaround time. Among dual testers (n=889, 18.5%), test type was the most important attribute, and preference was given to both antibody and viral tests. Noninvasive dual testers (n=1578, 32.9%) were most strongly influenced by specimen type and test type, preferring saliva and cheek swab specimens and both antibody and viral tests. Among hesitant home testers (n=171, 3.6%), the venue was the most important attribute; notably, this group was the most likely to opt out of testing. In addition to variability in preferences for testing features, heterogeneity was observed in the distribution of certain demographic characteristics (age, race/ethnicity, education, and employment), history of SARS-CoV-2 testing, COVID-19 diagnosis, and concern about the pandemic. Simulation models predicted that testing uptake would increase from 81.6% (with a status quo scenario of polymerase chain reaction by nasal swab in a provider's office and a turnaround time of several days) to 98.1% by offering additional scenarios using less invasive specimens, both viral and antibody tests from a single specimen, faster turnaround time, and at-home testing.

CONCLUSIONS

We identified substantial differences in preferences for SARS-CoV-2 testing and found that offering additional testing options would likely increase testing uptake in line with public health goals. Additional studies may be warranted to understand if preferences for testing have changed since the availability and widespread uptake of vaccines.

An update on host immunity correlates and prospects of re-infection in COVID-19

Reinfection with SARS-CoV-2 is not frequent yet the incidence rate of it is increasing globally owing to the slow emergence of drift variants that pose a perpetual threat to vaccination strategies and have a greater propensity for disease reoccurrence. Long-term protection against SARS-CoV-2 reinfection relies on the induction of the innate as well as the adaptive immune response endowed with immune memory. However, a multitude of factors including the selection pressure, the waning immunity against SARS-CoV-2 over the first year after infection possibly favors evolution of more infectious immune escape variants, amplifying the risk of reinfection. Additionally, the correlates of immune protection, the novel SARS-CoV-2 variants of concern (VOC), the durability of the adaptive and mucosal immunity remain major challenges for the development of therapeutic and prophylactic interventions. Interestingly, a recent body of evidence indicated that the gastrointestinal (GI) tract is another important target organ for SARS-CoV-2 besides the respiratory system, potentially increasing the likelihood of reinfection by impacting the microbiome and the immune response via the gut-lung axis. In this review, we summarized the latest development in SARS-CoV-2 reinfection, and explored the untapped potential of trained immunity. We also highlighted the immune memory kinetics of the humoral and cell-mediated immune response, genetic drift of the emerging viral variants, and discussed the current challenges in vaccine development. Understanding the dynamics and the quality of immune response by unlocking the power of the innate, humoral and cell-mediated immunity during SARS-CoV-2 reinfection would open newer avenues for drug discovery and vaccine designs.

RT-PCR Detection of SARS-CoV-2 among Individuals from the Upper Silesian Region-Analysis of 108,516 Tests

Background: The COVID-19 pandemic triggered by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has left a huge mark on everyday lives, introducing restrictions and plunging the global economy. This study aimed to analyze the available epidemiological data from the register of one of the largest laboratories testing for SARS-CoV-2 in the Silesian voivodship of Poland. Methods: This analysis is based upon the epidemiological records collected between 30 March 2020, and 30 April 2021, by the Silesian Park of Medical Technology Kardio-Med Silesia (Zabrze, Poland). In addition, we performed SARS-CoV-2 variant detection in samples from patients reinfected with SARS-CoV-2. Results: Our results confirm that SARS-CoV-2 infections are more common in urban areas. Laboratory-confirmed COVID-19 cases represent 13.21% of all RT-PCR test results during the 13 months of our laboratory diagnostics for SARS-CoV-2 infections. Detection of SARS-CoV-2 variants in samples of potentially reinfected patients showed discrepancies in the results. Conclusions: Due to the higher risk of SARS-CoV-2 infection among the Upper Silesian population, the region is at greater risk of deteriorating economic situation and healthcare as compared to other areas of Poland. RT-PCR methods are inexpensive and suitable for large-scale screening, but they can be untrustworthy so detection of SARS-CoV-2 variants in samples should be confirmed by sequencing.

COVID-19 vaccination strategies depend on the underlying network of social interactions

Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, different mitigation and management strategies limiting economic and social activities have been implemented across many countries. Despite these strategies, the virus continues to spread and mutate. As a result, vaccinations are now administered to suppress the pandemic. Current COVID-19 epidemic models need to be expanded to account for the change in behaviour of new strains, such as an increased virulence and higher transmission rate. Furthermore, models need to account for an increasingly vaccinated population. We present a network model of COVID-19 transmission accounting for different immunity and vaccination scenarios. We conduct a parameter sensitivity analysis and find the average immunity length after an infection to be one of the most critical parameters that define the spread of the disease. Furthermore, we simulate different vaccination strategies and show that vaccinating highly connected individuals first is the quickest strategy for controlling the disease.

Rapidly Self-Sterilizing PPE Capable of Destroying 100% of Microbes in 30-60 Seconds

The continued proliferation of superbugs in hospitals and the coronavirus disease 2019 (COVID-19) has created an acute worldwide demand for sustained broadband pathogen suppression in households, hospitals, and public spaces. In response, we have created a highly active, self-sterilizing copper configuration capable of inactivating a wide range of bacteria and viruses in 30-60 seconds. The highly active material destroys pathogens faster than any conventional copper configuration and acts as quickly as alcohol wipes and hand sanitizers. Unlike the latter, our copper material does not release volatile compounds or leave harmful chemical residues and maintains its antimicrobial efficacy over sustained use; it is shelf stable for years. We have performed rigorous testing in accordance with guidelines from U.S. regulatory agencies and believe that the material could offer broad spectrum, non-selective defense against most microbes via integration into masks, protective equipment, and various forms of surface coatings.

COVID-19 Vaccination: The Mainspring of Challenges and the Seed of Remonstrance

As of March 2020, the time when the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a pandemic, our existence has been threatened and the lives of millions have been claimed. With this ongoing global issue, vaccines are considered of paramount importance in curtailing the outbreak and probably a prime gamble to bring us back to 'ordinary life'. To date, more than 200 vaccine candidates have been produced, many of which were approved by the Food and Drug Administration (FDA) for emergency use, with the research and discovery phase of their production process passed over. Capering such a chief practice in COVID-19 vaccine development, and manufacturing vaccines at an unprecedented speed brought many challenges into play and raised COVID-19 vaccine remonstrance. In this review, we highlight relevant challenges to global COVID-19 vaccine development, dissemination, and deployment, particularly at the level of large-scale production and distribution. We also delineate public perception on COVID-19 vaccination and outline the main facets affecting people's willingness to get vaccinated.

A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection

Background: The emergence of novel variants has been a great deal of international concern since the recently published data suggest that previous infections with SARS-CoV-2 may not protect an individual from new variants. We report a patient had two distinct episodes of COVID-19 with different variants of SARS-CoV-2. Methods: The nasopharyngeal samples collected from the two episodes were subjected to whole-genome sequencing and comparative genome analysis. Results: The first infection presented with mild symptoms, while the second infection presented with severe outcomes which occurred 74 days after the patient recovered from the first episode. He had elevated C-reactive protein, ferritin, and bilateral consolidation as a sign of acute infection. Genome analysis revealed that the strains from the first and second episodes belonged to two distinct Nexstrain clades 20B and 20I and Pangolin lineages B.1.1.25 and B.1.1.7, respectively. A total of 36 mutations were observed in the episode-2 strain when compared with the reference strain Wuhan-Hu-1. Among them, eight mutations were identified in the receptor-binding domain (RBD). Conclusion: Our findings concern whether the immunity acquired by natural infection or mass vaccination could confer adequate protection against the constantly evolving SARS-CoV-2. Therefore, continuous monitoring of genetic variations of SARS-CoV-2 strains is crucial for interventions such as vaccine and drug designs, treatment using monoclonal antibodies, and patient management.

Recurrent SARS-CoV-2 infections and their potential risk to public health - a systematic review

OBJECTIVE

To inform quarantine and contact-tracing policies concerning re-positive cases-cases testing positive among those recovered.

MATERIALS AND METHODS

We systematically reviewed and appraised relevant literature from PubMed and Embase for the extent of re-positive cases and their epidemiological characteristics.

RESULTS

In 90 case reports/series, a total of 276 re-positive cases were found. Among confirmed reinfections, 50% occurred within 90 days from recovery. Four reports related onward transmission. In thirty-five observational studies, rate of re-positives ranged from zero to 50% with no onward transmissions reported. In eight reviews, pooled recurrence rate ranged from 12% to 17.7%. Probability of re-positive increased with several factors.

CONCLUSION

Recurrence of a positive SARS-CoV-2 test is commonly reported within the first weeks following recovery from a first infection.

How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology

We hypothesized that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, including generating reduced susceptibility in children. To determine what the prepandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 y of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.8 y (95% CI 6.3 to 8.1) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission.

Synopsis of symptoms of COVID-19 during second wave of the pandemic in India

COVID-19 was caused by the original coronavirus, severe acute respiratory syndrome associated coronavirus-2 (SARS CoV2), which originated in Wuhan, China. COVID-19 had a large breakout of cases in early 2020, resulting in an epidemic that turned into a pandemic. This quickly enveloped the global healthcare system. The principal testing method for COVID-19 detection, according to the WHO, is reverse transcription polymerase chain reaction (RT-PCR). Isolation of patients, quarantine, masking, social distancing, sanitizer use, and complete lockdown were all vital health-care procedures for everyone. With the 'new normal' and vaccination programmes, the number of cases and recovered patients began to rise months later. The easing of restrictions during the plateau phase resulted in a rebound of instances, which hit the people with more ferocity and vengeance towards the start of April 2021. Coronaviruses have evolved to cause respiratory, enteric, hepatic, and neurologic diseases, resulting in a wide range of diseases and symptoms such as fever, cough, myalgia or fatigue, shortness of breath, muscle ache, headache, sore throat, rhinorrhea, hemoptysis, chest pain, nausea, vomiting, diarrhoea, anosmia, and ageusia. Coronavirus infections can be mild, moderate, or severe in intensity. COVID-19 pulmonary dysfunction includes lung edoema, ground-glass opacities, surfactant depletion, and alveolar collapse. Patients who presented with gastrointestinal (GI) symptoms such as anorexia, nausea, vomiting, or diarrhoea had a higher risk of negative outcomes. COVID-19's influence on cognitive function is one of COVID-19's long-term effects. More clinical situations need to be reviewed by healthcare professionals so that an appropriate management protocol may be developed to reduce morbidity and death in future coming third/fourth wave cases.

Modelling COVID-19 dynamics and potential for herd immunity by vaccination in Austria, Luxembourg and Sweden

Against the COVID-19 pandemic, non-pharmaceutical interventions have been widely applied and vaccinations have taken off. The upcoming question is how the interplay between vaccinations and social measures will shape infections and hospitalizations. Hence, we extend the Susceptible-Exposed-Infectious-Removed (SEIR) model including these elements. We calibrate it to data of Luxembourg, Austria and Sweden until 15 December 2020. Sweden results having the highest fraction of undetected, Luxembourg of infected and all three being far from herd immunity in December. We quantify the level of social interaction, showing that a level around 1/3 of before the pandemic was still required in December to keep the effective reproduction number Refft below 1, for all three countries. Aiming to vaccinate the whole population within 1 year at constant rate would require on average 1,700 fully vaccinated people/day in Luxembourg, 24,000 in Austria and 28,000 in Sweden, and could lead to herd immunity only by mid summer. Herd immunity might not be reached in 2021 if too slow vaccines rollout speeds are employed. The model thus estimates which vaccination rates are too low to allow reaching herd immunity in 2021, depending on social interactions. Vaccination will considerably, but not immediately, help to curb the infection; thus limiting social interactions remains crucial for the months to come.

The SARS-CoV-2 pandemic: remaining uncertainties in our understanding of the epidemiology and transmission dynamics of the virus, and challenges to be overcome

Great progress has been made over the past 18 months in scientific understanding of the biology, epidemiology and pathogenesis of SARS-CoV-2. Extraordinary advances have been made in vaccine development and the execution of clinical trials of possible therapies. However, uncertainties remain, and this review assesses these in the context of virus transmission, epidemiology, control by social distancing measures and mass vaccination and the effect on all of these on emerging variants. We briefly review the current state of the global pandemic, focussing on what is, and what is not, well understood about the parameters that control viral transmission and make up the constituent parts of the basic reproductive number R 0. Major areas of uncertainty include factors predisposing to asymptomatic infection, the population fraction that is asymptomatic, the infectiousness of asymptomatic compared to symptomatic individuals, the contribution of viral transmission of such individuals and what variables influence this. The duration of immunity post infection and post vaccination is also currently unknown, as is the phenotypic consequences of continual viral evolution and the emergence of many viral variants not just in one location, but globally, given the high connectivity between populations in the modern world. The pattern of spread of new variants is also examined. We review what can be learnt from contact tracing, household studies and whole-genome sequencing, regarding where people acquire infection, and how households are seeded with infection since they constitute a major location for viral transmission. We conclude by discussing the challenges to attaining herd immunity, given the uncertainty in the duration of vaccine-mediated immunity, the threat of continued evolution of the virus as demonstrated by the emergence and rapid spread of the Delta variant, and the logistics of vaccine manufacturing and delivery to achieve universal coverage worldwide. Significantly more support from higher income countries (HIC) is required in low- and middle-income countries over the coming year to ensure the creation of community-wide protection by mass vaccination is a global target, not one just for HIC. Unvaccinated populations create opportunities for viral evolution since the net rate of evolution is directly proportional to the number of cases occurring per unit of time. The unit for assessing success in achieving herd immunity is not any individual country, but the world.

Six-month outcomes and effect of pulmonary rehabilitation among patients hospitalized with COVID-19: a retrospective cohort study

BACKGROUND

Patients appear to maintain sequelae post-coronavirus disease 2019 (COVID-19) affecting daily life and physical health. We investigated the changes in and the effects of pulmonary rehabilitation (PR) on exercise capacity and immunology six months after COVID-19 hospitalization.

METHODS

This retrospective cohort reviewed 233 COVID-19 patients admitted from 17 January 2020 to 29 February 2020. Ninety-eight patients who completed 2-week and 6-month follow-ups and tests were included. Among 98 patients, 27 completed at least five sessions of PR at the First Hospital of Changsha, China, during the 6-month convalescence were allocated to the PR group; the reminder who had not performed any PR were assigned to the control group. The primary outcome was the change in six-minute walk distance (6-MWD) between the 2-week and 6-month follow-ups, which was assessed via analysis of covariance with a covariate of propensity score that adjusted for the potential confounders. Secondary outcomes were the changes in 6-MWD, SARS-CoV-2 immunoglobulins, T-lymphocytes and blood chemistry, which were evaluated via paired tests.

RESULTS

Participants' ages ranged from 19 to 84 years (M = 47, standard deviation (SD)=15) 45.9% identified as male. During the 6-month convalescence, 6-MWD increased 27.0%, with a mean [95% CI] of 113 [92-134] m (p < .001). SARS-CoV-2 IgG and IgM decreased 33.3% (p = .002) and 43.8% (p = .009), CD4+ T cells increased 7.9% (p = .04), and the majority of blood chemistry significantly changed. The patients in the PR group acquired a greater increase in 6-MWD than those in control (unadjusted, 194 [167-221] m, p < .001; adjusted, 123 [68-181] m, p < .001), dose-responsiveness of PR on 6-MWD was observed (p < .001). No differences in immunity variables and blood chemistry were observed between groups.

CONCLUSIONS

These findings suggest PR may be a strategy to promote the improvement of exercise capacity after COVID-19.

Should Breakthrough SARS-CoV-2 Infection Affect Our Confidence in the COVID-19 Vaccines?

Coronavirus disease 2019 (COVID-19) vaccines have shown excellent clinical efficacy and effectiveness in real-world data. Although they are regarded as a means of ending the global pandemic, some individuals become infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after immunization. This growing evidence or lack of effectiveness has led to vaccine refusal. This paper sought to help the public gain a deeper understanding of breakthrough events creating the positive perception that vaccines remain effective in ending the pandemic. Discussions vital for the general public's active participation in vaccination are expressed to create confidence or provide a potential solution to the challenge of vaccine hesitancy.

Reinfection with new variants of SARS-CoV-2 after natural infection: a prospective observational cohort in 13 care homes in England

Background

Understanding the duration of protection and risk of reinfection after natural infection is crucial to planning COVID-19 vaccination for at-risk groups, including care home residents, particularly with the emergence of more transmissible variants. We report on the duration, neutralising activity, and protection against the alpha variant of previous SARS-CoV-2 infection in care home residents and staff infected more than 6 months previously.

Methods

We did this prospective observational cohort surveillance in 13 care homes in Greater London, England. All staff and residents were included. Staff and residents had regular nose and throat screening for SARS-CoV-2 by RT-PCR according to national guidelines, with ad hoc testing of symptomatic individuals. From January, 2021, antigen lateral flow devices were also used, but positive tests still required RT-PCR confirmation. Staff members took the swab samples for themselves and the residents. The primary outcome was SARS-CoV-2 RT-PCR positive primary infection or reinfection in previously infected individuals, as determined by previous serological testing and screening or diagnostic RT-PCR results. Poisson regression and Cox proportional hazards models were used to estimate protective effectiveness of previous exposure. SARS-CoV-2 spike, nucleoprotein, and neutralising antibodies were assessed at multiple timepoints as part of the longitudinal follow-up.

Findings

Between April 10 and Aug 3, 2020, we recruited and tested 1625 individuals (933 staff and 692 residents). 248 participants were lost to follow-up (123 staff and 125 residents) and 1377 participants were included in the follow-up period to Jan 31, 2021 (810 staff and 567 residents). There were 23 reinfections (ten confirmed, eight probable, five possible) in 656 previously infected individuals (366 staff and 290 residents), compared with 165 primary infections in 721 susceptible individuals (444 staff and 277 residents). Those with confirmed reinfections had no or low neutralising antibody concentration before reinfection, with boosting of titres after reinfection. Kinetics of binding and neutralising antibodies were similar in older residents and younger staff.

Interpretation

SARS-CoV-2 reinfections were rare in older residents and younger staff. Protection from SARS-CoV-2 was sustained for longer than 9 months, including against the alpha variant. Reinfection was associated with no or low neutralising antibody before reinfection, but significant boosting occurred on reinfection.

Funding

Public Health England.

Prior aerosol infection with lineage A SARS-CoV-2 variant protects hamsters from disease, but not reinfection with B.1.351 SARS-CoV-2 variant

The circulation of SARS-CoV-2 has resulted in the emergence of variants of concern (VOCs). It is currently unclear whether the previous infection with SARS-CoV-2 provides protection against reinfection with VOCs. Here, we show that low dose aerosol exposure to hCoV-19/human/USA/WA-CDC-WA1/2020 (WA1, lineage A), resulted in a productive mild infection. In contrast, a low dose of SARS-CoV-2 via fomites did not result in productive infection in the majority of exposed hamsters and these animals remained non-seroconverted. After recovery, hamsters were re-exposed to hCoV-19/South African/KRISP-K005325/2020 (VOC B.1.351) via an intranasal challenge. Seroconverted rechallenged animals did not lose weight and shed virus for three days. They had a little infectious virus and no pathology in the lungs. In contrast, shedding, weight loss and extensive pulmonary pathology caused by B.1.351 replication were observed in the non-seroconverted animals. The rechallenged seroconverted animals did not transmit the virus to naïve sentinels via direct contact transmission, in contrast to the non-seroconverted animals. Reinfection with B.1.351 triggered an anamnestic response that boosted not only neutralizing titres against lineage A, but also titres against B.1.351. Our results confirm that aerosol exposure is a more efficient infection route than fomite exposure. Furthermore, initial infection with SARS-CoV-2 lineage A does not prevent heterologous reinfection with B.1.351 but prevents disease and onward transmission. These data suggest that previous SARS-CoV-2 exposure induces partial protective immunity. The reinfection generated a broadly neutralizing humoral response capable of effectively neutralizing B.1.351 while maintaining its ability to neutralize the virus to which the initial response was directed against.

The mystery of COVID-19 reinfections: A global systematic review and meta-analysis

BACKGROUND

As the COVID-19 pandemic rages on, reports on disparities in vaccine roll out alongside COVID-19 reinfection have been emerging. We conducted a systematic review to assess the determinants and disease spectrum of COVID-19 reinfection.

MATERIALS AND METHODS

A comprehensive search covering relevant databases was conducted for observational studies reporting Polymerase Chain Reaction (PCR) confirmed infection and reinfection cases. A quality assessment tool developed by the National Institute of Health (NIH) for the assessment of case series was utilized. Meta-analyses were performed using RevMan 5.3 for pooled proportions of findings in first infection and reinfection with a 95% confidence interval (CI).

RESULTS

Eighty-one studies reporting 577 cases were included from 22 countries. The mean age of patients was 46.2 ± 18.9 years and 179 (31.0%) cases of comorbidities were reported. The average time duration between first infection and reinfection was 63.6 ± 48.9 days. During first infection and reinfection, fever was the most common symptom (41.4% and 36.4%, respectively) whilst anti-viral therapy was the most common treatment regimen administered (44.5% and 43.0%, respectively). Comparable odds of symptomatic presentation and management were reported for the two infections. However, a higher Intensive Care Unit (ICU) admission rate was observed in reinfection compared to first infection (10 vs 3). Ten deaths were reported with respiratory failure being the most common cause of death (7/10 deaths).

CONCLUSION

Our findings support immunization practices given increased ICU admissions and mortality in reinfections. Our cohort serves as a guide for clinicians and authorities in devising an optimal strategy for controlling the pandemic. (249 words).

Assessing the effects of non-pharmaceutical interventions on SARS-CoV-2 transmission in Belgium by means of an extended SEIQRD model and public mobility data

We present a compartmental extended SEIQRD metapopulation model for SARS-CoV-2 spread in Belgium. We demonstrate the robustness of the calibration procedure by calibrating the model using incrementally larger datasets and dissect the model results by computing the effective reproduction number at home, in workplaces, in schools, and during leisure activities. We find that schools and home contacts are important transmission pathways for SARS-CoV-2 under lockdown measures. School reopening has the potential to increase the effective reproduction number from Re=0.66±0.04 (95 % CI) to Re=1.09±0.05 (95 % CI) under lockdown measures. The model accounts for the main characteristics of SARS-CoV-2 transmission and COVID-19 disease and features a detailed representation of hospitals with parameters derived from a dataset consisting of 22 136 hospitalized patients. Social contact during the pandemic is modeled by scaling pre-pandemic contact matrices with Google Community Mobility data and with effectivity-of-contact parameters inferred from hospitalization data. The calibrated social contact model with its publically available mobility data, although coarse-grained, is a cheap and readily available alternative to social-epidemiological contact studies under lockdown measures, which were not available at the start of the pandemic.

Does infection with or vaccination against SARS-CoV-2 lead to lasting immunity?

Many nations are pursuing the rollout of SARS-CoV-2 vaccines as an exit strategy from unprecedented COVID-19-related restrictions. However, the success of this strategy relies critically on the duration of protective immunity resulting from both natural infection and vaccination. SARS-CoV-2 infection elicits an adaptive immune response against a large breadth of viral epitopes, although the duration of the response varies with age and disease severity. Current evidence from case studies and large observational studies suggests that, consistent with research on other common respiratory viruses, a protective immunological response lasts for approximately 5-12 months from primary infection, with reinfection being more likely given an insufficiently robust primary humoral response. Markers of humoral and cell-mediated immune memory can persist over many months, and might help to mitigate against severe disease upon reinfection. Emerging data, including evidence of breakthrough infections, suggest that vaccine effectiveness might be reduced significantly against emerging variants of concern, and hence secondary vaccines will need to be developed to maintain population-level protective immunity. Nonetheless, other interventions will also be required, with further outbreaks likely to occur due to antigenic drift, selective pressures for novel variants, and global population mobility.

Experimental re-infected cats do not transmit SARS-CoV-2

SARS-CoV-2 is the causative agent of COVID-19 and responsible for the current global pandemic. We and others have previously demonstrated that cats are susceptible to SARS-CoV-2 infection and can efficiently transmit the virus to naïve cats. Here, we address whether cats previously exposed to SARS-CoV-2 can be re-infected with SARS-CoV-2. In two independent studies, SARS-CoV-2-infected cats were re-challenged with SARS-CoV-2 at 21 days post primary challenge (DPC) and necropsies performed at 4, 7 and 14 days post-secondary challenge (DP2C). Sentinels were co-mingled with the re-challenged cats at 1 DP2C. Clinical signs were recorded, and nasal, oropharyngeal, and rectal swabs, blood, and serum were collected and tissues examined for histologic lesions. Viral RNA was transiently shed via the nasal, oropharyngeal and rectal cavities of the re-challenged cats. Viral RNA was detected in various tissues of re-challenged cats euthanized at 4 DP2C, mainly in the upper respiratory tract and lymphoid tissues, but less frequently and at lower levels in the lower respiratory tract when compared to primary SARS-CoV-2 challenged cats at 4 DPC. Viral RNA and antigen detected in the respiratory tract of the primary SARS-CoV-2 infected cats at early DPCs were absent in the re-challenged cats. Naïve sentinels co-housed with the re-challenged cats did not shed virus or seroconvert. Together, our results indicate that cats previously infected with SARS-CoV-2 can be experimentally re-infected with SARS-CoV-2; however, the levels of virus shed was insufficient for transmission to co-housed naïve sentinels. We conclude that SARS-CoV-2 infection in cats induces immune responses that provide partial, non-sterilizing immune protection against re-infection.

COVID-19 challenges: From SARS-CoV-2 infection to effective point-of-care diagnosis by electrochemical biosensing platforms

In January 2020, the World Health Organization (WHO) identified a new zoonotic virus, SARS-CoV-2, responsible for causing the COVID-19 (coronavirus disease 2019). Since then, there has been a collaborative trend between the scientific community and industry. Multidisciplinary research networks try to understand the whole SARS-CoV-2 pathophysiology and its relationship with the different grades of severity presented by COVID-19. The scientific community has gathered all the data in the quickly developed vaccines that offer a protective effect for all variants of the virus and promote new diagnostic alternatives able to have a high standard of efficiency, added to shorter response analysis time and portability. The industry enters in the context of accelerating the path taken by science until obtaining the final product. In this review, we show the principal diagnostic methods developed during the COVID-19 pandemic. However, when we observe the diagnostic tools section of an efficient infection outbreak containment report and the features required for such tools, we could observe a highlight of electrochemical biosensing platforms. Such devices present a high standard of analytical performance, are low-cost tools, easy to handle and interpret, and can be used in the most remote and low-resource regions. Therefore, probably, they are the ideal point-of-care diagnostic tools for pandemic scenarios.

Reinfection cases by closely related SARS-CoV-2 lineages in Southern Brazil

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic that started in late 2019 and still affects people's lives all over the world. Lack of protective immunity after primary infection has been involved with reported reinfection cases by SARS-CoV-2. In this study, we described two cases of reinfection caused by non-VOC (Variants of Concern) strains in southern Brazil, being one patient a healthcare worker. The four samples previously positive for SARS-CoV-2 by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) were sequenced by a high-performance platform and the genomic analysis confirmed that lineages responsible for infections were B.1.91 and B.1.1.33 (patient 1), and B.1.1.33 and B.1.1.28 (patient 2). The interval between the two positive RT-qPCR for patients 1 and 2 was 45 and 61 days, respectively. This data shows that patients may be reinfected even by very closely related SARS-CoV-2 lineages.

Drug-based therapeutic strategies for COVID-19-infected patients and their challenges

Emerging epidemic-prone diseases have introduced numerous health and economic challenges in recent years. Given current knowledge of COVID-19, herd immunity through vaccines alone is unlikely. In addition, vaccination of the global population is an ongoing challenge. Besides, the questions regarding the prevalence and the timing of immunization are still under investigation. Therefore, medical treatment remains essential in the management of COVID-19. Herein, recent advances from beginning observations of COVID-19 outbreak to an understanding of the essential factors contributing to the spread and transmission of COVID-19 and its treatment are reviewed. Furthermore, an in-depth discussion on the epidemiological aspects, clinical symptoms and most efficient medical treatment strategies to mitigate the mortality and spread rates of COVID-19 is presented.

Changes in COVID-19 vaccine acceptance rate among recovered critically Ill patients: A 12-month follow-up study

Introduction

We surveyed a cohort of patients who recovered from severe SARS-CoV-2 infection to determine the COVID-19 vaccination rate. We also compared the willingness to accept COVID-19 vaccine before and after its availability to assess changes in perception and attitude towards vaccination.

Materials and Methods

Recovered patients with severe hypoxemic respiratory failure from SARS-CoV-2 infection treated in the ICU at Grady Memorial Hospital, Atlanta, Georgia between April 1, 2020, and June 30, 2020 were followed up over a 1-year period to assess vaccine acceptability and acceptance rates, and changes in perception towards COVID-19 vaccination before and after vaccine availability.

Results

A total of 98 and 93 patients completed the initial and follow up surveys respectively. During the initial survey, 41% of the patients intended to receive vaccination, 46% responded they would not accept a vaccine against COVID-19 even if it were proven to be ‘safe and effective ‘and 13% undecided. During the follow up survey, 44% of the study cohort had received at least one dose of a COVID-19 vaccine. Major reasons provided by respondents for not accepting COVID-19 vaccine were lack of trust in the effectiveness of the vaccine, pharmaceutical companies, government, vaccine technology, fear of side effects and perceived immunity against COVID-19. Respondents were more likely to be vaccinated if recommended by their physicians (OR 6.4, 95% CI 2.8–8.3), employers (OR 2.5, 95% CI 1.9–5.8), and family and friends (OR 1.6, 95% CI 1.1–4.5).

Conclusion

We found a suboptimal COVID-19 vaccination rate in a cohort of patients who recovered from severe infection. COVID-19 vaccine information and recommendation by healthcare providers, employers, and family and friends may improve vaccination uptake.

Clinical outcomes of sofosbuvir-based antivirals in patients with COVID-19: a systematic review and meta-analysis of randomized trials

BACKGROUND

Several randomized trials have evaluated the effects of sofosbuvir-based direct-acting antivirals on the clinical outcomes in patients with COVID-19.

METHODS

A systematic literature search with no language restrictions was performed on electronic databases and preprint repositories to identify eligible randomized trials published up to 8 July 2021. A random-effects model was used to estimate the pooled odds ratio (OR) for outcomes of interest with the use of sofosbuvir combined with direct-acting antiviral agents relative to the nonuse of sofosbuvir-based direct-acting antiviral agents at 95% confidence intervals (CI).

RESULTS

The meta-analysis of 11 trials (n = 2,161) revealed statistically significant reduction in the odds of mortality (pooled odds ratio = 0.59; 95% confidence interval 0.36 to 0.99) but no statistically significant difference in the odds of development of composite endpoint of severe illness (pooled odds ratio = 0.79; 95% confidence interval 0.43 to 1.44) with the administration of sofosbuvir-based direct-acting antiviral agents among patients with COVID-19, relative to non-administration of sofosbuvir-based direct-acting antiviral agents.Subgroup analysis with seven trials involving sofosbuvir-daclatasvir revealed no significant mortality benefit (pooled odds ratio = 0.77; 95% confidence interval 0.48 to 1.22).

CONCLUSION

Sofosbuvir-based direct-acting antiviral agents have no protective effects against the development of severe illness in patients with COVID-19 with the current dosing regimen. Whether sofosbuvir-based direct-acting antiviral agents could offer mortality benefits would require further investigations.

COVID-19 reinfection: the role of natural immunity, vaccines, and variants

The COVID-19 pandemic has altered innumerable lives. Although recent mass vaccinations offer a glimmer of hope, the rising death toll and new variants continue to dominate the current scenario. As we begin to understand more about SARS-CoV-2 infections, the territory of reinfections with COVID-19 remains unexplored. In this review, we will discuss several aspects of reinfection: (a) How is COVID-19 reinfection characterized? (b) Does prior literature differentiate between reinfection and reactivation? (c) What SARS-CoV-2 strains do the vaccines target and can they protect against new strains? Larger and longer timeline studies are needed to understand reinfection risks. With the ongoing distribution of the SARS-CoV-2 vaccines to provide protection, the understanding of the possibility for SARS-CoV-2 reinfection remains critical.

Abbreviations CDC: Centers for Disease ControlSARS-CoV-2: Severe acute respiratory syndrome coronavirus 2COVID-19: Coronavirus disease 2019RT-PCR: Reverse Transcription Polymerase Chain ReactionPASC: Post-Acute Sequelae of SARS-CoV-2 infection

Activity-based epidemic propagation and contact network scaling in auto-dependent metropolitan areas

We build on recent work to develop a fully mechanistic, activity-based and highly spatio-temporally resolved epidemiological model which leverages person-trajectories obtained from an activity-based model calibrated for two full-scale prototype cities, consisting of representative synthetic populations and mobility networks for two contrasting auto-dependent city typologies. We simulate the propagation of the COVID-19 epidemic in both cities to analyze spreading patterns in urban networks across various activity types. Investigating the impact of the transit network, we find that its removal dampens disease propagation significantly, suggesting that transit restriction is more critical for mitigating post-peak disease spreading in transit dense cities. In the latter stages of disease spread, we find that the greatest share of infections occur at work locations. A statistical analysis of the resulting activity-based contact networks indicates that transit contacts are scale-free, work contacts are Weibull distributed, and shopping or leisure contacts are exponentially distributed. We validate our simulation results against existing case and mortality data across multiple cities in their respective typologies. Our framework demonstrates the potential for tracking epidemic propagation in urban networks, analyzing socio-demographic impacts and assessing activity- and mobility-specific implications of both non-pharmaceutical and pharmaceutical intervention strategies.

Clinical practice in COVID-19: The most frequently asked questions to infectious diseases specialists

Since the emergence of the disease caused by the severe respiratory syndrome coronavirus 2 (SARS-CoV-2) - COVID-19 - in late December 2019, a vast number of publications on the subject appeared in peer-reviewed journals and preprints. Despite the significant amount of available information, infectious disease physicians are requested to solve questions from colleagues, patients, and relatives on a daily basis. Here, we aim to describe the evidence supporting the answers for frequently asked questions, based on a literature review. We created a web-based questionnaire which was distributed to a group of 70 infectious disease specialists and medical residents, asking what questions and issues they most frequently faced. The 10 most frequent questions guided the topics for a narrative review. We provide evidence and consensus-based information on subjects such as infection and transmission, isolation, management of COVID-19 confirmed cases, reinfection, clinical-therapeutic management, vaccination, and antibodies post-infection/vaccination. Correctly clarifying doubts and providing clear information to physicians, patients, and family members helps to better manage COVID-19 in the community and the hospital settings.

Identifying Inconclusive Data in the SARS-CoV-2 Molecular Diagnostic Using Nucleocapsid Phosphoprotein Gene as Target

CONTEXT

The gold standard test to identify the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in coronavirus disease 2019 (COVID-19) patients is the real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR), but the inconclusive data and presence of false positive diagnosis remain the major problem of this approach.

OBJECTIVE

To compare the fitness of two primers sets to the SARS-CoV-2 nucleocapsid phosphoprotein (NP) gene in the molecular diagnosis of COVID-19, we verify the inconclusive data and confidence of high cycle threshold (Ct) values in the SARS-CoV-2 detection.

DESIGN

The 970 patient samples were tested using United States Centers for Disease Control and Prevention protocol. We compared the fitness of two primers sets to two different regions of NP gene. In addition, we check the consistency of positive samples with high Ct values by retesting extracted SARS-CoV-2 RNA or by second testing of patients.

RESULTS

The N1 and N2 displayed similar fitness during testing with no differences between Ct values. Then, we verified security range Cts related to positive diagnostic with Ct above 34 failing in 21/32 (65.6%) after retesting of samples. The samples patients with Ct above 34.89 that were doubly positive revealed a low sensitivity (52.4%) and specificity (63.6%) of the test in samples with Ct above 34.

CONCLUSIONS

It is secure to use one primer set to the NP gene to identify SARS-CoV-2 in samples. However, samples with high Ct values may be considered inconclusive and retested to avoid false positive diagnosis.

PD-1 blockade counteracts post-COVID-19 immune abnormalities and stimulates the anti-SARS-CoV-2 immune response

A substantial proportion of patients who have recovered from coronavirus disease-2019 (COVID-19) experience COVID-19–related symptoms even months after hospital discharge. We extensively immunologically characterized patients who recovered from COVID-19. In these patients, T cells were exhausted, with increased PD-1⁺ T cells, as compared with healthy controls. Plasma levels of IL-1β, IL-1RA, and IL-8, among others, were also increased in patients who recovered from COVID-19. This altered immunophenotype was mirrored by a reduced ex vivo T cell response to both nonspecific and specific stimulation, revealing a dysfunctional status of T cells, including a poor response to SARS-CoV-2 antigens. Altered levels of plasma soluble PD-L1, as well as of PD1 promoter methylation and PD1-targeting miR–15-5p, in CD8⁺ T cells were also observed, suggesting abnormal function of the PD-1/PD-L1 immune checkpoint axis. Notably, ex vivo blockade of PD-1 nearly normalized the aforementioned immunophenotype and restored T cell function, reverting the observed post–COVID-19 immune abnormalities; indeed, we also noted an increased T cell–mediated response to SARS-CoV-2 peptides. Finally, in a neutralization assay, PD-1 blockade did not alter the ability of T cells to neutralize SARS-CoV-2 spike pseudotyped lentivirus infection. Immune checkpoint blockade ameliorates post–COVID-19 immune abnormalities and stimulates an anti–SARS-CoV-2 immune response.