Comparative genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible.

Background: In recent months, multiple cases of confirmed SARS-CoV-2 reinfection have been reported. However, accurate epidemiological and virological data, including genomic analysis where possible, are required to differentiate cases of prolonged viral RNA shedding (i.e. intermittent detection) from true reinfection. The objective of this review was to systematically identify and summarise all cases of SARS-CoV-2 reinfection confirmed by comparative genomic analysis. Methods: A protocol based on Cochrane rapid review methodology was employed. Databases and pre-print servers were searched until 9/11/2020. Results: Ten studies, representing 17 patients, were identified (mean age=40; 71% male). The time interval between primary infection and reinfection ranged from 13 to 142 days (median: 60).Comparative whole genome sequencing confirmed reinfection in 14 patients (the primary and secondary infections were caused by different viruses). A further three cases had strong, but not confirmed evidence of reinfection, as only partial genomes were retrieved on primary infection.Across 12 studies that reported the number of single nucleotide polymorphisms (SNPs) comparing the first and second genomes, between 8 and 24 SNPs were discovered. With an average SARS-CoV-2 mutation acquisition rate of 1-2 per month, in all cases it is likely that the secondary infection was caused by a different SARS-CoV-2 virus, rather than prolonged shedding of viral RNA from the primary infection.In five reinfection cases, the primary and secondary infections were caused by different SARS-CoV-2 lineages/clades, strongly indicating that infections were caused by different viruses. Conclusion: Comparative genomic analyses from 14 patients confirm that SARS-CoV-2 reinfection can occur.

Irish Media Coverage of COVID-19 Evidence-Based Research Reports From One National Agency.

BACKGROUND: How research findings are presented through domestic news can influence behaviour and risk perceptions, particularly during emergencies such as the coronavirus disease 2019 (COVID-19) pandemic. Monitoring media communications to track misinformation and find information gaps is an important component of emergency risk communication. Therefore, this study investigated the traditional media coverage of nine selected COVID-19 evidence-based research reports and associated press releases (PRs) published during the initial phases of the pandemic (April to July 2020) by one national agency. METHODS: NVivo was used for summative content analysis. 'Key messages' from each research report were proposed and 488 broadcast, print, and online media sources were coded at the phrase level. Manifest content was coded and counted to locate patterns in the data (what and how many) while latent content was analysed to further investigate these patterns (why and how). This included the coding of the presence of political and public health actors in coverage. RESULTS: Coverage largely did not misrepresent the results of the reports, however, selective reporting and the variability in the use of quotes from governmental and public health stakeholders changed and contextualised results in different manners than perhaps originally intended in the PR. Reports received varying levels of media attention. Coverage focused on more 'human-interest' stories (eg, spread of COVID-19 by children and excess mortality) as opposed to more technical reports (eg, focusing on viral load, antibodies, testing, etc). CONCLUSION: Our findings provide a case-study of European media coverage of evidence reports produced by a national agency. Results highlighted several strengths and weaknesses of current communication efforts.

Pharmacological interventions to prevent Covid-19 disease: A rapid review.

The aim of this rapid review was to determine the effectiveness of pharmacological interventions (excluding vaccines) to prevent coronavirus disease 2019 (Covid-19) or reduce the severity of disease. A systematic search of published peer-reviewed articles and non-peer-reviewed pre-prints was undertaken from 1 January 2020 to 17 August 2021. Four randomised controlled trials (RCTs) and one non-RCT were included; three trials (two RCTs and one non-RCT) tested ivermectin with or without carrageenan. While all reported some potential protective effect of ivermectin, these trials had a high risk of bias and the certainty of evidence was deemed to be 'very low'. One RCT tested bamlanivimab compared to placebo and reported a significantly reduced incidence of Covid-19 in the intervention group; this trial had a low risk of bias however the certainty of evidence was deemed 'very low'. The fifth RCT tested casirivimab plus imdevimab versus placebo and reported that the combination of monoclonal antibodies significantly reduced the incidence of symptomatic and asymptomatic SARS-CoV-2 infection, viral load, duration of symptomatic disease and the duration of a high viral load; this trial was deemed to have a low risk of bias, and the certainty of evidence was 'low'. The designations 'low' and 'very low' regarding the certainty of evidence indicate that the estimate of effect is uncertain and therefore is unsuitable for informing decision-making. At the time of writing, there is insufficient high quality evidence to support the use of pharmacological interventions to prevent Covid-19.

Quantifying the risk of SARS-CoV-2 reinfection over time.

Despite over 140 million SARS-CoV-2 infections worldwide since the beginning of the pandemic, relatively few confirmed cases of SARS-CoV-2 reinfection have been reported. While immunity from SARS-CoV-2 infection is probable, at least in the short term, few studies have quantified the reinfection risk. To our knowledge, this is the first systematic review to synthesise the evidence on the risk of SARS-CoV-2 reinfection over time. A standardised protocol was employed, based on Cochrane methodology. Electronic databases and preprint servers were searched from 1 January 2020 to 19 February 2021. Eleven large cohort studies were identified that estimated the risk of SARS-CoV-2 reinfection over time, including three that enrolled healthcare workers and two that enrolled residents and staff of elderly care homes. Across studies, the total number of PCR-positive or antibody-positive participants at baseline was 615,777, and the maximum duration of follow-up was more than 10 months in three studies. Reinfection was an uncommon event (absolute rate 0%-1.1%), with no study reporting an increase in the risk of reinfection over time. Only one study estimated the population-level risk of reinfection based on whole genome sequencing in a subset of patients; the estimated risk was low (0.1% [95% CI: 0.08-0.11%]) with no evidence of waning immunity for up to 7 months following primary infection. These data suggest that naturally acquired SARS-CoV-2 immunity does not wane for at least 10 months post-infection. However, the applicability of these studies to new variants or to vaccine-induced immunity remains uncertain.

Interventions in an Ambulatory Setting to Prevent Progression to Severe Disease in Patients With COVID-19: A Systematic Review.

OBJECTIVE: To conduct a systematic review on the effectiveness and safety of pharmacological and nonpharmacological interventions, in the ambulatory setting, aimed at preventing severe disease in patients with COVID-19. DATA SOURCES: Electronic databases (PubMed, EMBASE, and EuropePMC) were searched on January 6, 2021. STUDY SELECTION AND DATA EXTRACTION: A systematic review was conducted, adhering to PRISMA guidelines. The quality of individual trials was assessed using the Cochrane Risk-of-Bias Tool 2, and the certainty of evidence was assessed using GRADE. DATA SYNTHESIS: The collective search retrieved 3818 citations. Eight trials relating to 9 pharmacological interventions were identified. No evidence for nonpharmacological interventions was identified. Low certainty evidence of effectiveness in preventing severe disease was found for fluvoxamine (absolute difference: -8.7%; 95% CI: -1.8% to -16.4%) and bamlanivimab plus etesevimab (absolute difference: -4.9%; 95% CI: -0.8% to -8.9%). Both trials were limited by small sample sizes and short durations of follow-up. In addition, very low certainty evidence of effect was found for ivermectin plus doxycycline and sulodexide. Based on published data, insufficient evidence of effect was found for bamlanivimab (monotherapy), casirivimab plus imdevimab, ivermectin (monotherapy), nitazoxanide, and peginterferon lambda. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE: This review assessed all ambulatory treatments for COVID-19 that may improve patient outcomes and reduce hospitalizations. CONCLUSION: Recent trials have shown promising results for a number of pharmacological agents to treat COVID-19 in the ambulatory setting. However, larger, more robust trials are needed to support the routine use of these agents outside of monitored clinical trials.

Airborne transmission of SARS-CoV-2 via aerosols.

A key consideration in the Covid-19 pandemic is the dominant modes of transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The objective of this review was to synthesise the evidence for the potential airborne transmission of SARS-CoV-2 via aerosols. Systematic literature searches were conducted in PubMed, Embase, Europe PMC and National Health Service UK evidence up to 27 July 2020. A protocol was published and Cochrane guidance for rapid review methodology was adhered to throughout. Twenty-eight studies were identified. Seven out of eight epidemiological studies suggest aerosol transmission may occur, with enclosed environments and poor ventilation noted as possible contextual factors. Ten of the 16 air sampling studies detected SARS-CoV-2 ribonucleic acid; however, only three of these studies attempted to culture the virus with one being successful in a limited number of samples. Two of four virological studies using artificially generated aerosols indicated that SARS-CoV-2 is viable in aerosols. The results of this review indicate there is inconclusive evidence regarding the viability and infectivity of SARS-CoV-2 in aerosols. Epidemiological studies suggest possible transmission, with contextual factors noted. Viral particles have been detected in air sampling studies with some evidence of clinical infectivity, and virological studies indicate these particles may represent live virus, adding further plausibility. However, there is uncertainty as to the nature and impact of aerosol transmission of SARS-CoV-2, and its relative contribution to the Covid-19 pandemic compared with other modes of transmission.

Immune response following infection with SARS-CoV-2 and other coronaviruses: A rapid review.

In this review, we systematically searched and summarized the evidence on the immune response and reinfection rate following SARS-CoV-2 infection. We also retrieved studies on SARS-CoV and MERS-CoV to assess the long-term duration of antibody responses. A protocol based on Cochrane rapid review methodology was adhered to and databases were searched from 1/1/2000 until 26/5/2020. Of 4744 citations retrieved, 102 studies met our inclusion criteria. Seventy-four studies were retrieved on SARS-CoV-2. While the rate and timing of IgM and IgG seroconversion were inconsistent across studies, most seroconverted for IgG within 2 weeks and 100% (N = 62) within 4 weeks. IgG was still detected at the end of follow-up (49-65 days) in all patients (N = 24). Neutralizing antibodies were detected in 92%-100% of patients (up to 53 days). It is not clear if reinfection with SARS-CoV-2 is possible, with studies more suggestive of intermittent detection of residual RNA. Twenty-five studies were retrieved on SARS-CoV. In general, SARS-CoV-specific IgG was maintained for 1-2 years post-infection and declined thereafter, although one study detected IgG up to 12 years post-infection. Neutralizing antibodies were detected up to 17 years in another study. Three studies on MERS-CoV reported that IgG may be detected up to 2 years. In conclusion, limited early data suggest that most patients seroconvert for SARS-CoV-2-specific IgG within 2 weeks. While the long-term duration of antibody responses is unknown, evidence from SARS-CoV studies suggest SARS-CoV-specific IgG is sustained for 1-2 years and declines thereafter.

SARS-CoV-2 detection, viral load and infectivity over the course of an infection.

OBJECTIVES: To summarise the evidence on the detection pattern and viral load of SARS-CoV-2 over the course of an infection (including any asymptomatic or pre-symptomatic phase), and the duration of infectivity. METHODS: A systematic literature search was undertaken in PubMed, Europe PubMed Central and EMBASE from 30 December 2019 to 12 May 2020. RESULTS: We identified 113 studies conducted in 17 countries. The evidence from upper respiratory tract samples suggests that the viral load of SARS-CoV-2 peaks around symptom onset or a few days thereafter, and becomes undetectable about two weeks after symptom onset; however, viral loads from sputum samples may be higher, peak later and persist for longer. There is evidence of prolonged virus detection in stool samples, with unclear clinical significance. No study was found that definitively measured the duration of infectivity; however, patients may not be infectious for the entire duration of virus detection, as the presence of viral ribonucleic acid may not represent transmissible live virus. CONCLUSION: There is a relatively consistent trajectory of SARS-CoV-2 viral load over the course of COVID-19 from respiratory tract samples, however the duration of infectivity remains uncertain.