Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020.
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ABSTRACT:
SUBMITTER: Smith MR
PROVIDER: S-EPMC8517019 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Following its emergence in late 2019, SARS-CoV-2 has caused a global pandemic resulting in unprecedented efforts to reduce transmission and develop therapies and vaccines (WHO Emergency Committee, 2020; Zhu et al ., 2020). Rapidly generated viral genome sequences have allowed the spread of the virus to be tracked via phylogenetic analysis (Hadfield et al ., 2018; Pybus et al ., 2020; Worobey et al ., 2020). While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced, allowing continent-specific variants to emerge. However, within Europe travel resumed in the summer of 2020, and the impact of this travel on the epidemic is not well understood. Here we report on a novel SARS-CoV-2 variant, 20A.EU1, that emerged in Spain in early summer, and subsequently spread to multiple locations in Europe, accounting for the majority of sequences by autumn. We find no evidence of increased transmissibility of this variant, but instead demonstrate how rising incidence in Spain, resumption of travel across Europe, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions and quarantine requirements, we estimate 20A.EU1 was introduced hundreds of times to countries across Europe by summertime travellers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes.Caveats20A.EU1 most probably rose in frequency in multiple countries due to travel and difference in SARS-CoV-2 prevalence. There is no evidence that it spreads faster . There are currently no data to evaluate whether this variant affects the severity of the disease . While dominant in some countries, 20A.EU1 has not taken over everywhere and diverse variants of SARS-CoV-2 continue to circulate across Europe. 20A.EU1 is not the cause of the European 'second wave.'
| S-EPMC7709189 | biostudies-literature
Project description:BackgroundViral infections can cause significant morbidity in cystic fibrosis (CF). The current Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic could therefore have a serious impact on the health of people with CF (pwCF).MethodsWe used the 38-country European Cystic Fibrosis Society Patient Registry (ECFSPR) to collect case data about pwCF and SARS-CoV-2 infection.ResultsUp to 30 June 2020, 16 countries reported 130 SARS-CoV-2 cases in people with CF, yielding an incidence of 2.70/1000 pwCF. Incidence was higher in lung-transplanted patients (n=23) versus non-transplanted patients (n=107) (8.43 versus 2.36 cases/1000). Incidence was higher in pwCF versus the age-matched general population in the age groups <15, 15-24, and 25-49 years (p<0.001), with similar trends for pwCF with and without lung transplant. Compared to the general population, pwCF (regardless of transplantation status) had significantly higher rates of admission to hospital for all age groups with available data, and higher rates of intensive care, although not statistically significant. Most pwCF recovered (96.2%), however 5 died, of whom 3 were lung transplant recipients. The case fatality rate for pwCF (3.85%, 95% CI: 1.26-8.75) was non-significantly lower than that of the general population (7.46%; p=0.133).ConclusionsSARS-CoV-2 infection can result in severe illness and death for pwCF, even for younger patients and especially for lung transplant recipients. PwCF should continue to shield from infection and should be prioritized for vaccination.
| S-EPMC8053246 | biostudies-literature
Project description:BackgroundReported COVID-19 cases underestimate SARS-CoV-2 infections. We conducted a national probability survey of US households to estimate the cumulative incidence adjusted for antibody waning.MethodsFrom August-December 2020, a multistage random sample of US addresses were mailed a survey and materials to self-collect nasal swabs and dried blood spots. One adult household member completed the survey and mail specimens for viral detection with PCR and total (IgA, IgM, IgG) nucleocapsid antibody by a commercial, EUA-approved antigen capture assay. We estimated cumulative incidence of SARS-CoV-2 adjusted for waning antibodies and calculated reported fraction and infection fatality ratio (IFR). Differences in seropositivity among demographic, geographic and clinical subgroups were explored with weighted prevalence ratios (PR).ResultsAmong 39,500 sampled households, 4,654 respondents provided responded. Cumulative incidence adjusted for waning was 11.9% (95% credible interval (CrI): 10.5-13.5%) as of October 30, 2020. We estimated 30,332,842 (CrI: 26,703,753- 34,335,338) total infections in the U.S. adult population by October 30, 2020. Reported fraction was 17% and IFR was 0.85% among adults. Non-Hispanic Black (PR: 2.2) and Hispanic (PR: 3.1) persons were more likely than White non-Hispanic to be seropositive, as were those living in metropolitan areas (PR: 2.5).ConclusionsOne in 8 US adults had been infected with SARS-CoV-2 by late October 2020; but few had been accounted for in public health reporting. The scope of the COVID-19 pandemic is likely substantially underestimated by reported cases. Disparities in COVID-19 by race observed among reported cases cannot be attributed to differential diagnosis or reporting of infections in some population subgroups.
| S-EPMC8406864 | biostudies-literature
Project description:BackgroundFollowing a first wave in spring and gradual easing of lockdown, Luxembourg experienced an early second epidemic wave of SARS-CoV-2 before the start of summer school holidays on 15th July. This provided the opportunity to investigate the role of school-age children and school settings for transmission.MethodsWe compared the incidence of SARS-CoV-2 in school-age children, teachers and the general working population in Luxembourg during two epidemic waves: a spring wave from March-April 2020 corresponding to general lockdown with schools being closed and May-July 2020 corresponding to schools being open. We assessed the number of secondary transmissions occurring in schools between May and July 2020 using routine contact tracing data.ResultsDuring the first wave in March-April 2020 when schools were closed, the incidence in pupils peaked at 28 per 100,000, while during the second wave in May-July 2020 when schools were open, incidence peaked 100 per 100,000. While incidence of SARS-CoV-2 was higher in adults than in children during the first spring wave, no significant difference was observed during the second wave in early summer. Between May and July 2020, we identified a total of 390 and 34 confirmed COVID-19 cases among 90,150 school-age children and 11,667 teachers, respectively. We further estimate that 179 primary cases caused 49 secondary cases in schools. While some small clusters of mainly student-to-student transmission within the same class were identified, we did not observe any large outbreaks with multiple generations of infection.ConclusionsTransmission of SARS-CoV-2 within Luxembourg schools was limited during an early summer epidemic wave in 2020. Precautionary measures including physical distancing as well as easy access to testing, systematic contact tracing appears to have been successful in mitigating transmission within educational settings.
| S-EPMC8093902 | biostudies-literature
Project description:BackgroundA year following the onset of the COVID-19 pandemic, new infections and deaths continue to increase in Europe. Serological studies, through providing evidence of past infection, can aid understanding of the population dynamics of SARS-CoV-2 infection.ObjectivesThis systematic review of SARS-CoV-2 seroprevalence studies in Europe was undertaken to inform public health strategies including vaccination, that aim to accelerate population immunity.MethodsWe searched the databases Web of Science, MEDLINE, EMBASE, SCOPUS, Cochrane Database of Systematic Reviews and grey literature sources for studies reporting seroprevalence of SARS-CoV-2 antibodies in Europe published between 01/12/2019-30/09/20. We provide a narrative synthesis of included studies. Studies were categorized into subgroups including healthcare workers (HCWs), community, outbreaks, pregnancy and children/school. Due to heterogeneity in other subgroups, we only performed a random effects meta-analysis of the seroprevalence amongst HCWs stratified by their country.Results115 studies were included spanning 17 European countries, that estimated the seroprevalence of SARS-CoV-2 from samples obtained between November 2019 -August 2020. A total of 54/115 studies included HCWs with a reported seroprevalence among HCWs ranging from 0.7% to 45.3%, which did not differ significantly by country. In community studies significant heterogeneity was reported in the seroprevalence between different age groups and the majority of studies reported there was no significant difference by gender.ConclusionThis review demonstrates a wide heterogeneity in reported seroprevalence of SARS-CoV-2 antibodies between populations. Continued evaluation of seroprevalence is required to understand the impact of public health measures and inform interventions including vaccination programmes.
| S-EPMC8562786 | biostudies-literature
Project description:India, with around 15 million COVID-19 cases, recently became the second worst-hit nation by the SARS-CoV-2 pandemic. In this study, we analyzed the mutation and selection landscape of 516 unique and complete genomes of SARS-CoV-2 isolates from India in a 12-month span (from Jan to Dec 2020) to understand how the virus is evolving in this geographical region. We identified 953 genome-wide loci displaying single nucleotide polymorphism (SNP) and the Principal Component Analysis and mutation plots of the datasets indicate an increase in genetic variance with time. The 42% of the polymorphic sites display substitutions in the third nucleotide position of codons indicating that non-synonymous substitutions are more prevalent. These isolates displayed strong evidence of purifying selection in ORF1ab, spike, nucleocapsid, and membrane glycoprotein. We also find some evidence of localized positive selections ORF1ab, spike glycoprotein, and nucleocapsid. The CDSs for ORF3a, ORF8, nucleocapsid phosphoprotein, and spike glycoprotein were found to evolve at rapid rate. This study will be helpful in understanding the dynamics of rapidly evolving SARS-CoV-2.
| S-EPMC8547785 | biostudies-literature
Project description: Not available
| S-BSST379 | biostudies-other
Project description:There is an urgent public health need to better understand Severe Acute Respiratory Syndrome (SARS)-CoV-2/COVID-19, particularly how sequences of the viruses could lead to diverse incidence and mortality of COVID-19 in different countries. However, because of its unknown ancestors and hosts, elucidating the genetic variations of the novel coronavirus, SARS-CoV-2, has been difficult. Without needing to know ancestors, we identified an uneven distribution of local genome similarities among the viruses categorized by geographic regions, and it was strongly correlated with incidence and mortality. To ensure unbiased and origin-independent analyses, we used a pairwise comparison of local genome sequences of virus genomes by Basic Local Alignment Search Tool (BLAST). We found a strong statistical correlation between dominance of the SARS-CoV-2 in distributions of uneven similarities and the incidence and mortality of illness. Genomic annotation of the BLAST hits also showed that viruses from geographic regions with severe infections tended to have more dynamic genomic regions in the SARS-CoV-2 receptor-binding domain (RBD) and receptor-binding motif (RBM) of the spike protein (S protein). Dynamic domains in the S protein were also confirmed by a canyon region of mismatches coincident with RBM and RBD, without hits of alignments of 100% matching. Thus, our origin-independent analysis suggests that the dynamic and unstable SARS-CoV-2-RBD could be the main reason for diverse incidence and mortality of COVID-19 infection.
| S-EPMC7543285 | biostudies-literature
Project description:The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. In order to cast fresh light on the spread of the virus and on the effectiveness of the containment measures adopted globally, we used 26,869 SARS-CoV-2 genomes to build a phylogeny with 20,247 mutation events and adopted a phylogeographic approach. We confirmed that the phylogeny pinpoints China as the origin of the pandemic with major founders worldwide, mainly during January 2020. However, a single specific East Asian founder underwent massive radiation in Europe and became the main actor of the subsequent spread worldwide during March 2020. This lineage accounts for the great majority of cases detected globally and even spread back to the source in East Asia. Despite an East Asian source, therefore, the global pandemic was mainly fueled by its expansion across and out of Europe. It seems likely that travel bans established throughout the world in the second half of March helped to decrease the number of intercontinental exchanges, particularly from mainland China, but were less effective between Europe and North America where exchanges in both directions are visible up to April, long after bans were imposed.
| S-EPMC7693378 | biostudies-literature
Project description:The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We describe our laboratory experiences during a large contact tracing investigation, comparing previously published real-time RT-PCR assays in different PCR systems and a commercial kit. We found that assay performance using the same primers and probes with different PCR systems varied and the commercial kit performed well.
| S-EPMC7068163 | biostudies-literature