New SARS-CoV-2 variant of concern imported from the United Kingdom to Vietnam, December 2020.
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ABSTRACT:
SUBMITTER: Dao MH
PROVIDER: S-EPMC8013811 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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:Epidemiological and virological studies have revealed that SARS-CoV-2 variants of concern (VOCs) are emerging globally, including in Europe. The aim of this study was to evaluate the spread of B.1.1.7-lineage SARS-CoV-2 in southern Italy from December 2020-March 2021 through the detection of the S gene target failure (SGTF), which could be considered a robust proxy of VOC B.1.1.7. SGTF was assessed on 3075 samples from week 52/2020 to week 10/2021. A subset of positive samples identified in the Apulia region during the study period was subjected to whole-genome sequencing (WGS). A descriptive and statistical analysis of the demographic and clinical characteristics of cases according to SGTF status was performed. Overall, 20.2% of samples showed SGTF; 155 strains were confirmed as VOC 202012/01 by WGS. The proportion of SGTF-positive samples rapidly increased over time, reaching 69.2% in week 10/2021. SGTF-positive cases were more likely to be symptomatic and to result in hospitalization (p < 0.0001). Despite the implementation of large-scale non-pharmaceutical interventions (NPIs), such as the closure of schools and local lockdowns, a rapid spread of VOC 202012/01 was observed in southern Italy. Strengthened NPIs and rapid vaccine deployment, first among priority groups and then among the general population, are crucial both to contain the spread of VOC 202012/01 and to flatten the curve of the third wave.
| S-EPMC8125211 | biostudies-literature
Project description:We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69-V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.
| S-EPMC7848679 | biostudies-literature
Project description:A fast-spreading severe acute respiratory syndrome coronavirus 2 variant identified in the United Kingdom in December 2020 has raised international alarm. We analyzed data from 15 countries and estimated that the chance that this variant was imported into these countries by travelers from the United Kingdom by December 7 is >50%.
| S-EPMC8084518 | biostudies-literature
Project description:In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported.
| S-EPMC7920684 | biostudies-literature
Project description:ObjectiveThis study aimed to investigate coronavirus disease (COVID-19) epidemiology in Alberta, British Columbia, and Ontario, Canada.MethodsUsing data through December 1, 2020, we estimated time-varying reproduction number, Rt, using EpiEstim package in R, and calculated incidence rate ratios (IRR) across the 3 provinces.ResultsIn Ontario, 76% (92 745/121 745) of cases were in Toronto, Peel, York, Ottawa, and Durham; in Alberta, 82% (49 878/61 169) in Calgary and Edmonton; in British Columbia, 90% (31 142/34 699) in Fraser and Vancouver Coastal. Across 3 provinces, Rt dropped to ≤ 1 after April. In Ontario, Rt would remain < 1 in April if congregate-setting-associated cases were excluded. Over summer, Rt maintained < 1 in Ontario, ~1 in British Columbia, and ~1 in Alberta, except early July when Rt was > 1. In all 3 provinces, Rt was > 1, reflecting surges in case count from September through November. Compared with British Columbia (684.2 cases per 100 000), Alberta (IRR = 2.0; 1399.3 cases per 100 000) and Ontario (IRR = 1.2; 835.8 cases per 100 000) had a higher cumulative case count per 100 000 population.ConclusionsAlberta and Ontario had a higher incidence rate than British Columbia, but Rt trajectories were similar across all 3 provinces.
| S-EPMC8134904 | biostudies-literature
Project description:Although there have been several case reports and simulation models of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission associated with air travel, there are limited data to guide testing strategy to minimize the risk of SARS-CoV-2 exposure and transmission onboard commercial aircraft. Among 9853 passengers with a negative SARS-CoV-2 polymerase chain reaction test performed within 72 hours of departure from December 2020 through May 2021, five (0.05%) passengers with active SARS-CoV-2 infection were identified with rapid antigen tests and confirmed with rapid molecular test performed before and after an international flight from the United States to Italy. This translates to a case detection rate of 1 per 1970 travelers during a time of high prevalence of active infection in the United States. A negative molecular test for SARS-CoV-2 within 72 hours of international airline departure results in a low probability of active infection identified on antigen testing during commercial airline flight.
| S-EPMC8410576 | biostudies-literature
Project description:During the course of the coronavirus disease 2019 (COVID-19) pandemic, reports of a new multisystem inflammatory syndrome in children (MIS-C) have been increasing in Europe and the United States (1-3). Clinical features in children have varied but predominantly include shock, cardiac dysfunction, abdominal pain, and elevated inflammatory markers, including C-reactive protein (CRP), ferritin, D-dimer, and interleukin-6 (1). Since June 2020, several case reports have described a similar syndrome in adults; this review describes in detail nine patients reported to CDC, seven from published case reports, and summarizes the findings in 11 patients described in three case series in peer-reviewed journals (4-6). These 27 patients had cardiovascular, gastrointestinal, dermatologic, and neurologic symptoms without severe respiratory illness and concurrently received positive test results for SARS-CoV-2, the virus that causes COVID-19, by polymerase chain reaction (PCR) or antibody assays indicating recent infection. Reports of these patients highlight the recognition of an illness referred to here as multisystem inflammatory syndrome in adults (MIS-A), the heterogeneity of clinical signs and symptoms, and the role for antibody testing in identifying similar cases among adults. Clinicians and health departments should consider MIS-A in adults with compatible signs and symptoms. These patients might not have positive SARS-CoV-2 PCR or antigen test results, and antibody testing might be needed to confirm previous SARS-CoV-2 infection. Because of the temporal association between MIS-A and SARS-CoV-2 infections, interventions that prevent COVID-19 might prevent MIS-A. Further research is needed to understand the pathogenesis and long-term effects of this newly described condition.
| S-EPMC7561225 | biostudies-literature
Project description:Millions have died due to the COVID-19 pandemic. The irrepressible propensity of the pandemic, which was highlighted by the outbreak of the Delta variant, should not be underestimated. The Omicron SARS-CoV-2 variant is thought to have originated from Africa. Sequences of the omicron variant show that it carries the highest number of point mutations detected in a betacoronavirus. High hospitalization numbers due to the Omicron variant has retriggered precautionary restrictions and border closures even in countries which have attained herd immunity by mass vaccinations. Surveillance systems for accurate screening of the Omicron variant are needed to guide implementation of hygiene principles and restrictions. Development of vaccines against the variants is important as the pandemic evolves. Whether Omicron is the last variant depends on the success of the local and global public-health strategies against SARS-CoV-2.
| S-EPMC8768426 | biostudies-literature
Project description:The coding-complete genome sequence of a coronavirus strain, SARS-CoV-2/human/BGD/G039392/2021, obtained from a symptomatic male patient with coronavirus disease 2019 (COVID-19) in Dhaka, Bangladesh, is reported. The strain G039392 is 99.9% identical to the UK variant B.1.1.7.
| S-EPMC7909083 | biostudies-literature