SARS-CoV-2 Infections among Recent Organ Recipients, March-May 2020, United States.
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ABSTRACT:
SUBMITTER: Jones JM
PROVIDER: S-EPMC7853574 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:As a kind of human betacoronavirus, SARS-CoV-2 has endangered globally public health. As of January 2021, the virus had resulted in 2,209,195 deaths. By studying the evolution trend and characteristics of 265 SARS-CoV-2 strains in the United States from January to March, it is found that the strains can be divided into six clades, USA clade-1, USA clade-2, USA clade-3, USA clade-4, USA clade-5, and USA clade-6, in which US clade-1 may be the most ancestral clade, USA clade-2 is an interim clade of USA clade-1 and USA clade-3, the other three clades have similar codon usage pattern, while USA clade-6 is the newest and most adaptable clade. Mismatch analysis and protein alignment showed that the evolution of the clades arises from some special mutations in viral proteins, which may help the strain to invade, replicate, transcribe and so on. Compared with previous research and classifications, we suggest that clade O in GISAID should not be an independent clade and Wuhan-Hu-1 (EPI_ISL_402125) should not be an ancestral reference sequence. Our study decoded the evolutionary dynamic of SARS-CoV-2 in the early stage from the United States, which give some clues to infer the current evolution trend of SARS-CoV-2 and study the function of viral mutational protein.
| S-EPMC8426869 | biostudies-literature
Project description:ObjectiveSARS-CoV-2 testing is a critical component of preventing the spread of COVID-19. In the United States, people experiencing homelessness (PEH) have accessed testing at health clinics, such as those provided through Health Care for the Homeless (HCH) clinics or through community-based testing events at homeless service sites or encampments. We describe data on SARS-CoV-2 testing among PEH in US clinic- and community-based settings from March through November 2020.MethodsWe conducted a descriptive analysis of data from HCH clinics and community testing events. We used a standardized survey to request data from HCH clinics. We developed and made publicly available an online data entry portal to collect data from community-based organizations that provided testing for PEH. We assessed positivity rates across clinics and community service sites serving PEH and used generalized linear mixed models to account for clustering.ResultsThirty-seven HCH clinics reported providing 280 410 tests; 3.2% (n = 8880) had positive results (range, 1.6%-4.9%). By race, positivity rates were highest among people who identified as >1 race (11.6%; P < .001). During the reporting period, 22 states reported 287 community testing events and 14 116 tests; 7.1% (n = 1004) had positive results. Among facility types, day shelters (380 of 2697; 14.1%) and inpatient drug/alcohol rehabilitation facilities (32 of 251; 12.7%) reported the highest positivity rates.ConclusionsWhile HCH clinic data provided results for a larger number of patients, community-based testing data showed higher positivity rates. Clinic data demonstrated racial disparities in positivity. Community-based testing data provided information about SARS-CoV-2 transmission settings. Although these data provide information about testing, standard surveillance systems are needed to better understand the incidence of disease among PEH.
| S-EPMC9066227 | 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:The emergence and establishment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest (VOIs) and variants of concern (VOCs) highlight the importance of genomic surveillance. We propose a statistical learning strategy (SLS) for identifying and spatiotemporally tracking potentially relevant Spike protein mutations. We analyzed 167,893 Spike protein sequences from coronavirus disease 2019 (COVID-19) cases in the United States (excluding 21,391 sequences from VOI/VOC strains) deposited at GISAID from 19 January 2020 to 15 March 2021. Alignment against the reference Spike protein sequence led to the identification of viral residue variants (VRVs), i.e., residues harboring a substitution compared to the reference strain. Next, generalized additive models were applied to model VRV temporal dynamics and to identify VRVs with significant and substantial dynamics (false discovery rate q-value < 0.01; maximum VRV proportion >10% on at least one day). Unsupervised learning was then applied to hierarchically organize VRVs by spatiotemporal patterns and identify VRV-haplotypes. Finally, homology modeling was performed to gain insight into the potential impact of VRVs on Spike protein structure. We identified 90 VRVs, 71 of which had not previously been observed in a VOI/VOC, and 35 of which have emerged recently and are durably present. Our analysis identified 17 VRVs ~91 days earlier than their first corresponding VOI/VOC publication. Unsupervised learning revealed eight VRV-haplotypes of four VRVs or more, suggesting two emerging strains (B1.1.222 and B.1.234). Structural modeling supported a potential functional impact of the D1118H and L452R mutations. The SLS approach equally monitors all Spike residues over time, independently of existing phylogenic classifications, and is complementary to existing genomic surveillance methods.
| S-EPMC8777887 | biostudies-literature
Project description:By March 2020, COVID-19 led to thousands of deaths and disrupted economic activity worldwide. As a result of narrow case definitions and limited capacity for testing, the number of unobserved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during its initial invasion of the United States remains unknown. We developed an approach for estimating the number of unobserved infections based on data that are commonly available shortly after the emergence of a new infectious disease. The logic of our approach is, in essence, that there are bounds on the amount of exponential growth of new infections that can occur during the first few weeks after imported cases start appearing. Applying that logic to data on imported cases and local deaths in the United States through 12 March, we estimated that 108,689 (95% posterior predictive interval [95% PPI]: 1,023 to 14,182,310) infections occurred in the United States by this date. By comparing the model's predictions of symptomatic infections with local cases reported over time, we obtained daily estimates of the proportion of symptomatic infections detected by surveillance. This revealed that detection of symptomatic infections decreased throughout February as exponential growth of infections outpaced increases in testing. Between 24 February and 12 March, we estimated an increase in detection of symptomatic infections, which was strongly correlated (median: 0.98; 95% PPI: 0.66 to 0.98) with increases in testing. These results suggest that testing was a major limiting factor in assessing the extent of SARS-CoV-2 transmission during its initial invasion of the United States.
| S-EPMC7486725 | biostudies-literature
Project description:This overview of severe acute respiratory syndrome coronavirus 2 circulation over 1.5 years in Guinea demonstrates that virus clades and variants of interest and concern were progressively introduced, mostly by travellers through Conakry, before spreading through the country. Sequencing is key to following virus evolution and establishing efficient control strategies.
| S-EPMC8798712 | biostudies-literature
Project description:SARS-CoV-2 infections among vaccinated nursing home residents increased after the Omicron variant emerged. Data on booster dose effectiveness in this population are limited. During July 2021-March 2022, nursing home outbreaks in 11 US jurisdictions involving >3 infections within 14 days among residents who had received at least the primary COVID-19 vaccine(s) were monitored. Among 2,188 nursing homes, 1,247 outbreaks were reported in the periods of Delta (n = 356, 29%), mixed Delta/Omicron (n = 354, 28%), and Omicron (n = 536, 43%) predominance. During the Omicron-predominant period, the risk for infection within 14 days of an outbreak start was lower among boosted residents than among residents who had received the primary vaccine series alone (risk ratio [RR] 0.25, 95% CI 0.19-0.33). Once infected, boosted residents were at lower risk for all-cause hospitalization (RR 0.48, 95% CI 0.40-0.49) and death (RR 0.45, 95% CI 0.34-0.59) than primary vaccine-only residents.
| S-EPMC10045674 | biostudies-literature
Project description: Not available
| S-BSST800 | biostudies-other
Project description:BackgroundStandardised surveillance of COVID-19 infections among healthcare personnel during the current pandemic was and is not available. In particular, the proportion of occupational infections among healthcare personnel and which workers among them are most at risk remains unclear.ObjectivesThe aim of this study was to analyse the reported COVID-19 cases among healthcare personnel in Frankfurt/Main during the first six months of the pandemic, to determine the number of occupational infections and thus to allow a better interpretation of the data published by the Robert Koch Institute.MethodsData from the Frankfurt/Main Health Protection Authority was analysed for the period from 1 March to 31 August 2020, and healthcare personnel were recruited for a cross-sectional survey. Three subgroups were defined and analysed according to whether the infectious contact occurred at work, in private or in an unknown setting.ResultsHealthcare personnel accounted for 11.8% (319/2700) of all reported COVID-19 cases in Frankfurt/Main during the period studied. In the survey, 47.2% of respondents reported that their infection was acquired in the workplace. There was an association of contact with COVID-19 patients as well as employment in the internal medicine ward and a reported work-related infection. Also apparent was an association between suspected occupational infections and consequently filed reports for alleged occupational disease.Discussion and conclusionHealth protection authorities are in a position to collect relevant data on work-related transmissions in healthcare occupations and workplaces and should generate standardised data on infected healthcare personnel. This data is necessary to take targeted infection control and prevention measures that protect healthcare personnel and their patients.
| S-EPMC8984668 | biostudies-literature
Project description:In 2020, SARS-CoV-2 spread across the United States (U.S.) in three phases distinguished by peaks in the numbers of infections and shifting geographical distribution. We investigated the viral genetic diversity in each phase using sequences publicly available prior to December 15 th , 2020, when vaccination was initiated in the U.S. In Phase 1 (winter/spring), sequences were already dominated by the D614G Spike mutation and by Phase 3 (fall), genetic diversity of the viral population had tripled and at least 54 new amino acid changes had emerged at frequencies above 5%, several of which were within known antibody epitopes. These findings highlight the need to track the evolution of SARS-CoV-2 variants in the U.S. to ensure continued efficacy of vaccines and antiviral treatments.One sentence summarySARS-CoV-2 genetic diversity in the U.S. increased 3-fold in 2020 and 54 emergent nonsynonymous mutations were detected.
| S-EPMC8202437 | biostudies-literature