Multiple clades of SARS-CoV-2 were introduced to Thailand during the first quarter of 2020.
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ABSTRACT:
SUBMITTER: Buathong R
PROVIDER: S-EPMC8251142 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: Not available
| S-BSST800 | biostudies-other
Project description:Since a novel beta-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019, there has been a rapid global spread of the virus. Genomic surveillance was conducted on samples isolated from infected individuals to monitor the spread of genetic variants of SARS-CoV-2 in Korea. The Korea Disease Control and Prevention Agency performed whole genome sequencing of SARS-CoV-2 in Korea for 1 year (January 2020 to January 2021). A total of 2,488 SARS-CoV-2 cases were sequenced (including 648 cases from abroad). Initially, the prevalent clades of SARS-CoV-2 were the S and V clades, however, by March 2020, GH clade was the most dominant. Only international travelers were identified as having G or GR clades, and since the first variant 501Y.V1 was identified (from a traveler from the United Kingdom on December 22nd, 2020), a total of 27 variants of 501Y.V1, 501Y.V2, and 484K.V2 have been classified (as of January 25th, 2021). The results in this study indicated that quarantining of travelers entering Korea successfully prevented dissemination of the SARS-CoV-2 variants in Korea.
| S-EPMC7899228 | biostudies-literature
Project description:Dengue is an arboviral disease highly endemic in Bangkok, Thailand. To characterize the current genetic diversity of dengue virus (DENV), we recruited patients with suspected DENV infection at the Hospital for Tropical Diseases, Bangkok, during 2018-2020. We determined complete nucleotide sequences of the DENV envelope region for 111 of 276 participant serum samples. All four DENV serotypes were detected, with the highest proportion being DENV-1. Although all DENV-1 sequences were genotype I, our DENV-1 sequences were divided into four distinct clades with different distributions in Asian countries. Two genotypes of DENV-2 were identified, Asian I and Cosmopolitan, which were further divided into two and three distinct clades, respectively. In DENV-3, in addition to the previously dominant genotype III, a cluster of 6 genotype I viruses only rarely reported in Thailand was also observed. All of the DENV-4 viruses belonged to genotype I, but they were separated into three distinct clades. These results indicated that all four serotypes of DENV with multiple genotypes and/or clades co-circulate in Bangkok. Continuous investigation of DENV is warranted to further determine the relationship between DENV within Thailand and neighboring countries in Southeast Asia and Asia.
| S-EPMC8482112 | 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:Non-healthcare workers with a high potential for exposure to severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) may contribute to the virus spreading. Data among asymptomatic and high exposure risk populations is still scarce, in particular Chiang Mai and Lamphun provinces, Thailand. We conducted a cross-sectional observational study aiming to assess the prevalence of SARS-CoV-2 RNA positivity, anti-SARS-CoV-2 IgM/IgG, and potential associated factors among asymptomatic/mild symptomatic individuals with a high exposure risk in Chiang Mai and Lamphun provinces, during the second wave of outbreak in Thailand (November 2020-January 2021). Socio-demographic data was collected through an on-line questionnaire prior to collection of nasopharyngeal/throat swab samples and blood samples tested for SARS-CoV-2 RNA (DaAn Gene, China) and anti-SARS-CoV-2 IgM/IgG antibodies (commercial lateral flow immunoassays), respectively. Univariable and multivariable logistic regression analysis were used to analyze associated factors. None of 1,651 participants were found positive for SARS-CoV-2 RNA (0%, 95% confidence intervals, CI: 0-0.2). Fourteen were positive for anti-SARS-CoV-2 IgM/IgG antibodies (0.9%, 95% CI: 0.5-1.4), including 7 positives for IgM and 7 positives for IgG (0.4%, 95% CI: 0.2-0.9). Being over 50 years old was independently associated with virus exposure (OR: 5.8, 95% CI: 1.0-32.1%, p = 0.045). Despite high exposure risk, no current infection was found, and a very high proportion was still susceptible to SARS-CoV-2 infection and would clearly benefit from vaccination. Continuing active surveillance, rolling out of vaccination and monitoring response to vaccine will help better control the COVID-19 spread.
| S-EPMC8809620 | biostudies-literature
Project description:ObjectivesFirst responders, including firefighters, emergency medical technicians (EMTs), paramedics, and law enforcement officers, are working on the front lines to fight the COVID-19 pandemic and facing an increased risk of infection. This study assessed the seroprevalence of SARS-CoV-2 infection among first responders in northeastern Ohio.MethodsA survey and immunoglobulin G antibody test against SARS-CoV-2 nucleocapsid protein were offered to University Hospitals Health System-affiliated first-responder departments during May to September 2020. The survey contained questions about demographic characteristics and history of SARS-CoV-2 infection. A total of 3080 first responders with diverse job assignments from more than 400 fire and police departments participated in the study.ResultsOf 3080 participants, 73 (2.4%) were seropositive and 26 (0.8%) had previously positive real-time polymerase chain reaction results. Asymptomatic infection accounted for 46.6% (34 of 73) of seropositivity. By occupation, rates of seropositivity were highest among administration/support staff (3.8%), followed by paramedics (3.0%), EMTs (2.6%), firefighters (2.2%), and law enforcement officers (0.8%). Work-associated exposure rates to COVID-19 patients were: paramedics (48.2%), firefighters (37.1%), EMTs (32.3%), law enforcement officers (7.7%), and administration/support staff (4.4%). Self-reported community exposure was positively correlated with self-reported work-associated exposure rate (correlation coefficient = 0.99). Neither self-reported community nor work-associated exposure was correlated with SARS-CoV-2 seroprevalence. We found no significant difference in seroprevalence among sex/gender or age groups; however, Black participants had a higher positivity rate than participants of other racial groups despite reporting lower exposure.ConclusionsDespite the high work-associated exposure rate to SARS-CoV-2 infection, first responders with various roles demonstrated seroprevalence no higher than their administrative/supportive colleagues, which suggests infection control measures are effective in preventing work-related infection.
| S-EPMC9692179 | biostudies-literature
Project description:We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.
| S-EPMC7427299 | biostudies-literature
Project description:BackgroundIn December 2019, the COVID-19 pandemic initially erupted from a cluster of pneumonia cases of unknown origin in the city of Wuhan, China. Presently, it has almost reached 94 million cases worldwide. Lebanon on the brink of economic collapse and its healthcare system thrown into turmoil, has previously managed to cope with the initial SARS-CoV-2 wave. In this study, we sequenced 11 viral genomes from positive cases isolated between 2 February 2020 and 15 March 2020.MethodsSequencing data was quality controlled, consensus sequences generated, and a maximum-likelihood tree was generated with IQTREE v2. Genetic lineages were assigned with Pangolin v1.1.14 and single nucleotide variants (SNVs) were called from read files and manually curated from consensus sequence alignment through JalView v2.11 and the genomic mutational interference with molecular diagnostic tools was assessed with the CoV-GLUE pipeline. Phylogenetic analysis of whole genome sequences confirmed a multiple introduction scenario due to international travel.ResultsThree major lineages were identified to be circulating in Lebanon in the studied period. The B.1 (20A clade) was the most prominent, followed by the B.4 lineage (19A clade) and the B.1.1 lineage (20B clade). SNV analysis showed 15 novel mutations from which only one was observed in the spike region.
| S-EPMC8447710 | biostudies-literature
Project description:In Jan 2020, the outbreak of the 2019 novel coronavirus (SARS-CoV-2) in Wuhan, Hubei Province of China spread increasingly to other countries worldwide which WHO declared it as a public health emergency of international concern. Iran was included in the affected countries. Throat swab specimens were collected and tested by using real-time reverse transcription PCR (RT-PCR) kit targeting the E region for screening and RNA dependent RNA polymerase for confirmation. Conventional RT-PCR was conducted for the N region and the PCR products were sequenced by Sanger sequencing. The first seven cases of SARS-CoV-2 infections were identified in Qom, Iran. This report describes the clinical and epidemiological features of the first cases of SARS-CoV-2 confirmed in Iran. Future research should focus on finding the routes of transmission for this virus, including the possibility of transmission from foreign tourists to identify the possible origin of SARS-CoV-2 outbreak in Iran.
| S-EPMC7554384 | biostudies-literature
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) pandemic in humans since late 2019. Here, we investigated SARS-CoV-2 infection in dogs and cats during COVID-19 quarantine at private veterinary hospitals in Thailand. From April to May 2021, we detected SARS-CoV-2 in three out of 35 dogs and one out of nine cats from four out of 17 households with confirmed COVID-19 patients. SARS-CoV-2 RNA was detected from one of the nasal, oral, rectal and environmental swabs of dog-A (15 years old, mixed breed, male dog), cat-B (1 year old, domestic shorthair, male cat), dog-C (2 years old, mixed breed, female dog) and dog-D (4 years old, Pomeranian, female dog). The animals tested positive for SARS-CoV-2 RNA from 4 to 30 days after pet owners were confirmed to be COVID-19 positive. The animals consecutively tested positive for SARS-CoV-2 RNA for 4 to 10 days. One dog (dog-A) showed mild clinical signs, while the other dogs and a cat remained asymptomatic during quarantine at the hospitals. SARS-CoV-2 specific neutralizing antibodies were detected in both the dogs and cat by surrogate virus neutralization tests. Phylogenetic and genomic mutation analyses of whole genome sequences of three SARS-CoV-2 strains from the dogs and cat revealed SARS-CoV-2 of the Alpha variant (B.1.1.7 lineage). Our findings are suggestive of human-to-animal transmission of SARS-CoV-2 in COVID-19-positive households and contamination of viral RNA in the environment. Public awareness of SARS-CoV-2 infection in pet dogs and cats in close contact with COVID-19 patients should be raised.
| S-EPMC8661729 | biostudies-literature