Genome Characterization of COVID-19 Lineage B.1.1.7 Detected in the First Six Patients of a Cluster Outbreak - Shenzhen City, Guangdong Province, China, May 2021.
Ontology highlight
ABSTRACT:
SUBMITTER: He Y
PROVIDER: S-EPMC8393023 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundThis study was conducted to identify epidemiological characteristics of the first documented CHIK fever outbreak in China and evaluate the effect of the preventive measures taken.Methodology/principal findingsFrom September 1 to October 29, 2010, China's first documented outbreak of CHIK fever occurred in the Xincun community of Wanjiang District of Dongguan city, Guangdong province; 253 case-patients were recorded, of which 129 were laboratory confirmed, with an attack rate of 1%. Before September 18(th) the number of CHIK fever cases remained relatively low in the Xincun community; from September 19(th) onwards, the number of cases increased drastically, with an outbreak peak on October 4(th). Cases were distributed across nine small village groups in the Xincun community, with an attack rate of 0-12% at the village level. The household attack rates ranged between 20% and 100%. No significant difference was found in the attack rate between males and females. There was a significant difference in the attack rate in different age groups (chi-square=18.35, p=0.005); highest in patients aged 60 years or older and the lowest in patients aged under 10. The major clinical characteristics of patients are fever (100%), joint pain (79%) and rash (54%). Phylogenetic analysis of the E1 gene on the five earliest confirmed cases showed that the strains of CHIKV isolated from their sera were highly homologous (up to 99%) with isogeneic strains isolated in Thailand in 2009. After control measures were taken, including killing adult mosquitoes and cleaning breeding habitats of Aedes mosquitoes, the Breteau index and Mosq-ovitrap index decreased rapidly, and the outbreak ended on October 29.Conclusion/significanceThe infection source of the outbreak was imported. Cases showed obvious temporal, spatial, and population aggregation during the outbreak. Comprehensive control measures based on reducing the density of Aedes mosquitoes were effective in controlling the epidemic.
| S-EPMC3420915 | biostudies-literature
Project description:What is known about this topic?Coronavirus disease 2019 (COVID-19) is widespread globally. In China, COVID-19 has been well controlled and has appeared only in importation-related cases. Local epidemics occur sporadically in China and have been contained relatively quickly.What is added by this report?Epidemiological investigation with genome sequence traceability analysis showed that the first case of COVID-19 in Nangong City acquired infection from a confirmed case from Shijiazhuang City; infection subsequently led to 76 local cases. All cases were associated with the index case, and most were located in Fenggong Street and did not spread outside of Nangong City. The main routes of transmission were family clusters, intra-unit transmission, and nosocomial transmission.What are the implications for public health practice?This study highlights new techniques for rapidly tracing cases and identifying COVID-19 transmission chains. The different epidemiological characteristics in Nangong City, from the earliest stages of the outbreak, suggest that allocation of health sources for prevention and treatment were reasonable. Preventing transmission within medical institutions and isolation facilities and strengthening management in the community should be priorities for COVID-19 control during a city lockdown.
| S-EPMC8422181 | biostudies-literature
Project description:A disease outbreak with dengue-like symptoms was reported in Guangdong Province, China, in October 2010. Testing results confirmed that the pathogen causing the outbreak was chikungunya virus. Phylogenic analysis indicated that this virus was a member of the Indian Ocean clade of the East/Center/South African subgroup of chikungunya virus.
| S-EPMC3309566 | biostudies-literature
Project description:One week after second vaccinations were administered, an outbreak of B.1.1.7 lineage severe acute respiratory syndrome coronavirus 2 infections occurred in a long-term care facility in Berlin, Germany, affecting 16/20 vaccinated and 4/4 unvaccinated residents. Despite considerable viral loads, vaccinated residents experienced mild symptoms and faster time to negative test results.
| S-EPMC8314829 | biostudies-literature
Project description: Not available
| S-EPMC8392896 | biostudies-literature
Project description:Health-risk assessments of temperature are central to determine total non-accidental human mortality; however, few studies have investigated the effect of temperature on accidental human mortality. We performed a time-series study combined with a distributed lag non-linear model (DLNM) to quantify the non-linear and delayed effects of daily mean temperature on accidental human mortality between 2013 and 2017 in Shenzhen, China. The threshold for effects of temperature on accidental human mortality occurred between 5.6?°C and 18.5?°C. Cold exposures, but not hot exposures, were significantly associated with accidental human mortality. All of the observed groups were susceptible to cold effects, with the strongest effects presented in females (relative risk [RR]: 3.14, 95% confidence interval (CI) [1.44-6.84]), followed by poorly educated people (RR: 2.63, 95% CI [1.59-4.36]), males (RR: 1.79, 95% CI [1.10-2.92]), and well-educated people (RR: 1.20, 95% CI [0.58-2.51]). Pooled estimates for cold effects at a lag of 0-21 days (d) were also stronger than hot effects at a lag of 0-2 d. Our results indicate that low temperatures increased the risk of accidental human mortality. Females and poorly educated people were more susceptible to the low temperatures. These findings imply that interventions which target vulnerable populations during cold days should be developed to reduce accidental human mortality risk.
| S-EPMC7242478 | biostudies-literature
Project description:On January 5 2021, Ecuadorian COVID-19 genomic surveillance program detected a suspicious case of the B.1.1.7 lineage (alpha variant) of SARS-CoV-2 in Los Rios province, later confirmed by genome sequencing. The patient travelled from the UK by the end of December 2020. By contact tracing, several new cases were detected confirming B.1.1.7 transmission and spreading in Ecuador.
| S-EPMC8664343 | biostudies-literature
Project description:During 2018-2019, a severe human adenovirus (HAdV) infection outbreak occurred in southern China. Here, we screened 18 respiratory pathogens in 1704 children (≤ 14 years old) hospitalized with acute respiratory illness in Guangzhou, China, in 2019. In total, 151 patients had positive HAdV test results; 34.4% (52/151) of them exhibited severe illness. HAdV infection occurred throughout the year, with a peak in summer. The median patient age was 3.0 (interquartile range: 1.1-5.0) years. Patients with severe HAdV infection exhibited increases in 12 clinical indexes (P ≤ 0.019) and decreases in four indexes (P ≤ 0.007), compared with patients exhibiting non-severe infection. No significant differences were found in age or sex distribution according to HAdV infection severity (P > 0.05); however, the distributions of comorbid disease and HAdV co-infection differed according to HAdV infection severity (P < 0.05). The main epidemic types were HAdV-3 (47.0%, 71/151) and HAdV-7 (46.4%, 70/151). However, the severe illness rate was significantly higher in patients with HAdV-7 (51.4%) than in patients with HAdV-3 (19.7%) and other types of HAdV (20%) (P < 0.001). Sequencing analysis of genomes/capsid genes of 13 HAdV-7 isolates revealed high similarity to previous Chinese isolates. A representative HAdV-7 isolate exhibited a similar proliferation curve to the curve described for the epidemic HAdV-3 strain Guangzhou01 (accession no. DQ099432) (P > 0.05); the HAdV-7 isolate exhibited stronger virulence and infectivity, compared with HAdV-3 (P < 0.001). Overall, comorbid disease, HAdV co-infection, and high virulence and infectivity of HAdV-7 were critical risk factors for severe HAdV infection; these data can facilitate treatment, control, and prevention of HAdV infection.
| S-EPMC9243629 | biostudies-literature
Project description: Not available
| S-EPMC8392786 | biostudies-literature
Project description:Within 5 weeks in 2021, B.1.1.7 became the dominant severe acute respiratory syndrome coronavirus 2 lineage at an outpatient testing site in Berlin, Germany. Compared with outpatients with wild-type virus infection, patients with B.1.1.7 had similar cycle threshold values, more frequent sore throat and travel history, and less frequent anosmia/ageusia.
| S-EPMC8237906 | biostudies-literature