Etiological identification and genetic source tracking of a cluster of cases with fever during the period of regular prevention and control of COVID-19 epidemic
Zhongguo Bingdubing Zazhi = Chinese Journal of Viral Diseases
; 13(2):120, 2023.
Article
in English
| ProQuest Central | ID: covidwho-2314222
ABSTRACT
Objective To identify the pathogen and track the genetic source of a cluster of cases with fever in a kindergarten in Fengtai district during the normalization of COVID-19 prevention and control in Beijing.Methods A descriptive analysis method was used to investigate this cluster of cases with fever in April 2021.Pharyngeal swabs were collected and viral nucleic acid was extracted, real-time PCR was performed to identify SARS-CoV-2 and other common respiratory virus. G gene of human metapneumovirus(hMPV) was amplified by RT-PCR and was then sequenced. BioEdit was used for G gene sequence analysis and the Neighbor-Joining model in MEGA 5. 0 software was used to construct the phylogenic tree of G gene. Results A total of 16 cases were reported in one class with the incidence of 53. 3%(16/30) during 8 days of a cluster outbreak. All pharyngeal swabs collected from 12 cases were tested SARS-CoV-2 negative, six were found to be hMPV positive by multiplex-PCR, and one was positive for both human adenovirus and hMPV. Full-length sequences of G genes were obtained from 2 strains of hMPV. Sequence analysis showed that both strains were hMPV B2 and the nucleic acid homology of G gene was 96. 73%-98. 01% with strains from Japan(LC337940, LC337935, LC1922349) in 2016 and over 98. 40%with strains from Shandong(OL625642, OL625644) in 2019, Henan MN944096 in 2019.Compared with the amino acid sequence of hMPV-B2 reference strain(AY297748), six amino acid insertions containing EKEKEK were identified between 161-166 amino acid location and N-glycosylation of G protein analysis showed that the two strains had four N-glycosylation sites. Conclusions The leading pathogen for this cluster outbreak is found to be hMPV-B2, which are highly homologous with strains from Japan, Shandong and Henan. Therefore, a non-stop surveillance of hMPV is necessary during the normalization control and prevention period for COVID-19.
Alternative Medicine; Epidemics; Pathogens; Nucleic acids; Amino acids; Sequence analysis; Severe acute respiratory syndrome coronavirus 2; Disease control; Amino acid sequence; Fever; COVID-19; Outbreaks; Clusters; Viral diseases; Prevention; Glycosylation; Viruses; Kindergarten; Pharynx; Homology; Coronaviruses; Strains (organisms); Japan
Full text:
Available
Collection:
Databases of international organizations
Database:
ProQuest Central
Type of study:
Etiology study
/
Observational study
Language:
English
Journal:
Zhongguo Bingdubing Zazhi = Chinese Journal of Viral Diseases
Year:
2023
Document Type:
Article
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