The genetic characteristics of human coronavirus OC43 in cases of severe acute respiratory infection
Chinese Journal of Virology
; 36(2):236-245, 2020.
Article
in Chinese
| GIM | ID: covidwho-1970921
ABSTRACT
Human coronavirus (HCoV) is one of the important pathogens of human respiratory tract infection. in order to clarify the genetic characteristics of HCoV-0C43 in severe acute respiratory infection (SARI) cases at the molecular level, a total of 374 samples obtained from SARI cases in Henan Province, China, in 2019 were screened for the nucleic acids of HCoV -0C43 by real - time polymerase chain reaction (PCR). Reverse transcription-PCR amplification and sequencing of spike (5) RNA-dependent RNA polymerase (12dRp) and nucleocapsid (N) was carried out in samples with positive detection of the nucleic acids of FICoV-0C43. Upon. combination Of 42 representative sequences obtained from the GenBank database, phylogenetic trees were constructed based on three full-length sequences of S, RdRp and N genes. The FICoV -0C43 strains obtained from SARI cases were genotyped and the genetic characteristics of three target genes were analyzed. Variations in the amino acids of S protein (an important antigen of HCoV-0C43) were also analyzed. Results showed that 15 (4.01%) out of 374 samples from SARI cases were positive for FICoV-0C43, and the full-length sequences of S, RdRp and N genes were obtained from 4 out of 15 samples. Based on the phylogenetic trees of these three target genes, three strains belonged to the U genotype and one strain belonged to the H genotype. Analysis of the amino - acid variations of S protein indicated that there were three special sites of amino - acid variation (L272P, P5165 and 5902A) among the G genotype strains in 2019, including the three strains in our study and USA /MN306041/SC0810/2019. Another special variation in amino acids (N484D) was found among the II genotype strains in 2019, including one strain in our study and USA/MN306043/SC0841/2019. Based on the genotype identification and genetic characteristics of HCoV-0C43 strains from SARI cases in Henan Province in 2019, baseline data for the study of molecular epidemiology of HCoV 0C43 in China have been provided.
genes; nucleotide sequences; human diseases; genetic variation; epidemiology; man; Severe acute respiratory syndrome coronavirus 2; Human coronavirus OC43; China; Homo; Hominidae; primates; mammals; vertebrates; Chordata; animals; eukaryotes; APEC countries; East Asia; Asia; high Human Development Index countries; upper-middle income countries; Severe acute respiratory syndrome-related coronavirus; Betacoronavirus; Coronavirinae; Coronaviridae; Nidovirales; positive-sense ssRNA Viruses; ssRNA Viruses; RNA Viruses; viruses; Betacoronavirus 1; DNA sequences; People's Republic of China; SARS-CoV-2; genetic variability; genotypic variability; genotypic variation
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Collection:
Databases of international organizations
Database:
GIM
Language:
Chinese
Journal:
Chinese Journal of Virology
Year:
2020
Document Type:
Article
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