| ProjectThis study was based on the 13th Five-Year Plan Major Project on Pathogenic Spectrum of Acute Febrile Infectious Diseases in Guangdong Province and the group’s previous research,analyzing the pathogenic spectrum of adult patients with respiratory tract infections under the normal management of SARS-CoV-2 pneumonia prevention and control in 2020-2021;The whole genome sequences of HCoV-HKU1,229E,OC43 and NL63 were obtained by sequencing positive samples or isolates of low pathogenic HCoVs using macro-genome sequencing technology,and the phylogenetic trees of HCoV-HKU1,229E,OC43 and NL63 were constructed to elucidate the evolutionary variation of HCoV-HKU1,229E,OC43 and NL63.Methods1.Using Guangdong Second People’s Hospital as the sentinel hospital,BALF and NPS were collected from patients with respiratory tract infections in this hospital from 2020.04-2021.11,and the pathogens in the samples were detected by multiplex RT-PCR to analyze the infection characteristics of the pathogenic spectrum of the patients.2.Attempted isolation of coronavirus OC43,NL63,and 229E using LLC-MK2,RD,and 293T cells to obtain virus strains.3.Sequencing of HCoV-HKU1,OC43,NL63,229E based on Nanopore and macro-genome sequencing technologies and analysis of their molecular evolutionary features.Results1.There was no difference between B ALF and NPS of virus and PJ detection,and both bacterial and MP detection rates were higher in BALF than in NPS.K.P had good consistency in detection in both samples,and the consistency in detection of other pathogens was average.2.A total of 409 patients with RTI were included in 2020-2021.The majority of RTI patients were elderly(48.66%),and the pathogen detection rate was higher in males(49.39%)than in females(24.69%).The overall pathogen positivity rate was 73.90%,and the pathogens were mainly viruses and bacteria,with a virus detection rate of 57.21%and a bacteria positivity rate of 38.39%.The top three viral detection rates were EBV(30.56%),CMV(16.38%),and AdV(11.49%);the top three bacterial detection rates were K.P(17.36%);S.A(13.45%),and Hi(8.80%);the infection types were mainly single infections,and the most mixed infections were EV virus mixed with other pathogens.3.Based on the whole genome sequence of HCoV-OC43 obtained by Nanopore triple sequencing,the results of the phylogenetic analysis showed that its genotype was K-type,and more nucleotide and amino acid mutations occurred in the N-terminal Domain and Receptor Binding Domain of the S protein.Conclusions1.BALF is recommended for pathogen detection in patients with bacterial pneumonia and mycoplasma pneumonia,while NPS can be collected for pathogen detection in patients with viral pneumonia.2.Adult RTI patients in Guangzhou were mostly elderly,and men were higher than women,with higher pathogen detection rates and complex and diverse pathogenic infections.The respiratory pathogen spectrum changed after the SARS-CoV-2 pandemic,and the pathogens with higher detection rates were EBV,AdV,CMV,MuV,K.P,S.A,Hi,MP,PJ,etc.while the detection rates of IFVA and IFVB were lower than those before the SARS-CoV-2 pandemic.3.The prevalent genotype of an HCoV-OC43 whole genome sequence in Guangzhou was K-type,and the NTD and RBD of its S protein are mutation-prone regions. |
