Molecular tracking of long-distance transmission events of COVID-19 by lorry drivers in Fujian province
10.3760/cma.j.cn112866-20220907-00193
- VernacularTitle:货车司机远距离传播新型冠状病毒肺炎事件的分子溯源
- Author:
Qi LIN
1
;
Zehui CHEN
;
Zhimiao HUANG
;
Xiaohong ZENG
;
Quwen LI
;
Yuwei WENG
Author Information
1. 福建省疾病预防控制中心 福建省人兽共患病研究重点实验室，福州 350012
- Keywords:
2019 novel coronavirus;
Omicron variant;
Whole-genome sequencing;
Source tracing analysis
- From:
Chinese Journal of Experimental and Clinical Virology
2023;37(1):55-60
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To confirm the cross-provincial long-distance transmission events of Coronavirus Disease 2019 (COVID-19) by lorry drivers, the origin of infections of the cases and the transmission routes were tracked.Methods:Nasopharyngeal swab specimens from five lorry driver cases of COVID-19, found in Zhangzhou city in March, 2022 when the local outbreaks occurred in adjacent Quanzhou city, Fujian province, were collected to perform 2019 novel coronavirus (2019-nCoV) targeted genome amplification and followed by next-generation sequencing. The sequences were submitted to online 2019-nCoV analysis platforms to classify the type of variant and mutation sites. Phylogenetic tree for the viruses were constructed by phylogenetic analysis software. Combined with the epidemiological investigation, the origin of infections of the cases and the transmission routes were deduced.Results:Five complete genome sequences, with 29 770-29 839 bp in length and 99.53% average genomic coverage, of 2019-nCoV were successfully obtained. The viruses were all Omicron variants and further divided into three different subclades of BA.2. Of the five strains of 2019-nCoV, three were highly similar to the viruses of two distinct lineages co-circulated in Quanzhou city during the period of local outbreak of COVID-19, respectively. Phylogenetic analysis also revealed that the viruses from three infected lorry drivers were highly homologous to that from local outbreaks in Quanzhou city. The viruses from the rest two cases had seven to fourteen nucleotide mutations (corresponding to 5-7 amino acid substitutions) when compared with the viruses in local outbreaks in Quanzhou city, which excluded the involvement of the two cases into the transmission chains of local outbreaks. Combined with the field epidemiological investigations, the result revealed that the origin of infection of 2019-nCoV of the two sporadic lorry driver cases was outside of Fujian province.Conclusions:With the aid of high-throughput sequencing and bioinformatics technology combined with field epidemiological investigations, we speculated in this study that at least three origins of infection of 2019-nCoV in five lorry driver cases and cross-provincial long-distance transmission via two sporadic cases infected outside Fujian province when they returned.
