Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 - May 2021.

Dan Liang; Tao Wang; Jiao Jiao LI; Da Wei Guan; Guan Ting Zhang; Yu Feng Liang; An An LI; Wen Shan Hong; Li Wang; Meng Lin Chen; Xiao Ling Deng; Feng Juan Chen; Xing Fei Pan; Hong Ling Jia; Chun Liang Lei; Chang Wen KE

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Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province, China, October 2020 - May 2021.

Author: Dan LIANG ^{1
,

2
,

3} ; Tao WANG ⁴ ; Jiao Jiao LI ⁵ ; Da Wei GUAN ³ ; Guan Ting ZHANG ⁶ ; Yu Feng LIANG ⁷ ; An An LI ⁷ ; Wen Shan HONG ⁴ ; Li WANG ⁶ ; Meng Lin CHEN ⁸ ; Xiao Ling DENG ³ ; Feng Juan CHEN ⁵ ; Xing Fei PAN ⁹ ; Hong Ling JIA ¹⁰ ; Chun Liang LEI ⁵ ; Chang Wen KE ^{2
,

7
,

11
,

12
,

13}
Author Information

1. Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, Guangdong, China
2. Guangzhou National Laboratory, Guangzhou 510700, Guangdong, China
3. Guangdong Provincial Center for disease control and prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, Guangdong, China.
4. Shantou University Medical College, Shantou 515041, Guangdong, China.
5. Guangzhou Eighth People's Hospital, Guangzhou 510030, Guangdong, China.
6. School of public health, Sun Yat-sen University, Guangzhou 510080, Guangdong, China.
7. School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
8. Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou 510535, Guangdong, China.
9. Department of Infectious Diseases, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong, China.
10. Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China.
11. Guangdong Provincial Center for disease control and prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou 511430, Guangdong, China
12. Shantou University Medical College, Shantou 515041, Guangdong, China
13. School of public health, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
Publication Type:Journal Article
Keywords: Next-Generation sequencing; Phylogenetic tree; Severe acute respiratory syndrome coronavirus 2; Variants
MeSH: Amino Acids; COVID-19/epidemiology*; Genomics; Humans; Mutation; Phylogeny; SARS-CoV-2/genetics*
From: Biomedical and Environmental Sciences 2022;35(5):393-401
CountryChina
Language:English
Abstract: Objective:The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARS-CoV-2 from imported cases admitted to the Guangzhou Eighth People's Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019 (COVID-19). The SARS-CoV-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated.
Methods:In total, 177 throat swab samples were obtained from COVID-19 patients (from October 2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-CoV-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants.
Results:We observed that the imported cases mainly occurred after January 2021, peaking in May 2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage (Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1a (ORF1a) protein had the highest mutation density at the nucleotide level, and the D614G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7b, and ORF9b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in PubMed among all missense mutations.
Conclusion:These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-CoV-2 in Guangdong Province, China.