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Virol J. 2017 Nov 22;14(1):230. doi: 10.1186/s12985-017-0896-0.

Prevalence and genetic diversity analysis of human coronaviruses among cross-border children.

Liu P1,2, Shi L2, Zhang W3, He J2, Liu C2, Zhao C2, Kong SK4, Loo JFC5,6, Gu D7,8, Hu L9,10.

Author information

1
Department of Health Inspection and Quarantine, School of Public Health, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
2
Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China.
3
Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, People's Republic of China.
4
Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China.
5
Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China. jackyfcloo@cuhk.edu.hk.
6
Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China. jackyfcloo@cuhk.edu.hk.
7
Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China. wanhood@163.com.
8
Shenzhen Academy of Inspection and Quarantine, Shenzhen, 518010, People's Republic of China. wanhood@163.com.
9
Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China. 18307550009@139.com.
10
Shenzhen Academy of Inspection and Quarantine, Shenzhen, 518010, People's Republic of China. 18307550009@139.com.

Abstract

BACKGROUND:

More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted.

METHODS:

A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature > 37.5 °C), from 2014 May to 2015 Dec. Viral nucleic acids were analyzed and sequenced to study the prevalence and genetic diversity of the four human coronaviruses. The statistical significance of the data was evaluated with Fisher chi-square test.

RESULTS:

78 (2.37%; 95%CI 1.8-2.8%) out of 3298 nasopharyngeal swabs specimens were found to be positive for OC43 (36;1.09%), HKU1 (34; 1.03%), NL63 (6; 0.18%) and 229E (2;0.01%). None of SARS or MERS was detected. The HCoVs predominant circulating season was in transition of winter to spring, especially January and February and NL63 detected only in summer and fall. Complex population with an abundant genetic diversity of coronaviruses was circulating and they shared homology with the published strains (99-100%). Besides, phylogenetic evolutionary analysis indicated that OC43 coronaviruses were clustered into three clades (B,D,E), HKU1 clustered into two clades(A,B) and NL63 clustered into two clades(A,B). Moreover, several novel mutations including nucleotides substitution and the insertion of spike of the glycoprotein on the viral surface were discovered.

CONCLUSIONS:

The detection rate and epidemic trend of coronaviruses were stable and no obvious fluctuations were found. The detected coronaviruses shared a conserved gene sequences in S and RdRp. However, mutants of the epidemic strains were detected, suggesting continuous monitoring of the human coronaviruses is in need among cross-border children, who are more likely to get infected and transmit the viruses across the border easily, in addition to the general public.

KEYWORDS:

Cross-border children; Genetic diversity; Human coronaviruses; Molecular epidemiology; Phylogenetic analysis

PMID:
29166910
PMCID:
PMC5700739
DOI:
10.1186/s12985-017-0896-0
[Indexed for MEDLINE]
Free PMC Article

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