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, 33 (1), 87-95

Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009-2016

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Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009-2016

Yun Luo et al. Virol Sin.

Abstract

Previous studies indicated that fruit bats carry two betacoronaviruses, BatCoV HKU9 and BatCoV GCCDC1. To investigate the epidemiology and genetic diversity of these coronaviruses, we conducted a longitudinal surveillance in fruit bats in Yunnan province, China during 2009-2016. A total of 59 (10.63%) bat samples were positive for the two betacorona-viruses, 46 (8.29%) for HKU9 and 13 (2.34%) for GCCDC1, or closely related viruses. We identified a novel HKU9 strain, tentatively designated as BatCoV HKU9-2202, by sequencing the full-length genome. The BatCoV HKU9-2202 shared 83% nucleotide identity with other BatCoV HKU9 stains based on whole genome sequences. The most divergent region is in the spike protein, which only shares 68% amino acid identity with BatCoV HKU9. Quantitative PCR revealed that the intestine was the primary infection organ of BatCoV HKU9 and GCCDC1, but some HKU9 was also detected in the heart, kidney, and lung tissues of bats. This study highlights the importance of virus surveillance in natural reservoirs and emphasizes the need for preparedness against the potential spill-over of these viruses to local residents living near bat caves.

Keywords: Betacoronavirus; Genetic diversity; Surveillance.

Conflict of interest statement

Conflict of interest

The authors declare that they have no conflict of interest.

Animal and Human Rights Statement

This study was approved by the Animal Ethics Committee of the Wuhan Institute of Virology. All institutional and national guidelines for the care and use of animals were followed.

Figures

Fig. 1
Fig. 1
Map of sampling sites in Yunnan province of China. Red regions indicate the four districts where bat samples were collected.
Fig. 2
Fig. 2
Phylogenetic analysis of the detected coronaviruses in this study. Partial RdRp sequences (A), complete nucleoprotein gene sequences (B), and full-length genomic sequence of BatCoV HKU9-2202 (C) were aligned with corresponding sequences of representative viral species in the genus Betacoronavirus. Phylogenetic trees were constructed using the neighbor-joining method implemented in MEGA7 and bootstrap values calculated from 1000 replicates. The sequence obtained in this study is labeled in color and named by the sample isolate identifier followed by bat species, location, and collection year.
Fig. 2
Fig. 2
Phylogenetic analysis of the detected coronaviruses in this study. Partial RdRp sequences (A), complete nucleoprotein gene sequences (B), and full-length genomic sequence of BatCoV HKU9-2202 (C) were aligned with corresponding sequences of representative viral species in the genus Betacoronavirus. Phylogenetic trees were constructed using the neighbor-joining method implemented in MEGA7 and bootstrap values calculated from 1000 replicates. The sequence obtained in this study is labeled in color and named by the sample isolate identifier followed by bat species, location, and collection year.
Fig. 3
Fig. 3
Tissue distribution of BatCoV HKU9 (A) and GCCDC1 (B) in positive bat samples.

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