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. 2022 Nov 3:13:1030545.
doi: 10.3389/fmicb.2022.1030545. eCollection 2022.

Surveillance of avian influenza viruses in live bird markets of Shandong province from 2013 to 2019

Ti Liu  1 , Yousong Peng  2 , Julong Wu  1 , Shangwen Lu  2 , Yujie He  1 , Xiyan Li  3 , Lin Sun  1 , Shaoxia Song  1 , Shengyang Zhang  1 , Zhong Li  1 , Xianjun Wang  1 , Shu Zhang  1 , Mi Liu  4 , Zengqiang Kou  1
Affiliations

Surveillance of avian influenza viruses in live bird markets of Shandong province from 2013 to 2019

Ti Liu et al. Front Microbiol. .

Abstract

Avian influenza viruses (AIVs) seriously affect the poultry industry and pose a great threat to humans. Timely surveillance of AIVs is the basis for preparedness of the virus. This study reported the long-term surveillance of AIVs in the live bird market (LBM) of 16 cities in Shandong province from 2013 to 2019. A total of 29,895 samples were obtained and the overall positive rate of AIVs was 9.7%. The H9 was found to be the most predominant subtype in most of the time and contributed most to the monthly positve rate of AIVs as supported by the univariate and multivariate analysis, while H5 and H7 only circulated in some short periods. Then, the whole-genome sequences of 62 representative H9N2 viruses including one human isolate from a 7-year-old boy in were determined and they were genetically similar to each other with the median pairwise sequence identities ranging from 0.96 to 0.98 for all segments. The newly sequenced viruses were most similar to viruses isolated in chickens in mainland China, especially the provinces in Eastern China. Phylogenetic analysis showed that these newly sequenced H9N2 viruses belonged to the same clade for all segments except PB1. Nearly all of these viruses belonged to the G57 genotype which has dominated in China since 2010. Finally, several molecular markers associated with human adaptation, mammalian virulence, and drug resistance were identified in the newly sequenced H9N2 viruses. Overall, the study deepens our understanding of the epidemic and evolution of AIVs and provides a basis for effective control of AIVs in China.

Keywords: H9N2 AIV; avian influenza viruses; epidemic; genotypes; surveillance.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Surveillance of AIVs in LBMs of Shandong province from 2013 to 2019. (A) The number of samples and positive rates of AIVs by city in Shandong province. The cities were colored by the positive rate. The numbers in parentheses referred to the number of samples surveyed in the city. (B) The monthly positive rate of different HA subtypes or subtype combinations of influenza A viruses.
Figure 2
Figure 2
Pairwise sequence identities of each segment between newly sequenced H9N2 viruses.
Figure 3
Figure 3
The phylogeny of H9N2 viruses on each segment. The newly sequenced H9N2 viruses were colored in red in the trees. The human isolate was marked with blue stars. The details of these trees were shown in Supplementary Figure S1.
Figure 4
Figure 4
The host, isolation location and year composition of the neighbors of newly sequenced H9N2 viruses isolated in the environment.
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