Exploring utility of genomic epidemiology to trace origins of highly pathogenic influenza A/H7N9 in Guangdong.

Ru Bai Reina S Sikkema Bas B Oude Munnink Cong Rong Li Jie Wu Lirong Zou Yi Jing Jing Lu Run Yu Yuan Ming Liao Marion Koopmans Chang-Wen Ke

Virus Evol

Department of Pathogenic Microbiolgy, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.

Published: July 2020

The first instance of highly pathogenic influenza A/H7N9 was identified in Guangdong in January 2017, prompting an investigation into its spread and characteristics from 2016 to 2017 by sequencing 297 viruses.* -
During this period, three lineages of A/H7N9 viruses were found to co-circulate in Guangdong: a local low pathogenic lineage (13%), a newly imported low pathogenic lineage (23%), and a highly pathogenic lineage (64%).* -
The study also revealed that the highly pathogenic lineage likely originated from previously circulating low pathogenic strains, and that there is limited spread of the highly pathogenic A/H7N9 to other provinces, with different cleavage site variants present in poultry

The first highly pathogenic (HP) influenza A/H7N9 was reported in Guangdong in January 2017. To investigate the emergence and spread of HP A/H7N9 in Guangdong province, we sequenced 297 viruses (58 HP A/H7N9, 19 low pathogenic (LP) A/H7N9, and 220 A/H9N2) during 2016-2017. Our analysis showed that during the fifth wave, three A/H7N9 lineages were co-circulating in Guangdong: the local LP Pearl River Delta (PRD) lineage (13%), the newly imported LP Yangtze River Delta (YRD) lineage (23%), and the HP YRD lineage (64%). Previously circulating YRD-lineage LP during the third wave evolved to the YRD-lineage HP A/H7N9 in Guangdong. All YRD-lineage LP detected during the fifth wave most likely originated from newly imported viruses into Guangdong. Genotype comparison of HP A/H7N9 suggests limited outward spread of HP A/H7N9 to other provinces. The distribution of HP A/H7N9 cleavage site variants on live poultry markets differed from that found in humans, suggesting a V1-type cleavage site may facilitate human infections.

Download full-text PDF	Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758296	PMC
http://dx.doi.org/10.1093/ve/veaa097	DOI Listing

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