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Virus Evol
. 2020 Dec 18;6(2):veaa097.
doi: 10.1093/ve/veaa097. eCollection 2020 Jul.
Exploring utility of genomic epidemiology to trace origins of highly pathogenic influenza A/H7N9 in Guangdong
Ru Bai, Reina S Sikkema 1 , Bas B Oude Munnink 1 , Cong Rong Li 2 , Jie Wu 3 , Lirong Zou 3 , Yi Jing 4 , Jing Lu 3 , Run Yu Yuan 3 , Ming Liao 2 , Marion Koopmans 1 , Chang-Wen Ke 3
Affiliations
- PMID: 33391821
- PMCID: PMC7758296
- DOI: 10.1093/ve/veaa097
Abstract
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.
Keywords: Guangdong; genomic epidemiology; highly pathogenic influenza A/H7N9; origins.