First genome report and analysis of chicken H7N9 influenza viruses with poly-basic amino acids insertion in the hemagglutinin cleavage site

Abstract

We report the full-length sequence of two chicken source influenza A (H7N9) viruses found in Guangdong live poultry market (LPM) during the most recent wave of human infections (from October 2016 to the present time). These viruses carry insertion of poly-basic amino acids (KGKRTAR/G) at the protease cleavage site of the HA protein, which were previously found in the highly pathogenic (HP) human influenza A (H7N9) [IAV(H7N9)] strains. Phylogenetic analysis of these two novel avian influenza viruses (AIVs) suggested that their genomes reassorted between the Yangtze River Delta (YRD) and Pearl River Delta (PRD) clades. Molecular clock analysis indicated that they emerged several months before the HP human strains. Collectively, our results suggest that IAV(H7N9) viruses evolve in chickens through antigenic drift to include a signature HP sequence in the HA gene, which highlights challenges in risk assessment and public health management of IAV(H7N9) infections at the human-animal interface.

The Protective Effects of the A/ZJU01/ PR8/2013 Split H7N9 Avian Influenza Vaccine Against Highly Pathogenic H7N9 in BALB/c Mice

“…Worryingly, it involved more confirmed cases than previous epidemics [18, 19]. The isolation of drug-resistant viruses and emergence of highly pathogenic strains in chickens and humans has become a domestic and international concern [7, 20, 21]. …”

The Pandemic Threat of Emerging H5 and H7 Avian Influenza Viruses

“…From December 2016 until September 2017, a total of 32 human infections with highly pathogenic H7N9 were reported [ 147 , 148 , 149 ], and all of the highly pathogenic variants belong to the Yangtze River Delta lineage [ 117 ]. Highly pathogenic H7N9 viruses were also isolated from chickens, suggesting the virus originated in these animals [ 116 , 117 , 150 , 151 ].…”

Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites

“…The optimal Waterman-Smith alignments of the insertions of 9-12 nucleotides in H7 HA segments of HPAI viruses from Italy, 1999Italy, -2001 (Banks et al 2001;Monne et al 2014), England, 2015 (H7N7) (Abdelwhab et al 2016), China, 2017 (H7N9) (Chen et al 2017) or laboratoryadapted H7N7 strain SC35 (Li et al 1990) with chicken rRNAs and other segments of the corresponding strains contained mismatches and therefore did not allow one to draw conclusions on the origins of these insertions. Using the insertions of 9 nucleotides for BLAST searches in the chicken genome was not possible because such short queries were rejected by the BLAST program.…”