New Threats from H7N9 Influenza Virus: Spread and Evolution of High- and Low-Pathogenicity Variants with High Genomic Diversity in Wave Five

Abstract

H7N9 virus has caused five infection waves since it emerged in 2013. The highest number of human cases was seen in wave 5; however, the underlying reasons have not been thoroughly elucidated. In this study, the geographical distribution, phylogeny, and genetic evolution of 240 H7N9 viruses in wave 5, including 35 new isolates from patients and poultry in nine provinces, were comprehensively analyzed together with strains from first four waves. Geographical distribution analysis indicated that the newly emerging highly pathogenic (HP) and low-pathogenicity (LP) H7N9 viruses were cocirculating, causing human and poultry infections across China. Genetic analysis indicated that dynamic reassortment of the internal genes among LP-H7N9/H9N2/H6Ny and HP-H7N9, as well as of the surface genes, between the Yangtze and Pearl River Delta lineages resulted in at least 36 genotypes, with three major genotypes (G1 [A/chicken/Jiangsu/SC537/2013-like], G3 [A/Chicken/Zhongshan/ZS/2017-like], and G11 [A/Anhui/40094/2015-like]). The HP-H7N9 genotype likely evolved from G1 LP-H7N9 by the insertion of a KRTA motif at the cleavage site (CS) and then evolved into 15 genotypes with four different CS motifs, including PKGR/G, PKGR/G, PKRR/G, and PKRR/G. Approximately 46% (28/61) of HP strains belonged to G3. Importantly, neuraminidase (NA) inhibitor (NAI) resistance (R292K in NA) and mammalian adaptation (e.g., E627K and A588V in PB2) mutations were found in a few non-human-derived HP-H7N9 strains. In summary, the enhanced prevalence and diverse genetic characteristics that occurred with mammalian-adapted and NAI-resistant mutations may have contributed to increased numbers of human infections in wave 5. The highest numbers of human H7N9 infections were observed during wave 5 from October 2016 to September 2017. Our results showed that HP-H7N9 and LP-H7N9 had spread virtually throughout China and underwent dynamic reassortment with different subtypes (H7N9/H9N2 and H6Ny) and lineages (Yangtze and Pearl River Delta lineages), resulting in totals of 36 and 3 major genotypes, respectively. Notably, the NAI drug-resistant (R292K in NA) and mammalian-adapted (e.g., E627K in PB2) mutations were found in HP-H7N9 not only from human isolates but also from poultry and environmental isolates, indicating increased risks for human infections. The broad dissemination of LP- and HP-H7N9 with high levels of genetic diversity and host adaptation and drug-resistant mutations likely accounted for the sharp increases in the number of human infections during wave 5. Therefore, more strategies are needed against the further spread and damage of H7N9 in the world.

Recombinant hemagglutinin produced from Chinese Hamster Ovary (CHO) stable cell clones and a PELC/CpG combination adjuvant for H7N9 subunit vaccine development

“…The fifth epidemic wave in 2016-2017 was the most severe with 759 confirmed human cases, probably due to the geographical spread of the virus from eastern China throughout the whole country [7]. More importantly, the H7N9 viruses isolated during the fifth epidemic wave have evolved into two distinct lineages, namely, the Yangtze River Delta and Pearl River Delta lineages [8][9][10]. Some of these fifth-epidemic-wave H7N9 isolates of Yangtze River Delta lineage carried polybasic amino acids at the HA1/HA2 cleavage site, a characteristic of highly pathogenic avian influenza viruses [11].…”

A novel H7N3 reassortant originating from the zoonotic H7N9 highly pathogenic avian influenza viruses that has adapted to ducks

“…Based on phylogenetic analysis of the HA gene, the zoonotic H7N9 AIVs have been classified into two main lineages, the Yangtze River Delta (YRD) and Pearl River Delta (PRD) lineages; the first H7N9 HPAIV was derived from the YRD lineage (D. Wang et al, ; Yang et al, ). Recent studies have shown that the YRD lineage was dominant in the distribution of zoonotic H7N9 AIVs in China (Qi et al, ; Quan et al, ).…”

Emergence of waterfowl‐originated gene cassettes in HPAI H7N9 viruses caused severe human infection in Fujian, China

“…Previous studies showed that the internal genes of the HPAI H7N9 viruses were derived from H7N9/H9N2 viruses; however, the internal genes of these HPAI H7 viruses, including the human virus, have three sources, H7N9/H9N2 from poultry, H5N6, and the Eurasian wild‐bird gene pool (Figure C‐H). PB2, PB1, PA, and NS genes were derived from H7N9/H9N2 or the Eurasian wild‐bird gene pool, while the NP gene was from H7N9/H9N2 from poultry, H5N6, or the Eurasian wild‐bird gene pool.…”

“…The HPAI H7N9 virus might have emerged in mid‐2016, according to a molecular clock model . Frequent reassortments of internal genes among H7N9 and H9N2 viruses have been observed in the HPAI H7N9 viruses, similar to those in the LPAI H7N9 viruses . As of December 19, 2018, twenty‐seven outbreaks in poultry have been reported in 12 provinces in China, about 900 000 poultry have been culled (http://www.oie.int).…”