Spatiotemporal Associations and Molecular Evolution of Highly Pathogenic Avian Influenza A H7N9 Virus in China from 2017 to 2021

Evolution and distribution of rabies viruses from a panorama view

Rabies kills more than 59,000 people annually, mainly in developing countries. Previous studies on the evolution and distribution of rabies viruses (RABVs) were scattered. Here, we explore the evolution and distribution of this deadly virus from a novel panorama view. Multiple bioinformatic software tools were employed to analyze the phylogenetic diversity, evolution, spatiotemporal, and distribution of RABVs. The analyses were based on 1,202 qualified full-length genomes of RABVs and numerous literatures. Of the 10 distinct phylogenetic clades of RABV that we identified, more frequent intra- and inter-clade recombination occurs in the sequences of Asian-SEA, Arctic, and Cosmopolitan clades isolated from China, while according to existing sequence information, RABV might originate from bats (posterior probability, PP = 0.75, PP = 0.60 inferred from N and L genes, separately) in North America (PP = 0.57, PP = 0.62 inferred from N and L genes, separately). Due to the difference in evolutionary rate of N (2.22 × 10-4 subs/site/year, 95% HPD 1.99-2.47 × 10-4 subs/site/year) and L genes (1.67 × 10-4 subs/site/year, 95% HPD 1.59-1.74 × 10-4 subs/site/year), the root age was 1,406.6 (95% HPD 1,291.2-1,518.2) and 1,122.7 (95% HPD 1,052.4-1,193.9) inferred from N and L genes, separately. Among other findings, Mephitidae plays an important role in the interspecific transmission and communication of RABV, which we found tends to spread to populations genetically proximate to the host. We also identified amino acids under positive selection in different genes of different clades as well as single nucleotide variation sites important for different lineages. IMPORTANCE Rabies virus is widely distributed all over the world, and wild animals are its largest potential reservoir. Our study offers a panorama view about evolution and distribution of rabies viruses and emphasizes the need to monitor the transmission dynamics of animal rabies.

Characterization of an H7N9 Influenza Virus Isolated from Camels in Inner Mongolia, China

The H7N9 subtype of influenza virus can infect birds and humans, causing great losses in the poultry industry and threatening public health worldwide. However, H7N9 infection in other mammals has not been reported yet. In the present study, one H7N9 subtype influenza virus, A/camel/Inner Mongolia/XL/2020 (XL), was isolated from the nasal swabs of camels in Inner Mongolia, China, in 2020. Sequence analyses revealed that the hemagglutinin cleavage site of the XL virus was ELPKGR/GLF, which is a low-pathogenicity molecular characteristic. The XL virus had similar mammalian adaptations to human-originated H7N9 viruses, such as the polymerase basic protein 2 (PB2) Glu-to-Lys mutation at position 627 (E627K) mutation, but differed from avian-originated H7N9 viruses. The XL virus showed a higher SA-α2,6-Gal receptor-binding affinity and better mammalian cell replication than the avian H7N9 virus. Moreover, the XL virus had weak pathogenicity in chickens, with an intravenous pathogenicity index of 0.01, and intermediate virulence in mice, with a median lethal dose of 4.8. The XL virus replicated well and caused clear infiltration of inflammatory cells and increased inflammatory cytokines in the lungs of mice. Our data constitute the first evidence that the low-pathogenicity H7N9 influenza virus can infect camels and therefore poses a high risk to public health. IMPORTANCE H5 subtype avian influenza viruses can cause serious diseases in poultry and wild birds. On rare occasions, viruses can cause cross-species transmission to mammalian species, including humans, pigs, horses, canines, seals, and minks. The H7N9 subtype of the influenza virus can also infect both birds and humans. However, viral infection in other mammalian species has not been reported yet. In this study, we found that the H7N9 virus could infect camels. Notably, the H7N9 virus from camels had mammalian adaption molecular markers, including altered receptor-binding activity on the hemagglutinin protein and an E627K mutation on the polymerase basic protein 2 protein. Our findings indicated that the potential risk of camel-origin H7N9 virus to public health is of great concern.

Reintroduction of highly pathogenic avian influenza A H7N9 virus in southwestern China

Highly pathogenic (HP) avian influenza A H7N9 virus has emerged in China since 2016. In recent years, it has been most prevalent in northern China. However, several strains of HP H7N9 reappeared in southwestern China (Yunnan Province) in 2021. As a result, we are wondering if these viruses have re-emerged in situ or been reintroduced. Here, we present phylogenetic evidence that the HP H7N9 viruses isolated in Yunnan emigrated from northern to southwestern China in 2020. The northern subregion of China has become a novel epicenter in HP H7N9 dissemination. Meanwhile, a cleavage motif re-emerged due to the T341I mutation, implying a parallel evolution. This cross-region transmission, which originated in non-adjacent provinces and traveled a great geographic distance in an unknown way, indicates that HP H7N9 dissemination did not halt in 2020, even under the shadow of the COVID-19 pandemic. Additional surveillance studies in poultry are required to determine the HP H7N9 virus's geographic distribution and spread.

A dominant internal gene cassette of high pathogenicity avian influenza H7N9 virus raised since 2018

The zoonotic H7N9 avian influenza virus emerged with the H9N2-origin internal gene cassette. Previous studies have reported that genetic reassortments with H9N2 were common in the first five human H7N9 epidemic waves. However, our latest work found that the circulating high pathogenicity H7N9 virus has established a dominant internal gene cassette and has decreased the frequency of reassortment with H9N2 since 2018. This dominant cassette of H7N9 was distinct from the cocirculating H9N2, although they shared a common ancestor. As a result, we suppose that this dominant cassette may benefit the viral population fitness and promote its continuous circulation in chickens.