Rapid Evolution of H7N9 Highly Pathogenic Viruses that Emerged in China in 2017

Pigs are considered as important hosts or “mixing vessels” for the generation of pandemic influenza viruses Systematic surveillance of influenza viruses in pigs is essential for early warning and preparedness for the next potential pandemic Here, we report on an influenza virus surveillance of pigs from 2011 to 2018 in China, and identify a recently emerged genotype 4 (G4) reassortant Eurasian avian-like (EA) H1N1 virus, which bears 2009 pandemic (pdm/09) and triple-reassortant (TR)-derived internal genes and has been predominant in swine populations since 2016 Similar to pdm/09 virus, G4 viruses bind to human-type receptors, produce much higher progeny virus in human airway epithelial cells, and show efficient infectivity and aerosol transmission in ferrets Moreover, low antigenic cross-reactivity of human influenza vaccine strains with G4 reassortant EA H1N1 virus indicates that preexisting population immunity does not provide protection against G4 viruses Further serological surveillance among occupational exposure population showed that 104% (35/338) of swine workers were positive for G4 EA H1N1 virus, especially for participants 18 y to 35 y old, who had 205% (9/44) seropositive rates, indicating that the predominant G4 EA H1N1 virus has acquired increased human infectivity Such infectivity greatly enhances the opportunity for virus adaptation in humans and raises concerns for the possible generation of pandemic viruses

https://www.pnas.org/content/pnas/117/29/17204.full.pdf

Prevalent Eurasian avian-like H1N1 swine influenza virus with 2009 pandemic viral genes facilitating human infection

Influenza A viruses (IAVs) possess a great zoonotic potential as they are able to infect different avian and mammalian animal hosts, from which they can be transmitted to humans. This is based on the ability of IAV to gradually change their genome by mutation or even reassemble their genome segments during co-infection of the host cell with different IAV strains, resulting in a high genetic diversity. Variants of circulating or newly emerging IAVs continue to trigger global health threats annually for both humans and animals. Here, we provide an introduction on IAVs, highlighting the mechanisms of viral evolution, the host spectrum, and the animal/human interface. Pathogenicity determinants of IAVs in mammals, with special emphasis on newly emerging IAVs with pandemic potential, are discussed. Finally, an overview is provided on various approaches for the prevention of human IAV infections.

Zoonotic Potential of Influenza A Viruses: A Comprehensive Overview.

How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study.

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The phylogenomics of evolving virus virulence

The 1918 H1N1 Spanish Influenza pandemic was the most severe pandemic in modern history. Unlike more recent pandemics, most of the 1918 H1N1 virus' genome was derived directly from an avian influenza virus. Recent avian-origin H5 A/goose/Guangdong/1/1996 (GsGd) and Asian H7N9 viruses have caused several hundred human infections with high mortality rates. While these viruses have not spread beyond infected individuals, if they evolve the ability to transmit efficiently from person-to-person, specifically via the airborne route, they will initiate a pandemic. Therefore, this review examines H5 GsGd and Asian H7N9 viruses that have caused recent zoonotic infections with a focus on viral properties that support airborne transmission. Several GsGd H5 and Asian H7N9 viruses display molecular changes that potentiate transmission and/or exhibit ability for limited transmission between ferrets. However, the hemagglutinin of these viruses is unstable; this likely represents the most significant obstacle to the emergence of a virus capable of efficient airborne transmission. Given the global disease burden of an influenza pandemic, continued surveillance and pandemic preparedness efforts against H5 GsGd and Asian lineage H7N9 viruses are warranted.

/pdf/the-pandemic-threat-of-emerging-h5-and-h7-avian-influenza-3gbkn1vzit.pdf

The Pandemic Threat of Emerging H5 and H7 Avian Influenza Viruses.

The novel low-pathogenic avian influenza A H7N9 viruses (LPAI H7N9 viruses) have been a threat to public health since their emergence in 2013 because of the high rates of mortality and morbidity that they cause. Recently, highly pathogenic variants of these avian influenza A H7N9 viruses (HPAI H7N9 viruses) have emerged and caused human infections and outbreaks among poultry in mainland China. However, it is still unclear how the HPAI H7N9 virus was generated and how it evolved and spread in China. Here, we show that the ancestor virus of the HPAI H7N9 viruses originated in the Yangtze River Delta region and spread southward to the Pearl River Delta region, possibly through live poultry trade. After introduction into the Pearl River Delta region, the origin LPAI H7N9 virus acquired four amino acid insertions in the hemagglutinin (HA) protein cleavage site and mutated into the HPAI H7N9 virus in late May 2016. Afterward, the HPAI H7N9 viruses further reassorted with LPAI H7N9 or H9N2 viruses locally and generated multiple different genotypes. As of 14 July 2017, the HPAI H7N9 viruses had spread from Guangdong Province to at least 12 other provinces. The rapid geographical expansion and genetic evolution of the HPAI H7N9 viruses pose a great challenge not only to public health but also to poultry production. Effective control measures, including enhanced surveillance, are therefore urgently needed.IMPORTANCE The LPAI H7N9 virus has caused five outbreak waves in humans and was recently reported to have mutated into highly pathogenic variants. It is unknown how the HPAI H7N9 virus originated, evolved, and disseminated in China. In this study, we comprehensively analyzed the sequences of HPAI H7N9 viruses from 28 human and 21 environmental samples covering eight provinces in China that were taken from November 2016 to June 2017. The results show that the ancestor virus of the HPAI H7N9 viruses originated in the Yangtze River Delta region. However, the insertion of four amino acids into the HA protein cleavage site of an LPAI H7N9 virus occurred in late May 2016 in the Pearl River Delta region. The mutated HPAI H7N9 virus further reassorted with LPAI H7N9 or H9N2 viruses that were cocirculating in poultry. Considering the rapid geographical expansion of the HPAI H7N9 viruses, effective control measures are urgently needed.

Genesis and Spread of Newly Emerged Highly Pathogenic H7N9 Avian Viruses in Mainland China.

To the Editor: We report a human infection with avian-like swine A(H1N1) influenza virus first identified through a surveillance system for influenza like illness (ILI) in mainland China. An influenza virus, isolated from a patient with ILI, was originally subtyped as influenza A(H1N1)pdm09 virus with a hemagglutination inhibition (HI) test, but it was identified as a Eurasian avian-like influenza A(H1N1) virus (EA-H1N1) by full genome sequencing on January 30, 2013. The virus was named A/Hebei-Yuhua/SWL1250/2012 (H1N1v) (HB/1250/12), according to the definition of the World Health Organization (1).

The case-patient was a 3-year-old boy who had symptoms of fever and sore throat; his highest body temperature was 38°C on December 9, 2012. He was brought for medical treatment to an influenza sentinel hospital in the city of Shijiazhuang in Hebei Province, China, on December 12. He recovered within a week without hospitalization and oseltamivir treatment. A throat swab specimen was collected and sent to the local Chinese Center for Disease Control and Prevention for virus isolation and characterization, according to the Guidelines of the Chinese National Influenza Surveillance Network. A retrospective investigation was conducted to identify the potential infection source and any other possible cases. The case-patient was previously healthy and had no history of close contact with animals (live or dead wild birds, poultry, and swine) within 2 weeks before the onset of symptoms, nor a history of travel. He lived with his sister and parents; all other family members did not develop influenza-like symptoms during the period of the investigation.

Sporadic human infections with swine influenza virus had been reported previously (2,3). Another case-patient, infected by EA-H1N1 influenza virus A/Jiangsu/1/2011(JS11) in early 2011, was reported (4,5). The genome sequences of the viruses isolated from the 2 case-patients showed high homology; the similarity of the polymerase basic protein 2 was 99.1%; of polymerase basic protein 1, 99.3%; of polymerase acidic protein, 98.9%; of hemagglutinin (HA), 99.1%; nucleocapsid protein, 99.1%; neuraminidase protein, 99.2%; matrix protein, 99.6% and of nonstructural protein, 99.2% (Global Initiative on Sharing Avian Influenza Data, GISAID, accession no.EPI301156–63 for JS11 and EPI438417–25 for HB/1250/12). The HB/1250/12 virus has the amino acids D (at site 190) and E (at site 225) within the HA protein, which are reported to be critical for enhancement of the HA affinity in binding to α-2,6–linked sialosides (6). The virus was resistant to amantadine and rimantadine with S31N (Ser→Asn) mutation in M2 gene, but was predicted to be susceptible to the neuraminidase inhibitor drugs oseltamivir and zanamivir on the basis of the neuraminidase gene.

HI test with ferret anti-serum against A(H1N1)pdm09 (CA09), seasonal H3N2(Vic11,BR10/07 and Perth09), classical swine subtype H1N1(NJ76), and the seasonal influenza subtype H1N1 viruses (BR59/07, SI06) showed that the HB/1250/12 virus is antigenically indistinguishable from NJ76 and CA09, but different from subtype H3N2 viruses (Vic11, BR10/07, and Perth09) and seasonal subtype H1N1 viruses(BR59/07, SI06) (Technical Appendix Table). These findings were consistent with results reported previously (7–9).

To estimate the susceptibility of human population to this virus, and to investigate whether seasonal trivalent inactivated influenza vaccine (TIV) could provide cross-protection, we collected serum samples from children, adults, and elderly adults, before and after 2012–2013 TIV vaccination, and the antibody against HB/1250/12 virus was tested by HI assay. The seroprotection antibody was defined as HI titers >40. Before vaccination, 28% of children (3–5 years) and 6.7% of adults (18–59 years) had HI titers >40, but elderly adults (>60 years) did not. Samples from 56% of children, 56.7% of adults, and 26.7% of elderly adults had HI titers >40 after TIV vaccination; however, a 4-fold antibody rise developed in <30% in any age group (Table). These results indicated that a proportion of cross-protective antibody against EA-H1N1 exists in children and adults, whereas elderly adults are the most susceptible to EA-H1N1 infection with no cross-protective antibody, the vaccination with TIV could not substantially improve the level of cross-reactive EA-H1N1 antibodies.



Table

Cross-reactive antibody response against avian-like influenza A(H1N1) virus in pediatric and adult recipients of seasonal trivalent inactivated influenza vaccines, China, 2013*†



Antisera from hyperimmune sheep are usually used for influenza virus typing and subtyping, the CA09 sheep antisera reacted well with the HB/1250/12 virus (Technical Appendix Table). This is the reason why the local Chinese Center for Disease Control and Prevention originally subtyped HB/1250/12 as A(H1N1)pdm09 virus. Such avian-like H1N1 virus could be missed with regular HI test. In addition, a large proportion of swine influenza infection cases are mild and even asymptomatic (2); thus, the human infections with swine influenza virus may have been underestimated in China.

This is the first human case of EA-H1N1 infection identified through the national ILI surveillance network in China, indicating that the influenza surveillance network not only plays a critical role in monitoring the seasonal influenza circulation and the vaccine virus selection, but also is useful for early detection of novel influenza viruses with pandemic potential. This study also highlighted the value of, and urgent demand for, a cost-effective sequencing platform on routine influenza surveillance for pandemic preparedness.

Technical Appendix: 
Table showing cross-reactive antibody response against avian-like influenza A(H1N1) virus in pediatric and adult recipients of seasonal trivalent inactivated influenza vaccines, China, 2013

Click here to view.(92K, pdf)

Shun-Xiang Qi

Papers

Genesis and Spread of Newly Emerged Highly Pathogenic H7N9 Avian Viruses in Mainland China.

Human infection with Eurasian avian-like influenza A(H1N1) virus, China.