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#Analysis of recent #scientific #information on #avian #influenza A(#H7N9) virus - 10 February 2017 (@WHO, edited)

  Title : #Analysis of recent #scientific #information on #avian #influenza A(#H7N9) virus - 10 February 2017. Subject : Avian Influenza, ...

6 Mar 2017

#Human #infection caused by an #avian #influenza #H7N9 virus with a polybasic cleavage site in #Taiwan, 2017 (J Formos Med Assoc., edited)


Title: #Human #infection caused by an #avian #influenza #H7N9 virus with a polybasic cleavage site in #Taiwan, 2017.

Subject: Avian Influenza, H7N9 subtype, new reassortant strain isolated from a human case in Taiwan,

Source: Journal of the Formosan Medical Association, full page: (LINK). Edited.

Code: [  R  ]


Human infection caused by an avian influenza A (H7N9) virus with a polybasic cleavage site in Taiwan, 2017


Ji-Rong Yang, Ming-Tsan Liu

Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan

Open Access / DOI: 


On February 4, 2017, the Centers for Disease Control, Taiwan reported the year’s first laboratory-confirmed human infection with avian influenza A (H7N9) virus, by three real-time reverse transcriptase polymerase chain reactions targeting three different segments of the matrix (M), hemagglutinin (HA), and neuraminidase (NA) genes. The patient is a 69-year old man who returned from the Guangdong province of mainland China and is currently in critical condition.

The avian influenza A virus was first identified in March 2013 in China, and it was found to cause a severe infection in humans.1

In this report, the virus (A/Taiwan/1/2017) was isolated from a sputum specimen of the patient by inoculating into embryonated chicken eggs.

The full-length genomic sequences were analyzed to investigate the phylogenetic and genetic characteristics of this virus (GISAID accession numbers EPI917062-EPI917069).

We constructed the phylogenetic trees for each genome segment using the program MEGA6 (Tempe, Arizona, United States).

Based on the analyzed phylogenies, the A/Taiwan/1/2017 virus is a novel reassortant belonging to a genotype whose genetic constellation has not been reported previously.

The HA and NA genes of this virus belong to the Yangtze River Delta lineage, along with the H7N9 viruses isolated from Jiangsu, Zhejiang, and Fujian provinces of China in 2016 and 2017.

This lineage is distinguished from the Pearl River Delta lineage that mainly comprises the virus strains isolated from Hong Kong and Guangdong province since 2014.

Phylogenies of the six internal genes of A/Taiwan/1/2017 revealed the viral PB1 and MP (matrix protein) genes located at clades together with those of the A/Anhui/1/2013 vaccine strain and recently isolated viruses from Jiangsu, Zhejiang, Fujian, and Guangdong provinces in 2016 and 2017.

The PB2 (polymerase basic protein 2), PA (polymerase acidic protein), and NS (non-structural protein) genes clustered together with early H7N9 viruses and could be separated from those of the 2016 and 2017 viruses.

These results indicate that the H7N9 viruses are continuously evolving through reassortment.

The molecular signatures of the A/Taiwan/1/2017 virus associated with host adaptation, receptor specificity, pathogenesis, and antiviral resistance were also investigated (Table 1).

The Q226L/I and G228S substitutions in the HA protein, which are the major two mutations contributing to the high-affinity binding of viruses to human receptors, were not identified in this virus.

However, several substitutions in HA were detected, namely S138A, T160A, and G186V.

Of particular note, the A/Taiwan/1/2017 virus has an insertion of three basic amino acid residues (RKR) at the cleavage site connecting the HA1 and HA2 peptide regions, carrying a signature (PKRKRTAR/GLF) of highly pathogenic avian influenza (HPAI) viruses.

This has been the first demonstration of such a molecular characteristic in an H7N9 virus since their emergence in 2013, according to the alignment of viral HA sequences available from the GISAID database.

In the PB2 protein, the E627K substitution was present, as in previous isolates.1, 2 Virulence-related signatures, such as the 90 amino acid-PB1-F2 protein, as well as the P42S and D92E substitutions in the NS1 protein, were also identified.

The R292K substitution in the NA protein, which is a signature related to antiviral drug susceptibility, was present in the A/Taiwan/1/2017 virus, suggesting that this virus had developed resistance to oseltamivir.

The relationship of these substitutions and the viral phenotype in avian and human populations remains unknown.


Table 1

[Molecular analysis of the imported A/Taiwan/1/2017 H7N9 virus]

[Determination of viral characteristics: Protein    - Position    - Mutation    - A/TW/1/2017    - Function]

  • PB2    - 627    - E→K    K    - Replication ability
    • 701    - D→N    - D    - Nuclear Import
    • 702    - K→R    - K    - Species-associated signature positions
  • PB1    - 368    - I→V    - V    - Increased transmission in ferrets
  • PB1-F2    - 66    - N→S    - N    - Induction of apoptosis
    • 87–90 aa in length    - 90 aa    - Increased pathogenicity in mice
  • PA    - 100    - V→A    - A    - Species-associated signature positions
    • 336    - L→M    - L    - Increased polymerase activity in mice
    • 356    - K→R    - R    - Species-associated signature positions
    • 409    - S→N    - N    - Species-associated signature positions
  • HA(H3 numbering)    - Cleavage site    - Basic aa insertion    - PEVP KRKR TARGL    - High pathogenesis in poultry
    • 138    - S→A    - A    - Increased binding to human-type influenza receptor
    • 160    - T→A    - A    - N-glycosylation loss and increased binding to human-type influenza receptor
    • 186    - G→V    - V    - Increased binding to human-type influenza receptor
    • 226    - Q→L    - Q    - Increased binding to human-type influenza receptor
    • 228    - G→S    - G    - Increased binding to human-type influenza receptor
  • NA(N2 numbering)    - 119    - E→V    - E    - Oseltamivir resistance
    • 222    - I→L    - I    - Oseltamivir resistance
    • 292    - R→K    - K    - Resistance to oseltamivir and zanamivir
  • M2    - 31    - S→N    - N    - Amantadine resistance
  • NS1    - 42    - P→S    - S    - Increased pathogenesis in mice
    • 92    - D→E    - D    - Altered virulence in mice
    • 205    - N→S    - S    - Altered antiviral response in host
    • 210    - G→R    - G    - Altered antiviral response in host


{aa} = amino acids;

{HA} = hemagglutinin;

{H3} = hemagglutinin subtype 3;

{M2} = matrix 2 protein;

{NA} = neuraminidase;

{N2} = neuraminidase subtype 2;

{NS} = non-structural protein;

{PA} = polymerase acidic protein;

{PB} = polymerase basic protein;

{PB1-F2} = polymerase basic protein 1 alternate reading frame 2.


The polybasic HA cleavage site is considered the primary virulence marker of HPAI viruses.3 The low pathogenic avian influenza subtypes H5 and H7 acquired multiple basic amino acids at the HA cleavage site after the viruses were introduced into domestic poultry.4

The early H7N9 viruses lacked the polybasic HA cleavage site, exhibiting low pathogenicity, and caused mild or no disease in poultry.1, 5

Based on our analysis, we found that the H7N9 virus acquired an additional three basic amino acids at the HA cleavage site for the first time, which probably increased its virulence in poultry.

We proposed that the acquired polybasic insertion in this virus may be attributed to persistent circulation in poultry species, and the H7N9-infected poultry may be the primary source of human infection.

Further investigation is needed to determine whether the polybasic HA cleavage site of the H7N9 virus is associated with more severe human disease.

Our results on the molecular characteristics of this novel H7N9 virus highlight challenges in risk assessment of the H7N9 virus at the human-animal interface.



  1. Gao, R., Cao, B., Hu, Y., Feng, Z., Wang, D., Hu, W. et al. Human infection with a novel avian-origin influenza A (H7N9) virus. N Engl J Med. 2013; 368: 1888–1897
  2. Yang, J.R., Kuo, C.Y., Huang, H.Y., Wu, F.T., Huang, Y.L., Cheng, C.Y. et al. Characterization of influenza A (H7N9) viruses isolated from human cases imported into Taiwan. PLoS One. 2015; 10: e0119792
  3. Horimoto, T. and Kawaoka, Y. Reverse genetics provides direct evidence for a correlation of hemagglutinin cleavability and virulence of an avian influenza A virus. J Virol. 1994; 68: 3120–3128
  4. Horimoto, T., Rivera, E., Pearson, J., Senne, D., Krauss, S., Kawaoka, Y. et al. Origin and molecular changes associated with emergence of a highly pathogenic H5N2 influenza virus in Mexico. Virology. 1995; 213: 223–230
  5. Chen, Y., Liang, W., Yang, S., Wu, N., Gao, H., Sheng, J. et al. Human infections with the emerging avian influenza A H7N9 virus from wet market poultry: clinical analysis and characterisation of viral genome. Lancet. 2013; 381: 1916–1925


Conflicts of interest: The authors have no conflicts of interest relevant to this article.

© 2017, Formosan Medical Association. Published by Elsevier Taiwan LLC.


Keywords: Research; Abstracts; H7N9; Avian Influenza; Human; China; poultry; Taiwan.