Diversity and distribution of type A influenza viruses: an updated panorama analysis based on protein sequences

Qingye Zhuang,
Suchun Wang,
Shuo Liu,
Guangyu Hou,
Jinping Li,
Wenming Jiang,
Kaicheng Wang,
Cheng Peng,
Dong Liu,
Aizhen GuoEmail author and
Jiming ChenEmail author View ORCID ID profile

Virology Journal201916:85

https://doi.org/10.1186/s12985-019-1188-7

Received: 1 March 2019
Accepted: 31 May 2019
Published: 26 June 2019

Abstract

Background

Type A influenza viruses (IAVs) cause significant infections in humans and multiple species of animals including pigs, horses, birds, dogs and some marine animals. They are of complicated phylogenetic diversity and distribution, and analysis of their phylogenetic diversity and distribution from a panorama view has not been updated for multiple years.

Methods

139,872 protein sequences of IAVs from GenBank were selected, and they were aligned and phylogenetically analyzed using the software tool MEGA 7.0. Lineages and subordinate lineages were classified according to the topology of the phylogenetic trees and the host, temporal and spatial distribution of the viruses, and designated using a novel universal nomenclature system.

Results

Large phylogenetic trees of the two external viral genes (HA and NA) and six internal genes (PB2, PB1, PA, NP, MP and NS) were constructed, and the diversity and the host, temporal and spatial distribution of these genes were calculated and statistically analyzed. Various features regarding the diversity and distribution of IAVs were confirmed, revised or added through this study, as compared with previous reports. Lineages and subordinate lineages were classified and designated for each of the genes based on the updated panorama views.

Conclusions

The panorama views of phylogenetic diversity and distribution of IAVs and their nomenclature system were updated and assumed to be of significance for studies and communication of IAVs.