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

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.

Keywords: Distribution; Diversity; Influenza virus; Nomenclature; Phylogenetics; Protein.

Fig. 1

Phylogenetic diversity and distribution of H1 subtypes of IAVs based on HA sequences. H1 subtype IAVs were classified into two primary lineages, H1.1 and H1.2. H1.1 mainly corresponded to H1 subtype AIVs and some SIVs which originated from the AIVs. H1.2 corresponded to classical H1 subtype HuIVs and SIVs

Fig. 2

Phylogenetic diversity and distribution of H2 subtypes of IAVs based on HA sequences. H2 subtype IAVs were classified into two primary lineages, largely corresponding to the AIVs isolated from the Western and Eastern Hemispheres, respectively

Fig. 3

Phylogenetic diversity and distribution of H3 subtypes of IAVs based on HA sequences. H3 subtype IAVs were classified into three primary lineages, H3.1, H3.2 and H3.3. H3.1 corresponded to H3 subtype AIVs, and several secondary lineages within H3.1, H3.1a-H3.1c, were designated. H3.2 corresponded to many HuIVs and SIVs circulating worldwide. H3.3 corresponded to the EIVs circulating from 1963 to nowadays

Fig. 4

Phylogenetic diversity and distribution of H4 subtypes of IAVs based on HA sequences. H4 subtype IAVs were classified into three primary lineages; H4.1 and H4.2 mainly corresponded to AIVs circulating in the North America; H4.3 corresponded to AIVs from both Hemispheres

Fig. 5

Phylogenetic diversity and distribution of H7 and H15 subtypes of IAVs based on HA sequences. H7 subtype IAVs were classified into three primary lineages, H7.1, H7.2 and H7.3. H7.1 and H7.2 mainly corresponded to H7 subtype AIVs circulating in the Western and Eastern Hemispheres. H7.3 corresponded to H7 subtype EIVs which have not been found after the 1970s. H15 subtype IAVs could be classified into two lineages, H15.1 and H15.2. H15.1 corresponded to AIVs isolated from Australia in the 1970s and the 1980s. H15.2 corresponded to AIVs isolated from Russia around the year 2010

Fig. 6

Phylogenetic diversity and distribution of H9 subtypes of IAVs based on HA sequences. H9 subtype IAVs were classified into two primary lineages, H9.1 and H9.2. H9.1 corresponded to some H9 subtype AIVs circulating worldwide. H9.2 corresponded to many AIVs circulating in the Eastern Hemisphere

Fig. 7

Phylogenetic diversity and distribution of H5 subtypes of IAVs based on HA sequences. H5 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 8

Phylogenetic diversity and distribution of H6 subtypes of IAVs based on HA sequences. H6 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 9

Phylogenetic diversity and distribution of H8 subtypes of IAVs based on HA sequences. H8 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 10

Phylogenetic diversity and distribution of H10 subtypes of IAVs based on HA sequences. H10 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 11

Phylogenetic diversity and distribution of H11 subtypes of IAVs based on HA sequences. H11 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 12

Phylogenetic diversity and distribution of H12 subtypes of IAVs based on HA sequences. H12 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 13

Phylogenetic diversity and distribution of H14 subtypes of IAVs based on HA sequences. H14 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 14

Phylogenetic diversity and distribution of H16 subtypes of IAVs based on HA sequences. H6 subtype IAVs were classified into two primary lineages, which mainly corresponded to AIVs circulating in the Western and Eastern Hemispheres

Fig. 15

Phylogenetic diversity and distribution of H13 subtypes of IAVs based on HA sequences. H13 subtype IAVs were classified into two global primary lineages

Fig. 16

Phylogenetic diversity and distribution of H17 and H18 subtypes of IAVs based on HA sequences. The phylogenetic tree covered some sequences of H1-H16 subtypes as references

Fig. 17

Phylogenetic diversity and distribution of N1 subtype IAVs based on NA sequences. N1 subtype IAVs were classified into three lineages, N1.1, N1.2 and N1.3, largely corresponding to avian, human, and classical swine N1 subtype IAVs

Fig. 18

Phylogenetic diversity and distribution of N2 subtype IAVs based on NA sequences. N2 subtype IAVs were classified into two primary lineages, N2.1 and N2.2, largely corresponding to avian and human/swine IAVs

Fig. 19

Phylogenetic diversity and distribution of N4 subtype IAVs based on NA sequences. N4 subtype IAVs were classified into two primary lineages, which mainly corresponded to the AIVs circulating in the Western and Eastern Hemispheres

Fig. 20

Phylogenetic diversity and distribution of N5 subtype IAVs based on NA sequences. N5 subtype IAVs were classified into two primary lineages, which mainly corresponded to the AIVs circulating in the Western and Eastern Hemispheres

Fig. 21

Phylogenetic diversity and distribution of N6 subtype IAVs based on NA sequences. N6 subtype IAVs were classified into two primary lineages, which mainly corresponded to the AIVs circulating in the Western and Eastern Hemispheres

Fig. 22

Phylogenetic diversity and distribution of N3 subtype IAVs based on NA sequences. N3 subtype IAVs were classified into two primary lineages

Fig. 23

Phylogenetic diversity and distribution of N9 subtype IAVs based on NA sequences. N9 subtype IAVs were classified into two primary lineages

Fig. 24

Phylogenetic diversity and distribution of N7 subtype IAVs based on NA sequences. N7 subtype IAVs were classified into three primary lineages. N7.1 corresponded to AIVs circulating in the Western Hemisphere; N7.2 corresponded to AIVs circulating in the Eastern Hemisphere; N7.3corresponded to EIVs

Fig. 25

Phylogenetic diversity and distribution of N8 subtype IAVs based on NA sequences. N8 subtype IAVs were classified into three primary lineages. N8.1 corresponded to AIVs circulating in the Western Hemisphere; N8.2 corresponded to AIVs circulating in the Eastern Hemisphere; N8.3 corresponded to EIVs

Fig. 26

Phylogenetic diversity and distribution of N10 and N11 subtype IAVs based on NA sequences. The phylogenetic tree covered some sequences of N1-N9 subtypes as references

Fig. 27

Phylogenetic diversity and distribution of IAVs based on PB2 gene sequences. Based on the viral PB2 gene sequences, IAVs were classified into four primary lineages, PB2.1, PB2.2, PB2.3, and PB2.4 which mainly corresponded to AIVs, HuIVs, SIVs, and EIVs

Fig. 28

Phylogenetic diversity and distribution of IAVs based on PB1 gene sequences. Based on the viral PB1 gene sequences, IAVs were classified into four primary lineages, PB1.1, PB1.2, PB1.3, and PB1.4 which mainly corresponded to AIVs, HuIVs, SIVs, and EIVs

Fig. 29

Phylogenetic diversity and distribution of IAVs based on PA gene sequences. Based on the viral PA gene sequences, IAVs were classified into four primary lineages, PA.1, PA.2, PA.3, and PA.4 which mainly corresponded to AIVs, HuIVs, SIVs, and EIVs

Fig. 30

Phylogenetic diversity and distribution of IAVs based on NP gene sequences. Based on the viral NP gene sequences, IAVs were classified into four primary lineages, NP.1, NP.2 and NP.3 which mainly corresponded to AIVs, HuIVs and SIVs

Fig. 31

Phylogenetic diversity and distribution of IAVs based on MP gene sequences. Based on the viral MP gene sequences, IAVs were classified into three primary lineages, MP.1, MP.2 and MP.3 which mainly corresponded to AIVs, HuIVs and EIVs

Fig. 32

Phylogenetic diversity and distribution of IAVs based on NS gene sequences. Based on the viral NS gene sequences, IAVs were classified into three primary lineages, NS.1, NS.2 and NS.3 which mainly corresponded to AIVs, AIVs and EIVs

Fig. 33

Phylogenetic tree of the viral HA gene representative sequences of H1 subtype. H1 subtype IAVs were classified into two primary lineages, H1.1 and H1.2, and each of them were further classified into four secondary lineages. Bootstrap values were given at relevant nodes