Highly pathogenic avian influenza virus of the A/H5N8 subtype, clade 2.3.4.4b, caused outbreaks in Kazakhstan in 2020

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Zoological Science

Main article text

 

Introduction

Materials & Methods

Collecting samples for the study

Molecular diagnostics and virus subtyping

Whole genome sequencing

Bioinformatics and phylogenetic analysis

Results

Bird flu in Northern Kazakhstan, 2020

Molecular variability of surface glycoproteins

Relation of Kazakhstan’s viruses to isolates in contemporary circulation

Discussion

Conclusions

Supplemental Information

Supplemental Tables

DOI: 10.7717/peerj.13038/supp-1

Alignment of the nucleotide sequences for the hemagglutinin (HA) segment used in this study

DOI: 10.7717/peerj.13038/supp-2

Alignment of the nucleotide sequences for the neuraminidase (NA) segment used in this study

DOI: 10.7717/peerj.13038/supp-3

Alignment of the nucleotide sequences for the PB1 segment used in this study

DOI: 10.7717/peerj.13038/supp-4

Alignment of the nucleotide sequences for the PB2 segment used in this study

DOI: 10.7717/peerj.13038/supp-5

Alignment of the nucleotide sequences for the PA segment used in this study

DOI: 10.7717/peerj.13038/supp-6

Alignment of the nucleotide sequences for the NP segment used in this study

DOI: 10.7717/peerj.13038/supp-7

Alignment of the nucleotide sequences for the MP segment used in this study

DOI: 10.7717/peerj.13038/supp-8

Alignment of the nucleotide sequences for the NS segment used in this study

DOI: 10.7717/peerj.13038/supp-9

Phylogenetic tree for the segment PB2

DOI: 10.7717/peerj.13038/supp-10

Phylogenetic tree for the segment PB1

DOI: 10.7717/peerj.13038/supp-11

Phylogenetic tree for the segment PA

DOI: 10.7717/peerj.13038/supp-12

Phylogenetic tree for the segment NP

DOI: 10.7717/peerj.13038/supp-13

Phylogenetic tree for the segment MP

DOI: 10.7717/peerj.13038/supp-14

Phylogenetic tree for the segment NS

DOI: 10.7717/peerj.13038/supp-15

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Asylulan Amirgazin, Talgat Karibayev, Maxat Berdikulov, Tamila Kozhakhmetova and Laura Syzdykova performed the experiments, prepared figures and/or tables, and approved the final draft.

Alexandr Shevtsov conceived and designed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Yerlan Ramankulov conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Alexandr V. Shustov conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The sequences of influenza virus genomic segments are available at the GISAID database (https://www.gisaid.org/): EPI1927648, EPI1927649, EPI1927650, EPI1882525, EPI1927651, EPI1882526, EPI1927652, EPI1927653, EPI1927654, EPI1927655, EPI1927656, EPI1882547, EPI1927657, EPI1882546, EPI1927658, EPI1927659, EPI1927660, EPI1927661, EPI1927662, EPI1882548, EPI1927663, EPI1882549, EPI1927664, EPI1927665, EPI1927666, EPI1927667, EPI1927668, EPI1882551, EPI1927669, EPI1882550, EPI1927670, EPI1927671, EPI1927694, EPI1927695, EPI1927696, EPI1882552, EPI1927697, EPI1882553, EPI1927698, EPI1927699, EPI1927700, EPI1927701, EPI1927702, EPI1882555, EPI1927703, EPI1882554, EPI1927704, EPI1927705, EPI1927706, EPI1927707, EPI1927708, EPI1882556, EPI1927709, EPI1882557, EPI1927710, EPI1927711, EPI1927712, EPI1927713, EPI1927714, EPI1882559, EPI1927715, EPI1882558, EPI1927716, EPI1927717, EPI1927718, EPI1927719, EPI1927720, EPI1882560, EPI1927721, EPI1882561, EPI1927722, EPI1927723, EPI1927724, EPI1927725, EPI1927726, EPI1882563, EPI1927727, EPI1882562, EPI1927728, EPI1927729.

Data Availability

The following information was supplied regarding data availability:

The GISAID accession numbers to sequences of Kazakhstan HPAI (H5N8) isolates, GISAID entities for prototypes from originating laboratories, phylogenetic trees and all multiple alignments (PB2, PB1, PA, HA, NP, NA, MP, NS) used in the study are available in the Supplemental File.

Funding

This research was funded by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (Grant No. AP09562122). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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