Article ; Online: Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high-throughput whole genome sequencing.
Influenza and other respiratory viruses
2024 Volume 18, Issue 1, Page(s) e13252
Abstract: Background: During the 2019 severe influenza season, New South Wales (NSW) experienced the highest number of cases in Australia. This study retrospectively investigated the genetic characteristics of influenza viruses circulating in NSW in 2019 and ... ...
| Abstract | Background: During the 2019 severe influenza season, New South Wales (NSW) experienced the highest number of cases in Australia. This study retrospectively investigated the genetic characteristics of influenza viruses circulating in NSW in 2019 and identified genetic markers related to antiviral resistance and potential virulence. Methods: The complete genomes of influenza A and B viruses were amplified using reverse transcription-polymerase chain reaction (PCR) and sequenced with an Illumina MiSeq platform. Results: When comparing the sequencing data with the vaccine strains and reference sequences, the phylogenetic analysis revealed that most NSW A/H3N2 viruses (n = 68; 94%) belonged to 3C.2a1b and a minority (n = 4; 6%) belonged to 3C.3a. These viruses all diverged from the vaccine strain A/Switzerland/8060/2017. All A/H1N1pdm09 viruses (n = 20) showed genetic dissimilarity from vaccine strain A/Michigan/45/2015, with subclades 6B.1A.5 and 6B.1A.2 identified. All B/Victoria-lineage viruses (n = 21) aligned with clade V1A.3, presenting triple amino acid deletions at positions 162-164 in the hemagglutinin protein, significantly diverging from the vaccine strain B/Colorado/06/2017. Multiple amino acid substitutions were also found in the internal proteins of influenza viruses, some of which have been previously reported in hospitalized influenza patients in Thailand. Notably, the oseltamivir-resistant marker H275Y was present in one immunocompromised patient infected with A/H1N1pdm09 and the resistance-related mutation I222V was detected in another A/H3N2-infected patient. Conclusions: Considering antigenic drift and the constant evolution of circulating A and B strains, we believe continuous monitoring of influenza viruses in NSW via the high-throughput sequencing approach provides timely and pivotal information for both public health surveillance and clinical treatment. |
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| MeSH term(s) | Humans ; Influenza, Human ; Retrospective Studies ; Herpesvirus 1, Cercopithecine/genetics ; Influenza A Virus, H3N2 Subtype/genetics ; New South Wales/epidemiology ; Phylogeny ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Influenza Vaccines ; Australia ; Seasons ; Whole Genome Sequencing |
| Chemical Substances | Hemagglutinin Glycoproteins, Influenza Virus ; Influenza Vaccines |
| Language | English |
| Publishing date | 2024-01-30 |
| Publishing country | England |
| Document type | Journal Article |
| ZDB-ID | 2274538-5 |
| ISSN | 1750-2659 ; 1750-2640 |
| ISSN (online) | 1750-2659 |
| ISSN | 1750-2640 |
| DOI | 10.1111/irv.13252 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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