Yolshin Nikita*, Komissarov Andrey, Lioznov Dmitry
Smorodintsev Research Institute of Influenza, Saint-Petersburg, Russia
Nikita.yolshin [at] gmail.com
Abstract
During the current epidemic season 2023-2024, approximately 1700 influenza viruses were sequenced at the Smorodintsev Influenza Research Institute from patients with acute respiratory viral infections from 20 regions of the Russian Federation. Next-generation sequencing technologies (Illumina NextSeq 2000, MGI DNBSEQ-G400) were utilized for sequencing. Genome assembly onto the reference was performed using bwa-mem2 2.2.1 and samtools 1.6 programs, with consensus generation by the ivar 1.3.2 tool. The tool fastqc 0.12.1 was used to assess the quality of data and trimmomatic 0.39 to trim the reads.
Genome alignment of the current season’s viruses with earlier variants revealed notable characteristics. The vast majority (99%) of influenza viruses sequenced in Russia belonged to type H3N2, clade 3c.2a1b.2a.2a.3a.1 (vaccine virus A/Thailand/8/2022-like), sharing substitutions E50K, I140K (antigenic site A), and I223V (antigenic site D). Within clade 2a.3a.1, a subgroup with N122D substitution (loss of a potential glycosylation site) was predominant, with 85% representation among Russian viruses. Notably, viruses within this subgroup commonly featured K276E substitution at HA antigenic site C.
Additionally, several influenza A H1N1 and influenza B samples were successfully sequenced during the season. All H1N1 samples fell within clade 6B.1A.5a.2a (A/Victoria/2570/2019 vaccine virus clade), with characteristic amino acid substitutions in HA, including K130N, N156K, L161I, V250A, and E506D. These viruses also encoded amino acid substitutions K54Q, A186T, E224A, R259K, and K308R in HA1, characteristic of 5a.2a viruses. Notably, 5a.2a.1 clade viruses and A/Sydney/5/2021-like viruses were not detected in Russia during this season. Several distinct groups of Russian isolates were identified within the 5a.2a clade, exhibiting specific amino acid substitutions such as T120A and K169Q (antigenic site Ca1), V321I, and P137S (A/Netherlands/10468/2023-like).
Influenza surveillance plays a critical role in monitoring and understanding the dynamic evolution of influenza viruses, aiding in the timely detection of emerging strains and informing public health measures to mitigate the impact of seasonal epidemics and potential pandemics.
Keywords: Influenza, H3N2, H1N1, surveillance, NGS