Two phylogenetic cohorts of the nucleocapsid protein NP and their correlation with the host range of influenza A viruses

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Аннотация

Influenza A virus has a wide natural areal among birds, mammals and humans. One of the main regulatory adaptors of the virus host range is the major NP protein of the viral nucleocapsid. Phylogenetic analysis of the NP protein of different viruses has revealed the existence of two phylogenetic cohorts in human influenza virus population. Cohort I includes classical human viruses that caused epidemics in 1957, 1968, 1977. Cohort II includes the H1N1/2009pdm virus, which had a mixed avian-swine origin, but caused global human pandemic. Also, the highly virulent H5N1 avian influenza virus emerged in 2021 and caused outbreaks of lethal infections in mammals, including humans, appeared to have the NP gene of the second phylogenetic cohort and, therefore, by the type of adaptation to human is similar to the H1N1/2009pdm virus and seems to possess a high epidemic potential for humans. The data obtained shed light on pathways and dynamics of avian influenza viruses adaptation to humans and propose phylogenetic algorithm for systemic monitoring of dangerous virus strains to predict epidemic harbingers and take immediate preventive measures.

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Авторлар туралы

A. Chernyshova

N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health

Email: zhirnov@inbox.ru

D.I. Ivanovsky Institute of Virology

Ресей, Moscow

O. Zhirnov

N.F. Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Health; The Russian-German Academy of Medico-Social and Biotechnological Sciences

Хат алмасуға жауапты Автор.
Email: zhirnov@inbox.ru

D.I. Ivanovsky Institute of Virology, Corresponding Member of the RAS

Ресей, Moscow; The Innovation Center of Skolkovo, Moscow

Әдебиет тізімі

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2. Fig. 1. Phylogenetic analysis of the primary structure of the NP protein of influenza A viruses of birds and mammals, including humans. The phylogenetic tree of the NP protein was constructed based on the NP protein sequences from the GISAID and GenBank databases. Influenza A viruses isolated from birds, pigs, minks, cats and other mammals, including humans, in the period 1957–2023 were studied. The MEGA-10 program (nearest neighbor algorithm - NJ) was used for the analysis. To construct the tree, 39 complete a.a. sequences of NP proteins were used for classical human influenza H1N1 viruses (1950–2008), the classical lineage of swine H1N1 strains (1961–2020), avian viruses of the H5N1 subtype (2014–2023), and H5N1 viruses from mammals (2021–2023). GenBank: AAA51491.1; AFM72964.1; ABD60794.1; AFM71861.1; ABW36337.1; ACD85158.1; ADM18085.1; AHB51548.1; ADG59708.1; ABI84963.1; APC57870.2; GISAID:EPI243398; EPI173795; EPI168140; EPI171494; EPI168127; EPI677976; EPI138999; EPI2760375; EPI2755515; EPI2755455; EPI2737210; EPI2761157; EPI886274; EPI1922958; EPI1229955; EPI2557220; EPI1248597; EPI2748090; EPI2616223; EPI2603677; EPI1998203; EPI2220590; EPI2158641; EPI2670207; EPI181378; EPI319186; EPI1673272; EPI2587076.

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3. Fig. 2. Comparison of amino acid patterns of the NP protein in influenza A viruses isolated from mammals and birds. The numbers of 15 amino acid positions (a.a.) that form genetic patterns in the NP protein (m.w. 70 kDa; 498 a.a.), characteristic of human, porcine, and avian viruses [4, 14], are shown from left to right in order from the N-terminal methionine. The upper part of the columns shows the phylogenetic clades of classical human influenza H1N1 viruses (Hu), classical swine H1N1 viruses (Sw), pandemic human influenza virus H1N1/2009pdm (Pdm09), H5N1 influenza viruses isolated from minks (Min), and the classical lineage of avian H5N1 viruses (Av). The lower horizontal part shows the values ​​of the proportion (%) of a.a. positions that coincide in this group of viruses with avian (Av) and human (Hu) genetic stamps (“genetic signatures”). The amino acid positions are shown in the generally accepted single-letter Latin notation in the Logos format (http://weblogo.threeplusone.com/). (*) The marked amino acid positions have heterogeneity in viral populations, in which the amino acid indicated after the slash is found in 10–20% of viral isolates. To identify the amino acid variations, the amino acid positions in human viruses (white background) and avian viruses (gray background) are shown with different backgrounds. The horizontal dash indicates the background at amino acid position 313 NP, which differs from that in both reference viruses.

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