Phylogenetic analysis of variants of the Puumala virus (Hantaviridae:  Orthohantavirus ) circulating in the Saratov region

Yaroslav M. Krasnov; Краснов Ярослав Михайлович; Ekaterina V. Naidenova; Найденова Екатерина Владимировна; Natalia P. Guseva; Гусева Наталья Петровна; Tatyana A. Polunina; Полунина Татьяна Алексеевна; Natalya A. Sharapova; Шарапова Наталья Анатольевна; Ekaterina A. Sosedova; Соседова Екатерина Анатольевна; Nina V. Kotova; Котова Нина Владимировна; Kirill S. Zakharov; Захаров Кирилл Сергеевич; Andrey V. Kazantsev; Казанцев Андрей Владимирович; Irina V. Domanina; Доманина Ирина Владимировна; Vladimir N. Chekashov; Чекашов Владимир Николаевич; Mikhail M. Shilov; Шилов Михаил Михайлович; Evgeniy N. Kondratiev; Кондратьев Евгений Николаевич; Natalya A. Osina; Осина Наталья Александровна; Vladimir V. Kutyrev; Кутырев Владимир Викторович

doi:10.36233/0507-4088-224

Phylogenetic analysis of variants of the Puumala virus (Hantaviridae: Orthohantavirus) circulating in the Saratov region

Authors: Krasnov Y.M.¹, Naidenova E.V.¹, Guseva N.P.¹, Polunina T.A.¹, Sharapova N.A.¹, Sosedova E.A.¹, Kotova N.V.¹, Zakharov K.S.¹, Kazantsev A.V.¹, Domanina I.V.¹, Chekashov V.N.¹, Shilov M.M.¹, Kondratiev E.N.¹, Osina N.A.¹, Kutyrev V.V.¹
Affiliations:
1. Russian Research Anti-Plague Institute «Microbe»
Issue: Vol 69, No 2 (2024)
Pages: 162-174
Section: ORIGINAL RESEARCH
URL: https://journals.rcsi.science/0507-4088/article/view/256877
DOI: https://doi.org/10.36233/0507-4088-224
EDN: https://elibrary.ru/ijmubu
ID: 256877

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Abstract

The objective is to determine the complete nucleotide sequence and conduct a phylogenetic analysis of genome variants of the Puumala virus isolated in the Saratov region.

Materials and methods. The samples for the study were field material collected in the Gagarinsky (formerly Saratovsky), Engelssky, Novoburassky and Khvalynsky districts of the Saratov region in the period from 2019 to 2022. To specifically enrich the Puumala virus genome in the samples, were used PCR and developed a specific primer panel. Next, the resulting PCR products were sequenced and the fragments were assembled into one sequence for each segment of the virus genome. To construct phylogenetic trees, the maximum parsimony algorithm was used.

Results. Genetic variants of the Puumala virus isolated in the Saratov region have a high degree of genome similarity to each other, which indicates their unity of origin. According to phylogenetic analysis, they all form a separate branch in the cluster formed by hantaviruses from other subjects of the Volga Federal District. The virus variants from the Republics of Udmurtia and Tatarstan, as well as from the Samara and Ulyanovsk regions, are closest to the samples from the Saratov region.

Conclusion. The data obtained show the presence of a pronounced territorial confinement of strains to certain regions or areas that are the natural biotopes of their carriers. This makes it possible to fairly accurately determine the territory of possible infection of patients and/or the circulation of carriers of these virus variants based on the sequence of individual segments of their genome.

Keywords

hantaviruses, Puumala orthohantavirus, nucleotide sequence, Saratov region, Phylogeography