vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJGB-23-97vavilov-3984Research ArticleЭВОЛЮЦИОННАЯ КОМПЬЮТЕРНАЯ БИОЛОГИЯEVOLUTIONARY COMPUTATIONAL BIOLOGYО пространстве вариантов генетических последовательностей SARS-CoV-2On the space of SARS-CoV-2 genetic sequence variantshttps://orcid.org/0000-0003-1108-1486ПальяновА. Ю.PalyanovA. Yu.

Novosibirsk

palyanov@iis.nsk.suhttps://orcid.org/0000-0002-1783-5798ПальяноваН. В.PalyanovaN. V.

Novosibirsk

Институт систем информатики им. А.П. Ершова Сибирского отделения Российской академии наук; Научно-исследовательский институт вирусологии, Федеральный исследовательский центр фундаментальной и трансляционной медицины; Новосибирский национальный исследовательский государственный университетРоссияA.P. Ershov Institute of Informatics Systems of the Siberian Branch of the Russian Academy of Sciences; Research Institute of Virology, Federal Research Center of Fundamental and Translational Medicine of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityRussian FederationНаучно-исследовательский институт вирусологии, Федеральный исследовательский центр фундаментальной и трансляционной медициныРоссияResearch Institute of Virology, Federal Research Center of Fundamental and Translational Medicine of the Siberian Branch of the Russian Academy of SciencesRussian Federation202311122023277839850Copyright © Пальянов А.Ю., Пальянова Н.В., 20232023Пальянов А.Ю., Пальянова Н.В.Palyanov A.Y., Palyanova N.V.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3984

Пандемия коронавирусной инфекции, вызванная вирусом SARS-CoV-2, которой человечество противостояло с использованием новейших достижений науки, оставила после себя в том числе обширные генетические данные. Ежедневно начиная с конца 2019 г. в мире собирались образцы геномов вируса, что предоставляет возможность детально проследить его эволюцию с момента возникновения до настоящего времени. Накопленная статистика результатов экспресс-тестирования показала, что число подтвержденных случаев заражения SARS-CoV-2 составило не менее 767.5 млн (9.5 % нынешнего населения Земли без учета бессимптомников), а число секвенированных геномов вируса – более 15.7 млн (что составляет чуть более 2 % от общего числа заразившихся). Эти новые данные потенциально несут в себе информацию о механизмах изменчивости и распространения вируса, его взаимодействия с иммунной системой человека, об основных параметрах, характеризующих механизмы развития пандемии, и многое другое. В этой статье мы анализируем пространство возможных вариантов генетических последовательностей SARS-CoV-2 как с математической точки зрения, так и с учетом биологических ограничений, присущих этой системе (основанных на общебиологических знаниях и учитывающих особенности данного конкретного вируса). Для этого мы разработали программное обеспечение, способное загружать и анализировать нуклеотидные последовательности SARSCoV-2 в формате FASTA, определять позиции 5’ и 3’ UTR, число и расположение неидентифицированных нуклеотидов (“N”), осуществлять выравнивание относительно референсной последовательности посредством вызова предназначенных для этого программ, определять мутации, делеции и вставки, а также рассчитывать различные характеристики геномов вирусов с заданным шагом по времени (дни, недели, месяцы и т. д.). Полученные данные свидетельствуют о том, что, несмотря на кажущееся математическое многообразие возможных вариантов изменения вируса во времени, коридор эволюционной траектории, которым прошел коронавирус, представляется достаточно узким. Это дает основание полагать, что он в некоторой степени детерминирован, что позволяет надеяться на возможность моделирования эволюции коронавируса.

The coronavirus pandemic caused by the SARS-CoV-2 virus, which humanity resisted using the latest advances in science, left behind, among other things, extensive genetic data. Every day since the end of 2019, samples of the virus genomes have been collected around the world, which makes it possible to trace its evolution in detail from its emergence to the present. The accumulated statistics of testing results showed that the number of confirmed cases of SARS-CoV-2 infection was at least 767.5 million (9.5 % of the current world population, excluding asymptomatic people), and the number of sequenced virus genomes is more than 15.7 million (which is over 2 % of the total number of infected people). These new data potentially contain information about the mechanisms of the variability and spread of the virus, its interaction with the human immune system, the main parameters characterizing the mechanisms of the development of a pandemic, and much more. In this article, we analyze the space of possible variants of SARS-CoV-2 genetic sequences both from a mathematical point of view and taking into account the biological limitations inherent in this system, known both from general biological knowledge and from the consideration of the characteristics of this particular virus. We have developed software capable of loading and analyzing SARS-CoV-2 nucleotide sequences in FASTA format, determining the 5’ and 3’ UTR positions, the number and location of unidentified nucleotides (“N”), performing alignment with the reference sequence by calling the program designed for this, determining mutations, deletions and insertions, as well as calculating various characteris tics of virus genomes with a given time step (days, weeks, months, etc.). The data obtained indicate that, despite the apparent mathematical diversity of possible options for changing the virus over time, the corridor of the evolutionary  trajectory that the coronavirus has passed through seems to be quite narrow. Thus it can be assumed that it is determined to some extent, which allows us to hope for a possibility of modeling the evolution of the coronavirus. 

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The authors declare that there are no conflicts of interest present.