The Colorado potato beetle (CPB) is one of the most serious insect pests due to its high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses which infect leaf feeding beetles is scarce. We performed a metagenomic analysis of 297 CPB genomic and transcriptomic samples from the public National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database. The reads that were not aligned to the reference genome were assembled with metaSPAdes, and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. A total of 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders, and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: those that are homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Additionally, the full-length genomes and near-full length genome sequences of several viruses were assembled. We also found sequences belonging to Bracoviriform viruses and, for the first time, experimentally validated the presence of bracoviral genetic fragments in the CPB genome. Our work represents the first attempt to discover the viral genetic material in CPB samples, and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB.

The Colorado potato beetle is one of the most devastating potato pests in the world. However, its viral pathogens, which might have potential in pest control, have remained unexplored. With high-throughput sequencing of Colorado potato beetle samples derived from prepupal larvae which died from an unknown infection, we have identified two previously unknown RNA viruses and assembled their nearly complete genome sequences. The subsequent genetic and phylogenetic analysis demonstrated that the viruses, tentatively named Leptinotarsa iflavirus 1 and Leptinotarsa solinvi-like virus 1, are the novel representatives of the Iflaviridae and Solinviviridae families, respectively. To the best of our knowledge, these are the first sequencing-confirmed insect viruses derived from Colorado potato beetle samples. We propose that Leptinotarsa iflavirus 1 may be associated with a lethal disease in the Colorado potato beetle.

Studies of HIV-1 molecular epidemiology describe significant differences in HIV infection spread across geographical areas. We examined 80 HIV-1 samples from the Jewish Autonomous Region of Russia in 2024. HIV-1 genome sequences for 12 samples revealed a novel HIV-1 called CRF173_63A6. HIV-1 CRF173_63A6 was found to have arisen through recombination between a specific Russian A6 subtype and the recombinant virus CRF63_02A6, which is responsible for the PWID-associated HIV outbreak in the Siberian region of Russia. Phylogenetic analysis of pol sequences previously deposited in Genbank showed that the CRF173_63A6 samples we described are grouped into a common phylogenetic cluster that includes 54 HIV-1 samples isolated in the JAR and other areas of the Russian Far East, indicating a wide distribution of this virus genovariant. This study once again proves the significant contribution of the key PWID group not only to the development of local Russian HIV epidemics, but also to the change in the characteristics of the circulating virus population.

С момента начала пандемии COVID-19 в 2020 году в России наблюдалось пять волн циркуляции SARS-CoV-2. Наблюдалась быстрая эволюция SARS-CoV-2, которая привела к появлению новых вариантов вируса, которые последовательно сменялись более адаптированным вариантом. Вариант Омикрон, выявленный в ноябре 2021 года, быстро распространяется в мире и в России и вытесняет предыдущий вариант Дельта. Целью данного исследования было описание результатов мониторинга и проведение сравнительной генетической характеристики изолятов варианта Омикрон вируса SARS-CoV-2, выделенных в России и секвенированных во ФБУН ГНЦ ВБ “Вектор” Роспотребнадзора. Материалы и методы: в качестве материала для исследования использовали мазки из рото- и носоглотки, собранные Центрами Гигиены и Эпидемиологии Роспотребнадзора. Секвенирование образцов с использованием Illumina Miseq. Биоинформатический анализ геномных данных проводился с помощью ряда программ, таких как FastQC (v.0.11.9), MAFFT (v.7.475), IQ-TREE, Pangolin (v.3.17), Minimap2 (v.2.17-r941), SnpEff (v.5.0e). Результаты и выводы: В работе было отсеквенировано и проанализировано 324 изолятов варианта Омикрон вируса SARS-CoV-2, выделенных в России в период с 13.12.2021 по 17.01.2022. Выделенные изоляты имели большинство основных характерных мутаций варианта Омикрон, включая 32 мутации в S-белке, которые могут быть ассоциированы с повышенной трансмиссивностью, уклонением от иммунного ответа и изменением тропизма и патогенности. Изоляты варианта Омикрон, выявленные в России, по основным генетическим маркерам сходны со штаммами, циркулирующими в мире, для которых было показано преимущество в заражении по сравнению с вариантом Дельта, снижение эффективности вакцин, но при этом, возможно, менее тяжелое течение заболевания. Вариант Омикрон на данное время считается опасным патогеном и необходимые меры предосторожности, профилактики и лечения являются актуальными на данном этапе пандемии.

The Colorado potato beetle (CPB) is one of the most serious insect pests with high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses, which infect leaf feeding beetles, is scarce. We performed the metagenomic analysis of 297 CPB genomic and transcriptomic samples from public NBCI SRA database. The reads that were not aligned to the reference genome were assembled with metaSPAdes and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: homologous to genetic sequences of insect viruses ( Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses ( Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae ), and endogenous retroviral elements ( Retroviridae, Metaviridae ). Also, the full-length genomes and near-full length genome sequences of several viruses were assembled. We have also found the sequences belonging to Bracoviriform viruses and for the first time experimentally validated the presence of bracoviral genetic fragments in CPB genome. Our work is the first attempt to discover the viral genetic material in CPB samples and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB. The analytical pipeline and additional materials are available at https://github.com/starchevskaya-maria17/uncoVir

The Colorado potato beetle is one of the most devastating potato pests widespread in the world. However, its viral pathogens remain highly unexplored. Here using SISPA high-throughput sequencing of Colorado potato beetle (CPB) samples derived from prepupal larvae that died from an unknown infection, we have identified two previously unknown viruses and assembled their full-length genomic sequences. The subsequent genetic and phylogenetic analysis of the obtained sequences demonstrated that the isolated viruses, named Leptinotarsa iflavirus 1 and Leptinotarsa solinvi-like virus 1 , are the novel representatives of Iflaviridae and Solinviviridae viral families, respectively. To the best of our knowledge, these are the first sequencing-confirmed insect viruses derived directly from CPB samples. And we also propose that Leptinotarsa iflavirus 1 may be associated with lethal disease in CPB.