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Johnson ML, Zwart MP. Robust Approaches to the Quantitative Analysis of Genome Formula Variation in Multipartite and Segmented Viruses. Viruses 2024; 16:270. [PMID: 38400045 PMCID: PMC10892338 DOI: 10.3390/v16020270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
When viruses have segmented genomes, the set of frequencies describing the abundance of segments is called the genome formula. The genome formula is often unbalanced and highly variable for both segmented and multipartite viruses. A growing number of studies are quantifying the genome formula to measure its effects on infection and to consider its ecological and evolutionary implications. Different approaches have been reported for analyzing genome formula data, including qualitative description, applying standard statistical tests such as ANOVA, and customized analyses. However, these approaches have different shortcomings, and test assumptions are often unmet, potentially leading to erroneous conclusions. Here, we address these challenges, leading to a threefold contribution. First, we propose a simple metric for analyzing genome formula variation: the genome formula distance. We describe the properties of this metric and provide a framework for understanding metric values. Second, we explain how this metric can be applied for different purposes, including testing for genome-formula differences and comparing observations to a reference genome formula value. Third, we re-analyze published data to illustrate the applications and weigh the evidence for previous conclusions. Our re-analysis of published datasets confirms many previous results but also provides evidence that the genome formula can be carried over from the inoculum to the virus population in a host. The simple procedures we propose contribute to the robust and accessible analysis of genome-formula data.
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Tsishevskaya AA, Alkhireenko DA, Bayandin RB, Kartashov MY, Ternovoi VA, Gladysheva AV. Untranslated Regions of a Segmented Kindia Tick Virus Genome Are Highly Conserved and Contain Multiple Regulatory Elements for Viral Replication. Microorganisms 2024; 12:239. [PMID: 38399643 PMCID: PMC10893285 DOI: 10.3390/microorganisms12020239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Novel segmented tick-borne RNA viruses belonging to the group of Jingmenviruses (JMVs) are widespread across Africa, Asia, Europe, and America. In this work, we obtained whole-genome sequences of two Kindia tick virus (KITV) isolates and performed modeling and the functional annotation of the secondary structure of 5' and 3' UTRs from JMV and KITV viruses. UTRs of various KITV segments are characterized by the following points: (1) the polyadenylated 3' UTR; (2) 5' DAR and 3' DAR motifs; (3) a highly conserved 5'-CACAG-3' pentanucleotide; (4) a binding site of the La protein; (5) multiple UAG sites providing interactions with the MSI1 protein; (6) three homologous sequences in the 5' UTR and 3' UTR of segment 2; (7) the segment 2 3' UTR of a KITV/2017/1 isolate, which comprises two consecutive 40 nucleotide repeats forming a Y-3 structure; (8) a 35-nucleotide deletion in the second repeat of the segment 2 3' UTR of KITV/2018/1 and KITV/2018/2 isolates, leading to a modification of the Y-3 structure; (9) two pseudoknots in the segment 2 3' UTR; (10) the 5' UTR and 3' UTR being represented by patterns of conserved motifs; (11) the 5'-CAAGUG-3' sequence occurring in early UTR hairpins. Thus, we identified regulatory elements in the UTRs of KITV, which are characteristic of orthoflaviviruses. This suggests that they hold functional significance for the replication of JMVs and the evolutionary similarity between orthoflaviviruses and segmented flavi-like viruses.
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Affiliation(s)
- Anastasia A. Tsishevskaya
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Russia; (A.A.T.); (D.A.A.); (R.B.B.); (M.Y.K.); (V.A.T.)
- Physics Department, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Daria A. Alkhireenko
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Russia; (A.A.T.); (D.A.A.); (R.B.B.); (M.Y.K.); (V.A.T.)
- Natural Sciences Department, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Roman B. Bayandin
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Russia; (A.A.T.); (D.A.A.); (R.B.B.); (M.Y.K.); (V.A.T.)
| | - Mikhail Yu. Kartashov
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Russia; (A.A.T.); (D.A.A.); (R.B.B.); (M.Y.K.); (V.A.T.)
| | - Vladimir A. Ternovoi
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Russia; (A.A.T.); (D.A.A.); (R.B.B.); (M.Y.K.); (V.A.T.)
| | - Anastasia V. Gladysheva
- State Research Center of Virology and Biotechnology «Vector», 630559 Kol’tsovo, Russia; (A.A.T.); (D.A.A.); (R.B.B.); (M.Y.K.); (V.A.T.)
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Litov AG, Okhezin EV, Kholodilov IS, Belova OA, Karganova GG. Conserved Sequences in the 5' and 3' Untranslated Regions of Jingmenvirus Group Representatives. Viruses 2023; 15:v15040971. [PMID: 37112951 PMCID: PMC10141212 DOI: 10.3390/v15040971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The Jingmenvirus group (JVG), with members such as Jingmen tick virus (JMTV), Alongshan virus (ALSV), Yanggou tick virus (YGTV), and Takachi virus (TAKV), is drawing attention due to evidence of it causing disease in humans and its unique genome architecture. In the current work, complete untranslated regions (UTRs) of four strains of ALSV and eight strains of YGTV were obtained. An analysis of these sequences, as well as JVG sequences from GenBank, uncovered several regions within viral UTRs that were highly conserved for all the segments and viruses. Bioinformatics predictions suggested that the UTRs of all the segments of YGTV, ALSV, and JMTV could form similar RNA structures. The most notable feature of these structures was a stable stem-loop with one (5' UTR) or two (3' UTR) AAGU tetraloops on the end of a hairpin.
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Affiliation(s)
- Alexander G Litov
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Egor V Okhezin
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan S Kholodilov
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Oxana A Belova
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
| | - Galina G Karganova
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Institute of Poliomyelitis), 108819 Moscow, Russia
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Kholodilov IS, Belova OA, Ivannikova AY, Gadzhikurbanov MN, Makenov MT, Yakovlev AS, Polienko AE, Dereventsova AV, Litov AG, Gmyl LV, Okhezin EV, Luchinina SV, Klimentov AS, Karganova GG. Distribution and Characterisation of Tick-Borne Flavi-, Flavi-like, and Phenuiviruses in the Chelyabinsk Region of Russia. Viruses 2022; 14:v14122699. [PMID: 36560703 PMCID: PMC9780909 DOI: 10.3390/v14122699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
In this work, we presented data from a two-year study of flavi-, flavi-like, and phenuiviruses circulation in the population of ixodid ticks in the Chelyabinsk region. We isolated three tick-borne encephalitis virus (TBEV) strains from I. persulcatus, which was not detected in the ticks of the genus Dermacentor. The virus prevalence ranged from 0.66% to 2.28%. The Yanggou tick virus (YGTV) is widespread in steppe and forest-steppe zones and is mainly associated with ticks of the genus Dermacentor. We isolated 26 strains from D. reticulatus, D. marginatus, and I. persulcatus ticks in the HAE/CTVM8 tick cell line. The virus prevalence ranged from 1.58% to 4.18% in D. reticulatus, ranged from 0.78% to 3.93% in D. marginatus, and was 0.66% in I. persulcatus. There was combined focus of TBEV and YGTV in the territory of the Chelyabinsk region. The Alongshan virus (ALSV) was found to be associated with I. persulcatus ticks and is spread in forest zone. We detected 12 amplicons and isolated 7 strains of ALSV in tick cells. The virus prevalence ranged from 1.13% to 6.00%. The phlebovirus Gomselga and unclassified phenuivirus Stavropol were associated with I. persulcatus and D. reticulatus ticks, respectively. Virus prevalence of the unclassified phenuivirus Stavropol in the Chelyabinsk region is lower than that in neighbouring regions.
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Affiliation(s)
- Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Anna Y. Ivannikova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Magomed N. Gadzhikurbanov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Marat T. Makenov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Alexander S. Yakovlev
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Alexandra E. Polienko
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Alena V. Dereventsova
- Laboratory of Biochemistry, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Alexander G. Litov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Larissa V. Gmyl
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Egor V. Okhezin
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | | | - Alexander S. Klimentov
- Laboratory of Biochemistry, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia
- Correspondence:
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Gaafar YZA, Rabenstein F, Zia A, Gaafar ARZA, Ziebell H. Molecular characterisation of a new tenuivirus from Festuca sp. Virus Res 2021; 304:198509. [PMID: 34302922 DOI: 10.1016/j.virusres.2021.198509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/15/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
A novel virus with a quadruple genome of negative-sense, single-stranded RNA was identified by high-throughput sequencing (HTS) in a grass sample from Saxony-Anhalt, Germany, and tentatively called Festuca stripe-associated virus (FSaV). The genome of FSaV consists of four segments and a total of 16,535 nucleotides (nt) which encode seven open reading frames (ORF). FSaV shares highest nt identity (between 72.84% to 80.74%) to Iranian wheat stripe virus (IWSV) and rice hoja blanca virus (RHBV). Additionally, pairwise comparisons between the amino acid sequences of the ORFs on the genome of FSaV and the corresponding ones on the genomes of the members of the Tenuvirus genus showed that FSaV shared 83.17% and 90.85% (amino acid) aa identity to IWSV. Moreover, the non-coding intergenic regions (ncIR) shared only between 49.5% to 60.87% nt identity to the corresponding regions on the IWSV genome. Based on the ICTV species demarcation, the results suggest that FSaV may represent a new species of the genus Tenuivirus. Plastid sequence analysis of the HTS data showed that the original host is a member of the genus Festuca most likely the species Festuca pratensis.
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Affiliation(s)
- Yahya Z A Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany
| | - Frank Rabenstein
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Quedlinburg, Saxony-Anhalt, Germany
| | - Amjad Zia
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany
| | - Abdel-Rhman Z A Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany.
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Kholodilov IS, Belova OA, Morozkin ES, Litov AG, Ivannikova AY, Makenov MT, Shchetinin AM, Aibulatov SV, Bazarova GK, Bell-Sakyi L, Bespyatova LA, Bugmyrin SV, Chernetsov N, Chernokhaeva LL, Gmyl LV, Khaisarova AN, Khalin AV, Klimentov AS, Kovalchuk IV, Luchinina SV, Medvedev SG, Nafeev AA, Oorzhak ND, Panjukova EV, Polienko AE, Purmak KA, Romanenko EN, Rozhdestvenskiy EN, Saryglar AA, Shamsutdinov AF, Solomashchenko NI, Trifonov VA, Volchev EG, Vovkotech PG, Yakovlev AS, Zhurenkova OB, Gushchin VA, Karan LS, Karganova GG. Geographical and Tick-Dependent Distribution of Flavi-Like Alongshan and Yanggou Tick Viruses in Russia. Viruses 2021; 13:458. [PMID: 33799742 PMCID: PMC7998622 DOI: 10.3390/v13030458] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 02/03/2023] Open
Abstract
The genus Flavivirus includes related, unclassified segmented flavi-like viruses, two segments of which have homology with flavivirus RNA-dependent RNA polymerase NS5 and RNA helicase-protease NS3. This group includes such viruses as Jingmen tick virus, Alongshan virus, Yanggou tick virus and others. We detected the Yanggou tick virus in Dermacentor nuttalli and Dermacentor marginatus ticks in two neighbouring regions of Russia. The virus prevalence ranged from 0.5% to 8.0%. We detected RNA of the Alongshan virus in 44 individuals or pools of various tick species in eight regions of Russia. The virus prevalence ranged from 0.6% to 7.8%. We demonstrated the successful replication of the Yanggou tick virus and Alongshan virus in IRE/CTVM19 and HAE/CTVM8 tick cell lines without a cytopathic effect. According to the phylogenetic analysis, we divided the Alongshan virus into two groups: an Ixodes persulcatus group and an Ixodes ricinus group. In addition, the I. persulcatus group can be divided into European and Asian subgroups. We found amino acid signatures specific to the I. ricinus and I. persulcatus groups and also distinguished between the European and Asian subgroups of the I. persulcatus group.
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Affiliation(s)
- Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Evgeny S. Morozkin
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Alexander G. Litov
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Anna Y. Ivannikova
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Marat T. Makenov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Alexey M. Shchetinin
- Pathogenic Microorganisms Variability Laboratory, Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.M.S.); (V.A.G.)
| | - Sergey V. Aibulatov
- Laboratory of Parasitic Arthropods, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (S.V.A.); (A.V.K.); (S.G.M.)
| | - Galina K. Bazarova
- Laboratory of Bacteriology, Altai Antiplague Station of Rospotrebnadzor, 649000 Gorno-Altaisk, Russia;
| | - Lesley Bell-Sakyi
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 5RF, UK;
| | - Liubov A. Bespyatova
- Laboratory for Animal and Plant Parasitology, Institute of Biology of Karelian Research Centre, Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (L.A.B.); (S.V.B.)
| | - Sergey V. Bugmyrin
- Laboratory for Animal and Plant Parasitology, Institute of Biology of Karelian Research Centre, Russian Academy of Sciences (IB KarRC RAS), 185910 Petrozavodsk, Russia; (L.A.B.); (S.V.B.)
| | - Nikita Chernetsov
- Laboratory of Ornithology, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Department of Vertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Liubov L. Chernokhaeva
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Larissa V. Gmyl
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Anna N. Khaisarova
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, 432005 Ulyanovsk, Russia; (A.N.K.); (A.A.N.); (P.G.V.)
| | - Alexei V. Khalin
- Laboratory of Parasitic Arthropods, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (S.V.A.); (A.V.K.); (S.G.M.)
| | - Alexander S. Klimentov
- Laboratory of Biochemistry, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia;
- Laboratory of Biology and Indication of Arboviruses, Department Ivanovsky Institute of Virology, Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Irina V. Kovalchuk
- Office of Rospotrebnadzor in the Stavropol Territory, 355008 Stavropol, Russia; (I.V.K.); (N.I.S.)
- Stavropol State Medical University, 355017 Stavropol, Russia
| | | | - Sergey G. Medvedev
- Laboratory of Parasitic Arthropods, Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (S.V.A.); (A.V.K.); (S.G.M.)
| | - Alexander A. Nafeev
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, 432005 Ulyanovsk, Russia; (A.N.K.); (A.A.N.); (P.G.V.)
| | | | - Elena V. Panjukova
- Institute of Biology, Komi Science Center, Ural Branch of Russian Academy of Sciences, 167982 Syktyvkar, Russia;
| | - Alexandra E. Polienko
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Kristina A. Purmak
- FBIH “Center for Hygiene and Epidemiology in the Stavropol kray”, 355008 Stavropol, Russia; (K.A.P.); (E.N.R.)
| | - Evgeniya N. Romanenko
- FBIH “Center for Hygiene and Epidemiology in the Stavropol kray”, 355008 Stavropol, Russia; (K.A.P.); (E.N.R.)
| | | | - Anna A. Saryglar
- Infectious Disease Hospital, 667003 Kyzyl, Russia; (N.D.O.); (A.A.S.)
| | - Anton F. Shamsutdinov
- Kazan Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor, 420015 Kazan, Russia; (A.F.S.); (V.A.T.)
| | - Nataliya I. Solomashchenko
- Office of Rospotrebnadzor in the Stavropol Territory, 355008 Stavropol, Russia; (I.V.K.); (N.I.S.)
- FBIH “Center for Hygiene and Epidemiology in the Stavropol kray”, 355008 Stavropol, Russia; (K.A.P.); (E.N.R.)
| | - Vladimir A. Trifonov
- Kazan Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor, 420015 Kazan, Russia; (A.F.S.); (V.A.T.)
- Kazan State Medical Academy—Branch Campus of the FSBEI FPE «Russian Medical Academy of Continuous Postgraduate Education» of the Ministry of Healthcare of the Russian Federation, 420012 Kazan, Russia
| | - Evgenii G. Volchev
- Institute of Living Systems Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia;
| | - Pavel G. Vovkotech
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, 432005 Ulyanovsk, Russia; (A.N.K.); (A.A.N.); (P.G.V.)
| | - Alexander S. Yakovlev
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
| | - Olga B. Zhurenkova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Vladimir A. Gushchin
- Pathogenic Microorganisms Variability Laboratory, Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.M.S.); (V.A.G.)
- Faculty of Biology, Lomonosov MSU, 119991 Moscow, Russia
| | - Lyudmila S. Karan
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (E.S.M.); (M.T.M.); (O.B.Z.); (L.S.K.)
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, “Chumakov Institute of Poliomyelitis and Viral Encephalitides” FSBSI “Chumakov FSC R&D IBP RAS”, 108819 Moscow, Russia; (I.S.K.); (O.A.B.); (A.G.L.); (A.Y.I.); (L.L.C.); (L.V.G.); (A.E.P.); (A.S.Y.)
- Institute for Translational Medicine and Biotechnology, Sechenov University, 119146 Moscow, Russia
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Kopanke J, Lee J, Stenglein M, Mayo C. In Vitro Reassortment between Endemic Bluetongue Viruses Features Global Shifts in Segment Frequencies and Preferred Segment Combinations. Microorganisms 2021; 9:microorganisms9020405. [PMID: 33669284 PMCID: PMC7920030 DOI: 10.3390/microorganisms9020405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Bluetongue virus (BTV) is an arthropod-borne pathogen that is associated with sometimes severe disease in both domestic and wild ruminants. Predominantly transmitted by Culicoides spp. biting midges, BTV is composed of a segmented, double-stranded RNA genome. Vector expansion and viral genetic changes, such as reassortment between BTV strains, have been implicated as potential drivers of ongoing BTV expansion into previously BTV-free regions. We used an in vitro system to investigate the extent and flexibility of reassortment that can occur between two BTV strains that are considered enzootic to the USA, BTV-2 and BTV-10. Whole genome sequencing (WGS) was coupled with plaque isolation and a novel, amplicon-based sequencing approach to quantitate the viral genetic diversity generated across multiple generations of in vitro propagation. We found that BTV-2 and BTV-10 were able to reassort across multiple segments, but that a preferred BTV-2 viral backbone emerged in later passages and that certain segments were more likely to be found in reassortant progeny. Our findings indicate that there may be preferred segment combinations that emerge during BTV reassortment. Moreover, our work demonstrates the usefulness of WGS and amplicon-based sequencing approaches to improve understanding of the dynamics of reassortment among segmented viruses such as BTV.
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Abstract
The genome of the influenza virus consists of eight distinct single-stranded RNA segments, each encoding proteins essential for the viral life cycle. When the virus infects a host cell, these segments must be replicated and packaged into new budding virions. The viral genome is assembled with remarkably high fidelity: experiments reveal that most virions contain precisely one copy of each of the eight RNA segments. Cell-biological studies suggest that genome assembly is mediated by specific reversible and irreversible interactions between the RNA segments and their associated proteins. However, the precise inter-segment interaction network remains unresolved. Here, we computationally predict that tree-like irreversible interaction networks guarantee high-fidelity genome assembly, while cyclic interaction networks lead to futile or frustrated off-pathway products. We test our prediction against multiple experimental datasets. We find that tree-like networks capture the nearest-neighbour statistics of RNA segments in packaged virions, as observed by electron tomography. Just eight tree-like networks (of a possible 262 144) optimally capture both the nearest-neighbour data and independently measured RNA–RNA binding and co-localization propensities. These eight do not include the previously proposed hub-and-spoke and linear networks. Rather, each predicted network combines hub-like and linear features, consistent with evolutionary models of interaction gain and loss.
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Affiliation(s)
- Nida Farheen
- Indian Institute of Science Education and Research, Pune 411008, India
| | - Mukund Thattai
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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Abstract
RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle. These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA. Genera that possess these genome types include, respectively, Orbivirus (e.g., Bluetongue virus), Dianthovirus (e.g., Red clover necrotic mosaic virus) and Alphainfluenzavirus (e.g., Influenza A virus). Despite their distinct genomic features and diverse host ranges (i.e., animals, plants, and humans, respectively) each of these viruses uses trans-acting RNA–RNA interactions (tRRIs) to facilitate co-packaging of their segmented genome. The tRRIs occur between different viral genome segments and direct the selective packaging of a complete genome complement. Here we explore the current state of understanding of tRRI-mediated co-packaging in the abovementioned viruses and examine other known and potential functions for this class of RNA–RNA interaction.
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Affiliation(s)
- Laura R Newburn
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - K Andrew White
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
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