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Morozova OV, Sashina TA, Epifanova NV, Velikzhanina EI, Novikova NA. Phylodynamic characteristics of reassortant DS-1-like G3P[8]-strains of rotavirus type A isolated in Nizhny Novgorod (Russia). Braz J Microbiol 2023; 54:2867-2877. [PMID: 37897627 PMCID: PMC10689624 DOI: 10.1007/s42770-023-01155-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Since 2013, there has been an increase in reports of the spread of a double intergroup reassortant strain of rotavirus type A (RVA) with the genotype G3P[8] and other genes belonging to the second genogroup I2-R2-C2-M2-A2-N2-T2-E2-H2. In our study, we provide a molecular genetic characterization of rotaviruses with genotype G3P[8]-I2 isolated in Nizhny Novgorod. In our study, we used RT-PCR, Sanger sequencing, RNA-PAGE methods. Phylogenetic and phylodynamic analysis were performed using the Bayesian approach. According to our study, there was a significant increase in the proportion of G3P[8] from 15% during the period of 2020-2021 to 53% during the period of 2021-2022 in Nizhny Novgorod, Russia. Phylogenetic analysis based on the VP4 gene revealed that DS-1-like RVAs isolated in Nizhny Novgorod belong to different clusters of the P[8]-3.1 lineage, with a level of variation ranging from 1.1% to 1.3%. Based on the VP6 gene, the equine-like RVAs identified by us carry genetic variants belonging to three distinct clusters of the lineage I2-V, with a variation level ranging from 2.0% to 4.5%. These data indicate the genotypic diversity of circulating DS-1-like G3 RVAs. Phylogenetic analysis of the VP7 gene allowed us to assign the isolates identified in our study to the G3-1 lineage. We estimated that the circulation of the most recent common ancestor of the spreading strains dates back to 2002. Additionally, we determined the typical level of mutations in the VP7 gene, which amounted to 2.14*10-3 substitutions/per site/per year.
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Affiliation(s)
- Olga V Morozova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia.
| | - T A Sashina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N V Epifanova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - E I Velikzhanina
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
| | - N A Novikova
- Department of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russia
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Louge Uriarte EL, Badaracco A, Spetter MJ, Miño S, Armendano JI, Zeller M, Heylen E, Späth E, Leunda MR, Moreira AR, Matthijnssens J, Parreño V, Odeón AC. Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas. Viruses 2023; 15:2115. [PMID: 37896894 PMCID: PMC10611311 DOI: 10.3390/v15102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Rotavirus A (RVA) causes diarrhea in calves and frequently possesses the G6 and P[5]/P[11] genotypes, whereas G8 is less common. We aimed to compare RVA infections and G/P genotypes in beef and dairy calves from major livestock regions of Argentina, elucidate the evolutionary origin of a G8 strain and analyze the G8 lineages, infer the phylogenetic relationship of RVA field strains, and investigate the evolution and spatio-temporal dynamics of the main G6 lineages in American countries. Fecal samples (n = 422) from diarrheic (beef, 104; dairy, 137) and non-diarrheic (beef, 78; dairy, 103) calves were analyzed by ELISA and semi-nested multiplex RT-PCR. Sequencing, phylogenetic, phylodynamic, and phylogeographic analyses were performed. RVA infections were more frequent in beef (22.0%) than in dairy (14.2%) calves. Prevalent genotypes and G6 lineages were G6(IV)P[5] in beef (90.9%) and G6(III)P[11] (41.2%) or mixed genotypes (23.5%) in dairy calves. The only G8 strain was phylogenetically related to bovine and artiodactyl bovine-like strains. Re-analyses inside the G8 genotype identified G8(I) to G8(VIII) lineages. Of all G6 strains characterized, the G6(IV)P[5](I) strains from "Cuenca del Salado" (Argentina) and Uruguay clustered together. According to farm location, a clustering pattern for G6(IV)P[5] strains of beef farms was observed. Both G6 lineage strains together revealed an evolutionary rate of 1.24 × 10-3 substitutions/site/year, and the time to the most recent common ancestor was dated in 1853. The most probable ancestral locations were Argentina in 1981 for G6(III) strains and the USA in 1940 for G6(IV) strains. The highest migration rates for both G6 lineages together were from Argentina to Brazil and Uruguay. Altogether, the epidemiology, genetic diversity, and phylogeny of RVA in calves can differ according to the production system and farm location. We provide novel knowledge about the evolutionary origin of a bovine G8P[11] strain. Finally, bovine G6 strains from American countries would have originated in the USA nearly a century before its first description.
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Affiliation(s)
- Enrique L. Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Alejandra Badaracco
- Instituto Nacional de Tecnología Agropecuaria, EEA Montecarlo, Av. El Libertador Nº 2472, Montecarlo CP3384, Misiones, Argentina;
| | - Maximiliano J. Spetter
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Samuel Miño
- Instituto Nacional de Tecnología Agropecuaria, EEA Cerro Azul, Ruta 14, km 836, Cerro Azul CP3313, Misiones, Argentina;
| | - Joaquín I. Armendano
- Facultad de Ciencias Veterinarias, Departamento de Fisiopatología, Centro de Investigación Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil CP7000, Buenos Aires, Argentina; (M.J.S.); (J.I.A.)
| | - Mark Zeller
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Elisabeth Heylen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Ernesto Späth
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
| | - María Rosa Leunda
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Innovación para la Producción Agropecuaria y el Desarrollo Sostenible, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (M.R.L.); (A.R.M.)
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, University of Leuven, Herestraat 49, 3000 Leuven, Belgium; (M.Z.); (E.H.)
| | - Viviana Parreño
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Virología e Innovaciones Tecnológicas, Nicolas Repetto y de los Reseros s/n, Hurlingham CP1686, Buenos Aires, Argentina
| | - Anselmo C. Odeón
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226, km 73.5, Balcarce B7620, Buenos Aires, Argentina; (E.S.); (A.C.O.)
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Sashina TA, Velikzhanina EI, Morozova OV, Epifanova NV, Novikova NA. Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia. Arch Virol 2023; 168:215. [PMID: 37524885 DOI: 10.1007/s00705-023-05838-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - E I Velikzhanina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - O V Morozova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
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Shikhevich S, Chadaeva I, Khandaev B, Kozhemyakina R, Zolotareva K, Kazachek A, Oshchepkov D, Bogomolov A, Klimova NV, Ivanisenko VA, Demenkov P, Mustafin Z, Markel A, Savinkova L, Kolchanov NA, Kozlov V, Ponomarenko M. Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24043996. [PMID: 36835409 PMCID: PMC9966505 DOI: 10.3390/ijms24043996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.
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Affiliation(s)
- Svetlana Shikhevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Bato Khandaev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rimma Kozhemyakina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anna Kazachek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Natalya V. Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel Demenkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Zakhar Mustafin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Arcady Markel
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir Kozlov
- Research Institute of Fundamental and Clinical Immunology (RIFCI) SB RAS, Novosibirsk 630099, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
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Degiuseppe JI, Torres C, Mbayed VA, Stupka JA. Phylogeography of Rotavirus G8P[8] Detected in Argentina: Evidence of Transpacific Dissemination. Viruses 2022; 14:v14102223. [PMID: 36298778 PMCID: PMC9609476 DOI: 10.3390/v14102223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023] Open
Abstract
Rotavirus is one of the leading causes of diarrhea in children. In 2018, G8P[8], an unusual association of genotypes, was detected with moderate frequency in symptomatic children in Argen-tina, unlike a previous sporadic identification in 2016. The aim of this study was to analyze the dissemination pattern of the G8P[8]-lineage IV strains detected in Argentina. Nucleotide sequences of the VP7 gene of Argentine G8P[8] strains (2016, 2018 and 2019) were studied by discrete phylodynamic analyses, together with other worldwide relevant G8-lineage IV strains. Bayes Factor (BF) was used to assess the strength of the epidemiological association between countries. Phylodynamic analyses determined an evolutionary rate of 3.7 × 10-3 (HDP95%: 1.4 × 10-3-8.2 × 10-3) substitutions/site/year. Likewise, the most recent common ancestor was 32.2 years old, dating back to 1986 (HDP95% = 1984-1988). The spatiotemporal dynamics analysis revealed South Korea as being the country of origin of the Argentine strains (posterior probability of the ancestral state: 0.8471), which was also evidenced by a significant rate of diffusion from South Korea to Argentina (BF: 55.1). The detection of G8 in South America in 2016-2017 was not related to the cases detected in 2018-2019, revealing a new G8 introduction to the region and supporting a transpacific dissemination.
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Affiliation(s)
- Juan Ignacio Degiuseppe
- Laboratorio de Gastroenteritis Virales, INEI-ANLIS “Dr. Carlos G. Malbrán”, Avenida Vélez Sarsfield 563, Ciudad de Buenos Aires 1281, Argentina
- Correspondence: ; Tel.: +54-9-11-5804-6039; Fax: +54-11-4301-7428
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina Junín 954, Ciudad de Buenos Aires 1113, Argentina
| | - Viviana Andrea Mbayed
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Argentina Junín 954, Ciudad de Buenos Aires 1113, Argentina
| | - Juan Andrés Stupka
- Laboratorio de Gastroenteritis Virales, INEI-ANLIS “Dr. Carlos G. Malbrán”, Avenida Vélez Sarsfield 563, Ciudad de Buenos Aires 1281, Argentina
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Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients. Int J Mol Sci 2022; 23:ijms23052835. [PMID: 35269977 PMCID: PMC8911431 DOI: 10.3390/ijms23052835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Although half of hypertensive patients have hypertensive parents, known hypertension-related human loci identified by genome-wide analysis explain only 3% of hypertension heredity. Therefore, mainstream transcriptome profiling of hypertensive subjects addresses differentially expressed genes (DEGs) specific to gender, age, and comorbidities in accordance with predictive preventive personalized participatory medicine treating patients according to their symptoms, individual lifestyle, and genetic background. Within this mainstream paradigm, here, we determined whether, among the known hypertension-related DEGs that we could find, there is any genome-wide hypertension theranostic molecular marker applicable to everyone, everywhere, anytime. Therefore, we sequenced the hippocampal transcriptome of tame and aggressive rats, corresponding to low and high stress reactivity, an increase of which raises hypertensive risk; we identified stress-reactivity-related rat DEGs and compared them with their known homologous hypertension-related animal DEGs. This yielded significant correlations between stress reactivity-related and hypertension-related fold changes (log2 values) of these DEG homologs. We found principal components, PC1 and PC2, corresponding to a half-difference and half-sum of these log2 values. Using the DEGs of hypertensive versus normotensive patients (as the control), we verified the correlations and principal components. This analysis highlighted downregulation of β-protocadherins and hemoglobin as whole-genome hypertension theranostic molecular markers associated with a wide vascular inner diameter and low blood viscosity, respectively.
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Ponomarenko MP, Chadaeva IV, Ponomarenko PM, Bogomolov AG, Oshchepkov DY, Sharypova EB, Suslov VV, Osadchuk AV, Osadchuk LV, Matushkin YG. A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential. Vavilovskii Zhurnal Genet Selektsii 2022; 26:96-108. [PMID: 35342855 PMCID: PMC8894618 DOI: 10.18699/vjgb-22-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
One of the greatest achievements of genetics in the 20th century is D.K. Belyaev’s discovery of destabilizing selection during the domestication of animals and that this selection affects only gene expression regulation (not gene structure) and inf luences systems of neuroendocrine control of ontogenesis in a stressful environment. Among the experimental data generalized by Belyaev’s discovery, there are also f indings about accelerated extinc tion of testes’ hormonal function and disrupted seasonality of reproduction of domesticated foxes in comparison
with their wild congeners. To date, Belyaev’s discovery has already been repeatedly conf irmed, for example, by independent
observations during deer domestication, during the use of rats as laboratory animals, after the reintroduction
of endangered species such as Przewalski’s horse, and during the creation of a Siberian reserve population
of the Siberian grouse when it had reached an endangered status in natural habitats. A genome-wide comparison
among humans, several domestic animals, and some of their wild congeners has given rise to the concept of self-domestication
syndrome, which includes autism spectrum disorders. In our previous study, we created a bioinformatic
model of human self-domestication syndrome using differentially expressed genes (DEGs; of domestic animals
versus their wild congeners) orthologous to the human genes (mainly, nervous-system genes) whose changes in
expression affect reproductive potential, i. e., growth of the number of humans in the absence of restrictions caused
by limiting factors. Here, we applied this model to 68 human genes whose changes in expression alter the reproductive
health of women and men and to 3080 DEGs of domestic versus wild animals. As a result, in domestic animals,
we identif ied 16 and 4 DEGs, the expression changes of which are codirected with changes in the expression of the
human orthologous genes decreasing and increasing human reproductive potential, respectively. The wild animals
had 9 and 11 such DEGs, respectively. This difference between domestic and wild animals was signif icant according
to Pearson’s χ2 test (p < 0.05) and Fisher’s exact test (p < 0.05). We discuss the results from the standpoint of restoration
of endangered animal species whose natural habitats are subject to an anthropogenic impact.
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Affiliation(s)
- M. P. Ponomarenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. V. Chadaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - P. M. Ponomarenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. G. Bogomolov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - D. Yu. Oshchepkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. B. Sharypova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - V. V. Suslov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. V. Osadchuk
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - L. V. Osadchuk
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - Yu. G. Matushkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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8
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Chadaeva I, Ponomarenko P, Kozhemyakina R, Suslov V, Bogomolov A, Klimova N, Shikhevich S, Savinkova L, Oshchepkov D, Kolchanov NA, Markel A, Ponomarenko M. Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation. Animals (Basel) 2021; 11:2667. [PMID: 34573632 PMCID: PMC8465180 DOI: 10.3390/ani11092667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022] Open
Abstract
Belyaev's concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized in commercial colors of the domesticated fox that never occur in the wild and has been confirmed in a wide variety of pet breeds. Many human disease models involving animals allow to test drugs before human testing. Perhaps this is why investigators doing transcriptomic profiling of domestic versus wild animals have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes of tame and aggressive rats, identified their differentially expressed genes (DEGs), and, for the first time, applied principal component analysis to compare them with all the known DEGs of domestic versus wild animals that we could find. Two principal components, PC1 and PC2, respectively explained 67% and 33% of differential-gene-expression variance (hereinafter: log2 value) between domestic and wild animals. PC1 corresponded to multiple orthologous DEGs supported by homologs; these DEGs kept the log2 value sign from species to species and from tissue to tissue (i.e., a common domestication pattern). PC2 represented stand-alone homologous DEG pairs reversing the log2 value sign from one species to another and from tissue to tissue (i.e., representing intraspecific and interspecific variation).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (P.P.); (R.K.); (V.S.); (A.B.); (N.K.); (S.S.); (L.S.); (D.O.); (N.A.K.); (A.M.)
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Sashina TA, Morozova OV, Epifanova NV, Kashnikov AU, Leonov AV, Novikova NA. [Molecular monitoring of the rotavirus ( Reoviridae: Sedoreovirinae: Rotavirus: Rotavirus A) strains circulating in Nizhny Novgorod (2012-2020): detection of the strains with the new genetic features]. Vopr Virusol 2021; 66:140-151. [PMID: 33993684 DOI: 10.36233/0507-4088-46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/15/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The pentavalent rotavirus vaccine has been registered in Russia, however, the vaccination coverage remains low, and an annual increase in the incidence of rotavirus infection is unavoidable. In this regard, molecular monitoring of rotaviruses in order to search for new variants possessing epidemic potential is an urgent task. MATERIAL AND METHODS PCR genotyping and VP4 and VP7 genes sequencing were used to characterize rotaviruses circulating in Nizhny Novgorod in 2012-2020. The phylogenetic analysis of the strains was carried out using the BEAST software package. RESULTS The spectrum included 17 genotypes with predominance of G9P[8] (37,4%). Detected in this study genotypes G1P[4], G1P[9], G2P[8], G4P[4], G4P[6], G8P[8], and G9P[4] were not previously identified in Nizhny Novgorod. The circulation of DS-1-like strains possessing genotypes G1P[8], G3P[8], G8P[8], or G9P[8] and a short RNA pattern had been shown. Rotaviruses of the common genotypes were genetically heterogeneous and belonged to different phylogenetic lineages and/or sublineages (P[4]-IV-a; P[4]-IV-b; P[8]-3.1; P[8]-3.3; P[8]-3.4 and P[8]-3.6; G1-I; G1-II; G2-IVa-1; G2-IVa-3; G3-1; G3-3; G4-I-c; G9-III; G9-VI). DISCUSSION These results extend the available data on the genotypic structure of rotavirus populations in Russia and show the genetic diversity of viral strains. G3P[8] DS-1-like viruses were representatives of the G3-1 lineage, new for the territory of Russia, and had the largest number of amino acid substitutions in the VP7 antigenic epitopes. CONCLUSION The emergence and spread of strains with new genetic features may allow rotavirus to overcome the immunological pressure formed by natural and vaccine-induced immunity, and maintain or increase the incidence of rotavirus infection.
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Affiliation(s)
- T A Sashina
- FSBI «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - O V Morozova
- FSBI «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - N V Epifanova
- FSBI «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - A U Kashnikov
- FSBI «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - A V Leonov
- FSBI «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
| | - N A Novikova
- FSBI «Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology» of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)
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Vasiliev G, Chadaeva I, Rasskazov D, Ponomarenko P, Sharypova E, Drachkova I, Bogomolov A, Savinkova L, Ponomarenko M, Kolchanov N, Osadchuk A, Oshchepkov D, Osadchuk L. A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes. Int J Mol Sci 2021; 22:2346. [PMID: 33652917 PMCID: PMC7956675 DOI: 10.3390/ijms22052346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq data to compare the effect of co-directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common ancestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene-markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson's χ2 test p < 0.001, Fisher's exact test p < 0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial distribution), thus enforcing the norm (wild type).
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Affiliation(s)
- Gennady Vasiliev
- Novosibirsk State University, 630090 Novosibirsk, Russia;
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Irina Drachkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Alexander Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ludmila Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
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Sashina TA, Morozova OV, Epifanova NV, Novikova NA. Genotype constellations of the rotavirus A strains circulating in Nizhny Novgorod, Russia, 2017-2018. INFECTION GENETICS AND EVOLUTION 2020; 85:104578. [PMID: 33010418 DOI: 10.1016/j.meegid.2020.104578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022]
Abstract
Currently, the full-genome-based classification is widely used to investigate rotavirus A (RVA) strains found in different countries around the world. However, the information on the full genotypes of rotaviruses circulating in Russia is limited. Using partial sequencing, this study determined the full genotype constellations of 15 RVA strains in total commonly detected in Nizhny Novgorod (European part of Russia) in 2017-2018, three from each of the following genotypes G1P[8], G4P[8], and G9P[8] and six from G2P[4]. There were two intergenogroup mono-reassortants possessing an identical genotype constellation of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 with the DS-1-like NSP4 gene of probably local origin. A variety of subgenotype lineages and their combinations of Wa-like rotaviruses and genetic heterogeneity among G9P[8] and G1P[8] strains were shown on the basis of phylogenetic analysis of each gene. Moreover, two distinct co-circulating variants that differed in all 11 genome segments were found among DS-1-like rotaviruses.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia.
| | - Olga V Morozova
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia
| | - Natalia V Epifanova
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia
| | - Nadezhda A Novikova
- Laboratory of Molecular Epidemiology of Viral Infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation 603 950, 71 Malaya Yamskaya Str., Nizhny Novgorod, Russia
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