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Pramono D, Sugimoto K, Kimura T, Miyake A, Nishigaki K. Characterization of the endogenous retrovirus-derived placenta-specific soluble protein EnvV-Fca from domestic cats. FEBS Lett 2024; 598:1792-1806. [PMID: 38604984 DOI: 10.1002/1873-3468.14873] [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: 01/06/2024] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024]
Abstract
Endogenous retroviruses (ERVs) are remnants of ancestral viruses in the host genome. The present study identified the expression of a defective retroviral env gene belonging to the ERV group V member Env (EnvV) in Felis catus (EnvV-Fca). EnV-Fca was specifically detected in the placental trophoblast syncytiotrophobic layer and expressed as a secreted protein in cultured cells. Genetic analyses indicated that EnvV2 genes are widely present in vertebrates and are under purifying selection among carnivores, suggesting a potential benefit for the host. This study suggests that birds, bats, and rodents carrying EnvV2 may play significant roles as intermediate vectors in spreading or cross-transmitting viruses among species. Our findings provide valuable insights into the evolution of ERV in vertebrate hosts.
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Affiliation(s)
- Didik Pramono
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Japan
| | - Kenji Sugimoto
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
| | - Tohru Kimura
- The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
| | - Ariko Miyake
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Japan
| | - Kazuo Nishigaki
- Laboratory of Molecular Immunology and Infectious Disease, Joint Graduate School of Veterinary Medicine, Yamaguchi University, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Japan
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2
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Chung HC, Kim SJ, Hwang SJ, Jeon YS, Song MS, Ko SH, Lee J, Choi Y, Chung CU, Lee JM. Identification and characterization of recent retrovirus in Rhinolophus ferrumequinum bats. Microbiol Spectr 2024; 12:e0432323. [PMID: 38687078 DOI: 10.1128/spectrum.04323-23] [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: 12/31/2023] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
An investigation into retrovirus was conducted in six species of bats (Myotis aurascens, Myotis petax, Myotis macrodactylus, Miniopterus fuliginosus, Rhinolophus ferrumequinum, and Pipistrellus abramus) inhabiting South Korea. Exogenous retroviruses (XRVs) were detected in the tissue samples of R. ferrumequinum individuals by PCR assay. Proviruses were identified in all tissue samples through viral quantification using a digital PCR assay per organ (lung, intestine, heart, brain, wing, kidney, and liver), with viral loads varying greatly between each organ. In phylogenetic analysis based on the whole genome, the Korean bat retroviruses and the R. ferrumequinum retrovirus (RfRV) strain formed a new clade distinct from the Gammaretrovirus clade. The phylogenetic results determined these viruses to be RfRV-like viruses. In the Simplot comparison, Korean RfRV-like viruses exhibited relatively strong fluctuated patterns in the latter part of the envelope gene area compared to other gene areas. Several point mutations within this region (6,878-7,774 bp) of these viruses were observed compared to the RfRV sequence. One Korean RfRV-like virus (named Y4b strain) was successfully recovered in the Raw 264.7 cell line, and virus particles replicated in the cells were confirmed by transmission electron microscopy. RfRVs (or RfRV-like viruses) have been spreading since their first discovery in 2012, and the Korean RfRV-like viruses were assumed to be XRVs that evolved from RfRV.IMPORTANCER. ferrumequinum retrovirus (RfRV)-like viruses were identified in greater horseshoe bats in South Korea. These RfRV-like viruses were considered exogenous retroviruses (XRVs) that emerged from RfRV. Varying amounts of provirus detected in different organs suggest ongoing viral activity, replication, and de novo integration in certain organs. Additionally, the successful recovery of the virus in the Raw 264.7 cell line provides strong evidence supporting their status as XRVs. These viruses have now been identified in South Korea and, more recently, in Kenya since RfRV was discovered in China in 2012, indicating that RfRVs (or RfRV-like viruses) have spread worldwide.
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Affiliation(s)
- Hee Chun Chung
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Sung Jae Kim
- Department of Companion Animal Health, Kyungbok University, Namyangju, South Korea
| | - Su Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Young Shin Jeon
- Department of Life Science, Dongguk University, Gyeongju, South Korea
| | - Min Sik Song
- Bio Institute, OPTOLANE Technologies Inc, Seongnam-si, Gyeonggi-do, South Korea
| | - Si Hwan Ko
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
| | - Jasper Lee
- Department of Microbiology, California University of Science and Medicine, Colton, California, USA
| | - Yoona Choi
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Chul Un Chung
- Department of Life Science, Dongguk University, Gyeongju, South Korea
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, South Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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3
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Albuquerque NK, Silva SP, Aragão CF, Cunha TCAS, Paiva FAS, Coelho TFSB, Cruz ACR. Virome analysis of Desmodus rotundus tissue samples from the Amazon region. BMC Genomics 2024; 25:34. [PMID: 38177994 PMCID: PMC10768307 DOI: 10.1186/s12864-023-09950-w] [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: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses. RESULTS Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages. CONCLUSION This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.
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Affiliation(s)
- Nádia K Albuquerque
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
| | - Sandro P Silva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Carine F Aragão
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Tânia Cristina A S Cunha
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Francisco A S Paiva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Taciana F S B Coelho
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Ana Cecília R Cruz
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil.
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Kamau J, Ergunay K, Webala PW, Justi SA, Bourke BP, Kamau MW, Hassell J, Chege MN, Mwaura DK, Simiyu C, Kibiwot S, Onyuok S, Caicedo-Quiroga L, Li T, Zimmerman DM, Linton YM. A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats. Viruses 2022; 14:v14122820. [PMID: 36560824 PMCID: PMC9785147 DOI: 10.3390/v14122820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND AND METHODS To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing. RESULTS Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified. CONCLUSIONS Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.
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Affiliation(s)
- Joseph Kamau
- One Health Centre, Institute of Primate Research (IPR), Nairobi 00502, Kenya
| | - Koray Ergunay
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara 06230, Turkey
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
- Correspondence:
| | - Paul W. Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Silvia A. Justi
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Brian P. Bourke
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Maureen W. Kamau
- Mpala Research Centre, Nanyuki 10400, Kenya
- Global Health Program, Smithsonian Conservation Biology Institute (SCBI), Front Royal, VA 22630, USA
| | - James Hassell
- Mpala Research Centre, Nanyuki 10400, Kenya
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT 06520, USA
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Mary N. Chege
- One Health Centre, Institute of Primate Research (IPR), Nairobi 00502, Kenya
| | - David K. Mwaura
- One Health Centre, Institute of Primate Research (IPR), Nairobi 00502, Kenya
| | - Cynthia Simiyu
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Sospeter Kibiwot
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Samson Onyuok
- Zoology Department, National Museums of Kenya, Nairobi 00100, Kenya
| | - Laura Caicedo-Quiroga
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
| | - Tao Li
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Dawn M. Zimmerman
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
- Zoology Department, National Museums of Kenya, Nairobi 00100, Kenya
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution Museum Support Center, Suitland, MD 20746, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD 20910, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC 20560, USA
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Van Brussel K, Mahar JE, Ortiz-Baez AS, Carrai M, Spielman D, Boardman WSJ, Baker ML, Beatty JA, Geoghegan JL, Barrs VR, Holmes EC. Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses. Virology 2022; 576:42-51. [PMID: 36150229 DOI: 10.1016/j.virol.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 01/04/2023]
Abstract
Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae, Coronaviridae and Rhabdoviridae, with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting (Coronaviridae, Caliciviridae, Retroviridae) and one possible mammalian-infecting (Birnaviridae) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus) and a novel bat sapovirus (Caliciviridae), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two sampling locations 1375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal samples for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution.
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Affiliation(s)
- Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia
| | - Maura Carrai
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China
| | - Derek Spielman
- School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Wayne S J Boardman
- School of Animal and Veterinary Sciences, Faculty of Science, Engineering and Technology, University of Adelaide, Adelaide, SA, 5371, Australia
| | - Michelle L Baker
- CSIRO Australian Centre for Disease Preparedness, Health and Biosecurity Business Unit, Geelong, VIC, 3220, Australia
| | - Julia A Beatty
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington, 5022, New Zealand
| | - Vanessa R Barrs
- Jockey Club College of Veterinary Medicine & Life Sciences, City University of Hong Kong, Kowloon Tong, People's Republic of China; Centre for Animal Health and Welfare, City University of Hong Kong, Kowloon Tong, People's Republic of China.
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, 2006, Australia.
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Cholleti H, de Jong J, Blomström AL, Berg M. Characterization of Pipistrellus pygmaeus Bat Virome from Sweden. Viruses 2022; 14:v14081654. [PMID: 36016275 PMCID: PMC9415950 DOI: 10.3390/v14081654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/27/2022] [Accepted: 07/24/2022] [Indexed: 11/25/2022] Open
Abstract
Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78–99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88–94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.
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Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
- Correspondence:
| | - Johnny de Jong
- Swedish Biodiversity Centre (CBM), Department of Urban and Rural Development, Swedish University of Agricultural Sciences (SLU), P.O. Box 7016, 750 07 Uppsala, Sweden;
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), P.O. Box 7028, 750 07 Uppsala, Sweden; (A.-L.B.); (M.B.)
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7
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Koch BF. SARS-CoV-2 and human retroelements: a case for molecular mimicry? BMC Genom Data 2022; 23:27. [PMID: 35395708 PMCID: PMC8992427 DOI: 10.1186/s12863-022-01040-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
Background The factors driving the late phase of COVID-19 are still poorly understood. However, autoimmunity is an evolving theme in COVID-19’s pathogenesis. Additionally, deregulation of human retroelements (RE) is found in many viral infections, and has also been reported in COVID-19. Results Unexpectedly, coronaviruses (CoV) – including SARS-CoV-2 – harbour many RE-identical sequences (up to 35 base pairs), and some of these sequences are part of SARS-CoV-2 epitopes associated to COVID-19 severity. Furthermore, RE are expressed in healthy controls and human cells and become deregulated after SARS-CoV-2 infection, showing mainly changes in long interspersed nuclear element (LINE1) expression, but also in endogenous retroviruses. Conclusion CoV and human RE share coding sequences, which are targeted by antibodies in COVID-19 and thus could induce an autoimmune loop by molecular mimicry. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01040-2.
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Affiliation(s)
- Benjamin Florian Koch
- Department of Internal Medicine, Nephrology, Goethe University Hospital, Johann Wolfgang Goethe University Frankfurt/Main, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
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8
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Bolatti EM, Viarengo G, Zorec TM, Cerri A, Montani ME, Hosnjak L, Casal PE, Bortolotto E, Di Domenica V, Chouhy D, Allasia MB, Barquez RM, Poljak M, Giri AA. Viral Metagenomic Data Analyses of Five New World Bat Species from Argentina: Identification of 35 Novel DNA Viruses. Microorganisms 2022; 10:microorganisms10020266. [PMID: 35208721 PMCID: PMC8880087 DOI: 10.3390/microorganisms10020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Bats are natural reservoirs of a variety of zoonotic viruses, many of which cause severe human diseases. Characterizing viruses of bats inhabiting different geographical regions is important for understanding their viral diversity and for detecting viral spillovers between animal species. Herein, the diversity of DNA viruses of five arthropodophagous bat species from Argentina was investigated using metagenomics. Fecal samples of 29 individuals from five species (Tadarida brasiliensis, Molossus molossus, Eumops bonariensis, Eumops patagonicus, and Eptesicus diminutus) living at two different geographical locations, were investigated. Enriched viral DNA was sequenced using Illumina MiSeq, and the reads were trimmed and filtered using several bioinformatic approaches. The resulting nucleotide sequences were subjected to viral taxonomic classification. In total, 4,520,370 read pairs were sequestered by sequencing, and 21.1% of them mapped to viral taxa. Circoviridae and Genomoviridae were the most prevalent among vertebrate viral families in all bat species included in this study. Samples from the T. brasiliensis colony exhibited lower viral diversity than samples from other species of New World bats. We characterized 35 complete genome sequences of novel viruses. These findings provide new insights into the global diversity of bat viruses in poorly studied species, contributing to prevention of emerging zoonotic diseases and to conservation policies for endangered species.
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Affiliation(s)
- Elisa M. Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Gastón Viarengo
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - Tomaz M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Agustina Cerri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, San Lorenzo 1949, Rosario 2000, Argentina;
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Lea Hosnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Pablo E. Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Eugenia Bortolotto
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Violeta Di Domenica
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - María Belén Allasia
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Rubén M. Barquez
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
| | - Adriana A. Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
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