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da Costa AC, Tozetto-Mendoza TR, Foro Ramos EDS, Bortoletto P, Ferreira NE, Honorato L, Garcia Barbosa EM, Paião HGO, de Souza AF, Linhares IM, Spandorfer SD, Leal E, Mendes-Correa MC, Witkin SS. First Detection and Characterization of Smacovirus in the Human Vagina in Two Sequential Samples over a Twelve-Day Interval. Viruses 2024; 16:1545. [PMID: 39459879 PMCID: PMC11512292 DOI: 10.3390/v16101545] [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: 08/20/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 10/28/2024] Open
Abstract
BACKGROUND Smacovirus is a CRESS-DNA virus identified almost exclusively in transient fecal samples from various vertebrate species. OBJECTIVE We evaluated human vaginal samples for the presence and maintenance of Smacovirus. METHODS Viral metagenomics analysis was performed on vaginal samples collected from 28 apparently healthy women in New York City, USA. Twenty-one of the women provided duplicate samples over a 12-21-day interval. RESULTS Phylogenetic analysis identified two samples from the same individual, collected over a twelve-day interval, that were positive for the complete Smacovirus genome. All detected sequence contigs belonged to a single variant of CRESS-DNA. CONCLUSIONS The continuous presence of Smacovirus in the human vagina over a twelve-day period was identified.
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Affiliation(s)
- Antonio Charlys da Costa
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Tania Regina Tozetto-Mendoza
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil; (E.d.S.F.R.); (E.L.)
| | - Pietro Bortoletto
- Boston IVF-The Eugin Group, Waltham 02451, MA, USA;
- Harvard Medical School, Boston 02115, MA, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston 02115, MA, USA
| | - Noely Evangelista Ferreira
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Layla Honorato
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Erick Matheus Garcia Barbosa
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Heuder Gustavo Oliveira Paião
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Amanda Fernandes de Souza
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Iara M. Linhares
- Department of Gynecology and Obstetrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, Brazil;
| | - Steven D. Spandorfer
- Center for Reproductive Medicine and Infertility, Weill Cornell Medicine, New York 10001, NY, USA;
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Brazil; (E.d.S.F.R.); (E.L.)
| | - Maria Cassia Mendes-Correa
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
| | - Steven S. Witkin
- Laboratorio de Virologia (LIM52), Departamento de Infectologia e Medicina Tropical, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Av. Dr Enéas de Carvalho Aguiar, 470, São Paulo 05403-000, Brazil; (A.C.d.C.); (N.E.F.); (L.H.); (E.M.G.B.); (H.G.O.P.); (A.F.d.S.); (M.C.M.-C.); (S.S.W.)
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York 10001, NY, USA
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Da Costa AC, Bortoletto P, Spandorfer SD, Tozetto-Mendoza TR, Linhares IM, Mendes-Correa MC, Witkin SS. Association between torquetenovirus in vaginal secretions and infertility: An exploratory metagenomic analysis. Am J Reprod Immunol 2023; 90:e13788. [PMID: 37881119 DOI: 10.1111/aji.13788] [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: 03/26/2023] [Revised: 06/20/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023] Open
Abstract
PROBLEM The association of viruses with infertility remains incompletely evaluated. METHOD OF STUDY Vaginal secretions from 46 women seeking treatment in the Center for Reproductive Medicine and Infertility at Weill Cornell Medicine were tested for viruses by metagenomic analysis by lab personnel blinded to all clinical data. RESULTS Torquetenovirus (TTV) was identified in 16 women, alphapapillomavirus in seven women and most were positive for bacteriophages. Twelve of the subjects were fertile and sought to freeze their oocytes for future implantation. These women were all negative for TTV. In contrast, 16 of the 34 women (47.1%) being treated for infertility were TTV-positive (p = .0035). Evaluating the women by cause of infertility, five of nine women (55.6%) whose male partner had inadequate sperm parameters and six of 14 women (42.9%) with defective ovulation were TTV positive (p = .0062 and p = .0171, respectively, vs. the fertile women). Alphapapillomavirus was identified in one (8.3%) fertile woman, five (35.7%) women with ovulation deficiency, and one (11.1%) woman with male factor infertility. These differences were not statistically significant. There were no differences in bacteriophage families or the presence of Lactobacillus phages between fertile or infertile women or between different causes of infertility. There was a negative association between TTV detection and Lactobacillus crispatus dominance in the vaginal microbiota (p = .0184), but no association between TTV detection and the presence of alphapapillomavirus or Candida species. CONCLUSION Detection of TTV in the vagina might be a biomarker for specific causes of infertility.
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Affiliation(s)
- A Charlys Da Costa
- Laboratory of Investigative Medicine in Virology (LIM 52), Department of Infectious Diseases, Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Pietro Bortoletto
- Boston IVF, Waltham, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Steven D Spandorfer
- Center for Reproductive Medicine and Infertility, Weill Cornell Medicine, New York, USA
| | - Tania Regina Tozetto-Mendoza
- Laboratory of Investigative Medicine in Virology (LIM 52), Department of Infectious Diseases, Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Iara M Linhares
- Department of Gynecology and Obstetrics, Faculty of Medicine of the University of Sao Paulo, Sao Paulo, Brazil
| | - Maria Cassia Mendes-Correa
- Faculty of Medicine of the University of São Paulo - São Paulo, Sao Paulo, Brazil
- Laboratory of Investigative Medicine in Virology (LIM-52), Sao Paulo, Brazil
| | - Steven S Witkin
- Laboratory of Investigative Medicine in Virology (LIM-52), Sao Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA
- Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
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Potapov S, Gorshkova A, Krasnopeev A, Podlesnaya G, Tikhonova I, Suslova M, Kwon D, Patrushev M, Drucker V, Belykh O. RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters. Int J Mol Sci 2023; 24:12049. [PMID: 37569424 PMCID: PMC10418309 DOI: 10.3390/ijms241512049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.
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Affiliation(s)
- Sergey Potapov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Anna Gorshkova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Andrey Krasnopeev
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Galina Podlesnaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Irina Tikhonova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Maria Suslova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Dmitry Kwon
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Maxim Patrushev
- National Research Center Kurchatov Institute, Academician Kurchatov Square 1, 123098 Moscow, Russia
| | - Valentin Drucker
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
| | - Olga Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia (O.B.)
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Demoliner M, Filippi M, Gularte JS, da Silva MS, de Almeida PR, Pereira VMDAG, Heldt FH, Spilki FR. Genome of a husavirus from Southern Brazil. Rev Inst Med Trop Sao Paulo 2023; 65:e5. [PMID: 36651466 PMCID: PMC9870242 DOI: 10.1590/s1678-9946202365005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/21/2022] [Indexed: 01/18/2023] Open
Abstract
New viruses of the Picornavirales order have been discovered with the increase in the number of sequences obtained by high-throughput sequencing, as well as human stool-associated RNA virus (husavirus [HuV]), found in human stool samples. However, there is much to be clarified about HuV. Its cellular host, evolutionary history, and other biological characteristics are still unknown. Therefore, samples collected from human beings and environmental samples in a watershed in Southern Brazil were processed for the metagenomic library. Upon metagenomic analysis, we identified a HuV (husavirus LMM_67754 OP019707) genome with 8,846 bp, which was reported for the first time in Southern Brazil. The new genome presents only 37% of nucleotide identity with Brazilian strains and more than 90% with genomes from China, Vietnam, Venezuela, and the Netherlands. The HuV phylogeny presents significant differences among genomes, probably because multiple introductions of the virus may have occurred. Many questions still need to be answered about HuV. Therefore, more sequences and studies on this virus are necessary to improve the comprehension of the unknown origin of Picornavirales.
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Affiliation(s)
- Meriane Demoliner
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Micheli Filippi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariana Soares da Silva
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | | | - Fágner Henrique Heldt
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, Rio Grande do Sul, Brazil
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do Socorro Fôro Ramos E, de Oliveira Ribeiro G, Villanova F, de Padua Milagres FA, Brustulin R, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, Luchs A, da Costa AC, Leal É. Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis. Viruses 2021; 13:2365. [PMID: 34960634 PMCID: PMC8704738 DOI: 10.3390/v13122365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 01/21/2023] Open
Abstract
Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.
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Affiliation(s)
- Endrya do Socorro Fôro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
| | - Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
| | - Flávio Augusto de Padua Milagres
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, Tocantins, Brazil
| | - Rafael Brustulin
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, Brazil;
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Virology Center, Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo 01246-000, São Paulo, Brazil;
| | - Antonio Charlys da Costa
- Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil;
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
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