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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: 1.0] [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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Hrdy J, Vasickova P. Virus detection methods for different kinds of food and water samples – The importance of molecular techniques. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Barsoum Z. Pediatric Astrovirus Gastroenteritis: One-Year Prospective Irish Study. Turk Arch Pediatr 2021. [PMID: 35110068 PMCID: PMC9476272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Pérot P, Lecuit M, Eloit M. Astrovirus Diagnostics. Viruses 2017; 9:v9010010. [PMID: 28085120 PMCID: PMC5294979 DOI: 10.3390/v9010010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 01/25/2023] Open
Abstract
Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
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Affiliation(s)
- Philippe Pérot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Institut Pasteur, Centre d'innovation et de Recherche Technologique (Citech), 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Paris Descartes University, Sorbonne Paris Cité, 75005, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, 75015 Paris, France.
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France.
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Abstract
Gastroenteritis is a clinical illness of humans and other animals that is characterized by vomiting and diarrhea and caused by a variety of pathogens, including viruses. An increasing number of viral species have been associated with gastroenteritis or have been found in stool samples as new molecular tools have been developed. In this work, a DNA microarray capable in theory of parallel detection of more than 100 viral species was developed and tested. Initial validation was done with 10 different virus species, and an additional 5 species were validated using clinical samples. Detection limits of 1 × 10(3) virus particles of Human adenovirus C (HAdV), Human astrovirus (HAstV), and group A Rotavirus (RV-A) were established. Furthermore, when exogenous RNA was added, the limit for RV-A detection decreased by one log. In a small group of clinical samples from children with gastroenteritis (n = 76), the microarray detected at least one viral species in 92% of the samples. Single infection was identified in 63 samples (83%), and coinfection with more than one virus was identified in 7 samples (9%). The most abundant virus species were RV-A (58%), followed by Anellovirus (15.8%), HAstV (6.6%), HAdV (5.3%), Norwalk virus (6.6%), Human enterovirus (HEV) (9.2%), Human parechovirus (1.3%), Sapporo virus (1.3%), and Human bocavirus (1.3%). To further test the specificity and sensitivity of the microarray, the results were verified by reverse transcription-PCR (RT-PCR) detection of 5 gastrointestinal viruses. The RT-PCR assay detected a virus in 59 samples (78%). The microarray showed good performance for detection of RV-A, HAstV, and calicivirus, while the sensitivity for HAdV and HEV was low. Furthermore, some discrepancies in detection of mixed infections were observed and were addressed by reverse transcription-quantitative PCR (RT-qPCR) of the viruses involved. It was observed that differences in the amount of genetic material favored the detection of the most abundant virus. The microarray described in this work should help in understanding the etiology of gastroenteritis in humans and animals.
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Abstract
Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.
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Affiliation(s)
- Albert Bosch
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
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