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Vila-Nistal M, Maestre-Carballa L, Martinez-Hernández F, Martinez-Garcia M. Novel RNA viruses from the Atlantic Ocean: Ecogenomics, biogeography, and total virioplankton mass contribution from surface to the deep ocean. Environ Microbiol 2023; 25:3151-3160. [PMID: 37696769 DOI: 10.1111/1462-2920.16502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/04/2023] [Indexed: 09/13/2023]
Abstract
Marine viruses play a major role in the energy and nutrient cycle and affect the evolution of their hosts. Despite their importance, there is still little knowledge about RNA viruses. Here, we have explored the Atlantic Ocean, from surface to deep (4.296 m), and used viromics and quantitative methods to unveil the genomics, biogeography, and the mass contribution of RNA viruses to the total viroplankton. A total of 2481 putative RNA viral contigs (>500 bp) and 107 larger bona fide RNA viral genomes (>2.5 kb) were identified; 88 of them representing novel viruses belonging mostly to two clades: Yangshan assemblage (sister clade to the class Alsuviricetes) and Nodaviridae. These viruses were highly endemic and locally abundant, with little or no presence in other oceans since only ≈15% of them were found in at least one of the Tara sampling metatranscriptomes. Quantitative data indicated that the abundance of RNA viruses in the surface and deep chlorophyll maximum zone was within ≈106 VLP/mL representing a potential contribution of 5.2%-24.4% to the total viroplankton community (DNA and RNA viruses), with DNA viruses being the predominant members (≈107 VLP/mL). However, for the deep sample, the observed trend was the opposite, although as further discussed, several biases should be considered. Together these results contribute to our understanding of the diversity, abundance, and distribution of RNA viruses in the oceans and provide a basis for further investigation into their ecological roles and biogeography.
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Affiliation(s)
- Marina Vila-Nistal
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Alicante, Spain
| | - Lucia Maestre-Carballa
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Alicante, Spain
| | | | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Alicante, Spain
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Li Y, Niu JW, Zhou X, Chu PP, Zhang KL, Gou HC, Yang DX, Zhang JF, Li CL, Liao M, Zhai SL. Development of a multiplex qRT-PCR assay for the detection of porcine epidemic diarrhea virus, porcine transmissible gastroenteritis virus and porcine Deltacoronavirus. Front Vet Sci 2023; 10:1158585. [PMID: 37008344 PMCID: PMC10060962 DOI: 10.3389/fvets.2023.1158585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
Currently, porcine coronaviruses are prevalent in pigs, and due to the outbreak of COVID-19, porcine coronaviruses have become a research hotspot. porcine epidemic diarrhea virus (PEDV), Transmissible Gastroenteritis Virus (TGEV), and Porcine Deltacoronavirus (PDCoV) mentioned in this study mainly cause diarrhea in pigs. These viruses cause significant economic losses and pose a potential public health threat. In this study, specific primers and probes were designed according to the M gene of PEDV, the S gene of TGEV, and the M gene of PDCoV, respectively, and TaqMan probe-based multiplex real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was developed for the simultaneous detection of PEDV, TGEV, and PDCoV. This method has high sensitivity and specificity, and the detection limit of each virus can reach 2.95 × 100 copies/μl. An assay of 160 clinical samples from pigs with diarrhea showed that the positive rates of PEDV, TGEV, and PDCoV were 38.13, 1.88, and 5.00%; the coinfection rates of PEDV+TGEV, PEDV+PDCoV, TGEV+PDCoV, PEDV+TGEV+PDCoV were 1.25, 1.25, 0, 0.63%, respectively. The positive coincidence rates of the multiplex qRT-PCR and single-reaction qRT-PCR were 100%. This method is of great significance for clinical monitoring of the porcine enteric diarrhea virus and helps reduce the loss of the breeding industry and control the spread of the disease.
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Affiliation(s)
- Yan Li
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Jia-Wei Niu
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Xia Zhou
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Pin-Pin Chu
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Kun-Li Zhang
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Hong-Chao Gou
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Dong-Xia Yang
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Jian-Feng Zhang
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Chun-Ling Li
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
| | - Ming Liao
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
- Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, China
| | - Shao-Lun Zhai
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, Guangdong, China
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Dominguez-Huerta G, Wainaina JM, Zayed AA, Culley AI, Kuhn JH, Sullivan MB. The RNA virosphere: How big and diverse is it? Environ Microbiol 2023; 25:209-215. [PMID: 36511833 PMCID: PMC9852017 DOI: 10.1111/1462-2920.16312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - James M Wainaina
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA
| | - Alexander I Culley
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA.,Center of Microbiome Science, Ohio State University, Columbus, Ohio, USA.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio, USA
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