Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation
Lumpy skin disease virus (LSDV), a double‐stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpect...
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| Veröffentlicht in: | Journal of medical virology 2024-08, Vol.96 (8), p.e29829-n/a |
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| description | Lumpy skin disease virus (LSDV), a double‐stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS‐CoV‐2 surveillance underwent whole‐genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract. |
| doi_str_mv | 10.1002/jmv.29829 |
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Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS‐CoV‐2 surveillance underwent whole‐genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract.</description><identifier>ISSN: 0146-6615</identifier><identifier>ISSN: 1096-9071</identifier><identifier>EISSN: 1096-9071</identifier><identifier>DOI: 10.1002/jmv.29829</identifier><identifier>PMID: 39109810</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Adult ; Animals ; Aquatic insects ; Bos taurus ; Bos taurus indicus ; Capripoxvirus ; COVID-19 - diagnosis ; COVID-19 - virology ; DNA viruses ; Female ; Gene sequencing ; Genome, Viral - genetics ; Genomes ; Genomic analysis ; Humans ; human–animal interface ; India ; Lumpy skin disease ; Lumpy Skin Disease - virology ; lumpy skin disease virus (LSDV) ; Lumpy skin disease virus - classification ; Lumpy skin disease virus - genetics ; Lumpy skin disease virus - isolation & purification ; Male ; Metagenomics ; Metagenomics - methods ; Microbiomes ; Microbiota - genetics ; Milk products ; Nasopharynx - microbiology ; Nasopharynx - virology ; Oropharynx - microbiology ; Oropharynx - virology ; Respiratory System - microbiology ; Respiratory System - virology ; Respiratory tract ; Respiratory tract diseases ; SARS-CoV-2 - classification ; SARS-CoV-2 - genetics ; SARS-CoV-2 - isolation & purification ; Severe acute respiratory syndrome coronavirus 2 ; Skin diseases ; Transmitters ; upper respiratory tract ; Urban areas ; Vectors ; Viral diseases ; Viruses ; Whole Genome Sequencing ; Zoonoses</subject><ispartof>Journal of medical virology, 2024-08, Vol.96 (8), p.e29829-n/a</ispartof><rights>2024 Wiley Periodicals LLC.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c2439-dd60d736b3850bb9b98cdf981f7b70d3e4bfe25192416efc729f153542eae6963</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjmv.29829$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjmv.29829$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,781,785,1418,27928,27929,45578,45579</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39109810$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tomar, Siddharth Singh</creatorcontrib><creatorcontrib>Khairnar, Krishna</creatorcontrib><title>Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation</title><title>Journal of medical virology</title><addtitle>J Med Virol</addtitle><description>Lumpy skin disease virus (LSDV), a double‐stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS‐CoV‐2 surveillance underwent whole‐genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract.</description><subject>Adult</subject><subject>Animals</subject><subject>Aquatic insects</subject><subject>Bos taurus</subject><subject>Bos taurus indicus</subject><subject>Capripoxvirus</subject><subject>COVID-19 - diagnosis</subject><subject>COVID-19 - virology</subject><subject>DNA viruses</subject><subject>Female</subject><subject>Gene sequencing</subject><subject>Genome, Viral - genetics</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Humans</subject><subject>human–animal interface</subject><subject>India</subject><subject>Lumpy skin disease</subject><subject>Lumpy Skin Disease - virology</subject><subject>lumpy skin disease virus (LSDV)</subject><subject>Lumpy skin disease virus - classification</subject><subject>Lumpy skin disease virus - genetics</subject><subject>Lumpy skin disease virus - isolation & purification</subject><subject>Male</subject><subject>Metagenomics</subject><subject>Metagenomics - methods</subject><subject>Microbiomes</subject><subject>Microbiota - genetics</subject><subject>Milk products</subject><subject>Nasopharynx - microbiology</subject><subject>Nasopharynx - virology</subject><subject>Oropharynx - microbiology</subject><subject>Oropharynx - virology</subject><subject>Respiratory System - microbiology</subject><subject>Respiratory System - virology</subject><subject>Respiratory tract</subject><subject>Respiratory tract diseases</subject><subject>SARS-CoV-2 - classification</subject><subject>SARS-CoV-2 - genetics</subject><subject>SARS-CoV-2 - isolation & purification</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Skin diseases</subject><subject>Transmitters</subject><subject>upper respiratory tract</subject><subject>Urban areas</subject><subject>Vectors</subject><subject>Viral diseases</subject><subject>Viruses</subject><subject>Whole Genome Sequencing</subject><subject>Zoonoses</subject><issn>0146-6615</issn><issn>1096-9071</issn><issn>1096-9071</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kU1P3DAQhi1UBFvaQ_9AZamX9hAY24kTHyvoBxWIC-01cpJx8TZf2PGi7a9n6AKHSpwseR4_M-OXsXcCjgWAPFkPm2NpKmn22EqA0ZmBUrxiKxC5zrQWxSF7HeMaACoj5QE7VIawSsCK_T3DBdvFTyOfHO_TMG95_ONH3vmINiLf-JAiD2i7yOl6uUF-kwY78jTPGKgQZx_sMoUtX4JtFz74NkyNnwak4m3yRHCXAj0MJNhgXPxv-9DwDdt3to_49vE8Yj-_frk-_Z5dXH07P_18kbUyVybrOg1dqXSjqgKaxjSmajtH07uyKaFTmDcOZSGMzIVG15bSOFGoIpdoURutjtjHnXcO022i_vXgY4t9b0ecUqwV_UpVQWkEoR_-Q9dTCiNNR5QptQRQBVGfdhQtGmNAV8_BDzZsawH1QyA1BVL_C4TY94_G1AzYPZNPCRBwsgPufI_bl031j8tfO-U9GcuXGQ</recordid><startdate>202408</startdate><enddate>202408</enddate><creator>Tomar, Siddharth Singh</creator><creator>Khairnar, Krishna</creator><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7TK</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>202408</creationdate><title>Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation</title><author>Tomar, Siddharth Singh ; Khairnar, Krishna</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2439-dd60d736b3850bb9b98cdf981f7b70d3e4bfe25192416efc729f153542eae6963</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Adult</topic><topic>Animals</topic><topic>Aquatic insects</topic><topic>Bos taurus</topic><topic>Bos taurus indicus</topic><topic>Capripoxvirus</topic><topic>COVID-19 - diagnosis</topic><topic>COVID-19 - virology</topic><topic>DNA viruses</topic><topic>Female</topic><topic>Gene sequencing</topic><topic>Genome, Viral - genetics</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Humans</topic><topic>human–animal interface</topic><topic>India</topic><topic>Lumpy skin disease</topic><topic>Lumpy Skin Disease - virology</topic><topic>lumpy skin disease virus (LSDV)</topic><topic>Lumpy skin disease virus - classification</topic><topic>Lumpy skin disease virus - genetics</topic><topic>Lumpy skin disease virus - isolation & purification</topic><topic>Male</topic><topic>Metagenomics</topic><topic>Metagenomics - methods</topic><topic>Microbiomes</topic><topic>Microbiota - genetics</topic><topic>Milk products</topic><topic>Nasopharynx - microbiology</topic><topic>Nasopharynx - virology</topic><topic>Oropharynx - microbiology</topic><topic>Oropharynx - virology</topic><topic>Respiratory System - microbiology</topic><topic>Respiratory System - virology</topic><topic>Respiratory tract</topic><topic>Respiratory tract diseases</topic><topic>SARS-CoV-2 - classification</topic><topic>SARS-CoV-2 - genetics</topic><topic>SARS-CoV-2 - isolation & purification</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Skin diseases</topic><topic>Transmitters</topic><topic>upper respiratory tract</topic><topic>Urban areas</topic><topic>Vectors</topic><topic>Viral diseases</topic><topic>Viruses</topic><topic>Whole Genome Sequencing</topic><topic>Zoonoses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tomar, Siddharth Singh</creatorcontrib><creatorcontrib>Khairnar, Krishna</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of medical virology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tomar, Siddharth Singh</au><au>Khairnar, Krishna</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation</atitle><jtitle>Journal of medical virology</jtitle><addtitle>J Med Virol</addtitle><date>2024-08</date><risdate>2024</risdate><volume>96</volume><issue>8</issue><spage>e29829</spage><epage>n/a</epage><pages>e29829-n/a</pages><issn>0146-6615</issn><issn>1096-9071</issn><eissn>1096-9071</eissn><abstract>Lumpy skin disease virus (LSDV), a double‐stranded DNA virus from the Capripoxvirus genus, primarily affects Bos indicus, Bos taurus breeds, and water buffalo. Arthropod vectors, including mosquitoes and biting flies, are the main LSDV transmitters. Although LSDV is not zoonotic, this study unexpectedly detected LSDV reads in the upper respiratory tract microbiome of humans from rural and urban areas in Maharashtra, India. Nasopharyngeal and oropharyngeal swab samples collected for SARS‐CoV‐2 surveillance underwent whole‐genome metagenomics sequencing, revealing LSDV reads in 25% of samples. Split kmer analysis provided insights into sample relatedness despite the low coverage of LSDV reads with the reference genome. Our findings, which include the detection of LSDV contigs aligning to specific locations on the reference genome, suggest a common source for LSDV reads, potentially shared water sources, or milk/milk products. Further investigation is needed to ascertain the mode of transmission and reason for the detection of LSDV reads in human upper respiratory tract.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>39109810</pmid><doi>10.1002/jmv.29829</doi><tpages>12</tpages></addata></record> |
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| subjects | Adult Animals Aquatic insects Bos taurus Bos taurus indicus Capripoxvirus COVID-19 - diagnosis COVID-19 - virology DNA viruses Female Gene sequencing Genome, Viral - genetics Genomes Genomic analysis Humans human–animal interface India Lumpy skin disease Lumpy Skin Disease - virology lumpy skin disease virus (LSDV) Lumpy skin disease virus - classification Lumpy skin disease virus - genetics Lumpy skin disease virus - isolation & purification Male Metagenomics Metagenomics - methods Microbiomes Microbiota - genetics Milk products Nasopharynx - microbiology Nasopharynx - virology Oropharynx - microbiology Oropharynx - virology Respiratory System - microbiology Respiratory System - virology Respiratory tract Respiratory tract diseases SARS-CoV-2 - classification SARS-CoV-2 - genetics SARS-CoV-2 - isolation & purification Severe acute respiratory syndrome coronavirus 2 Skin diseases Transmitters upper respiratory tract Urban areas Vectors Viral diseases Viruses Whole Genome Sequencing Zoonoses |
| title | Detection of lumpy skin disease virus reads in the human upper respiratory tract microbiome requires further investigation |
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