Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022
The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next‐...
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| Veröffentlicht in: | Journal of medical virology 2024-06, Vol.96 (6), p.e29706-n/a |
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| creator | Hikmat, Houmadi Le Targa, Lorlane Boschi, Celine Py, Justine Bedotto, Marielle Morand, Aurélie Cassir, Nadim Aherfi, Sarah La Scola, Bernard Colson, Philippe |
| description | The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next‐generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in‐house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co‐infection. Subsequent HAdV typing for HBoV1‐positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1‐associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation. |
| doi_str_mv | 10.1002/jmv.29706 |
| format | Article |
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Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next‐generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in‐house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co‐infection. Subsequent HAdV typing for HBoV1‐positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1‐associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.</description><identifier>ISSN: 0146-6615</identifier><identifier>ISSN: 1096-9071</identifier><identifier>EISSN: 1096-9071</identifier><identifier>DOI: 10.1002/jmv.29706</identifier><identifier>PMID: 38888111</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>adenovirus ; Adenoviruses ; Adolescent ; Adult ; Aged ; Amino acids ; Bacteriology ; Cardiology and cardiovascular system ; Child ; Child, Preschool ; Cluster analysis ; Clustering ; Coinfection - epidemiology ; Coinfection - virology ; coinfections ; DNA, Viral - genetics ; Emerging diseases ; evolution ; Female ; France - epidemiology ; Genetic Variation ; genome ; Genome, Viral - genetics ; Genomes ; Genomic analysis ; Genotype ; High-Throughput Nucleotide Sequencing ; human bocavirus ; Human bocavirus - classification ; Human bocavirus - genetics ; Human bocavirus - isolation & purification ; Human health and pathology ; Humans ; Infant ; Infectious diseases ; Life Sciences ; Male ; Microbiology and Parasitology ; Middle Aged ; Nasopharynx - virology ; Parasitology ; Parvoviridae Infections - epidemiology ; Parvoviridae Infections - virology ; Phylogeny ; Principal components analysis ; Respiratory diseases ; Rhinovirus ; Sequence Analysis, DNA ; Virology ; Young Adult</subject><ispartof>Journal of medical virology, 2024-06, Vol.96 (6), p.e29706-n/a</ispartof><rights>2024 The Author(s). published by Wiley Periodicals LLC.</rights><rights>2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.</rights><rights>2024. This article is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c3826-84ced07a43f653dde2f202e36f11239238bd5d07b5b45b5436cd61c373d844643</cites><orcidid>0000-0001-8006-7704 ; 0000-0001-6285-0308</orcidid></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.29706$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjmv.29706$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38888111$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://amu.hal.science/hal-04677926$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Hikmat, Houmadi</creatorcontrib><creatorcontrib>Le Targa, Lorlane</creatorcontrib><creatorcontrib>Boschi, Celine</creatorcontrib><creatorcontrib>Py, Justine</creatorcontrib><creatorcontrib>Bedotto, Marielle</creatorcontrib><creatorcontrib>Morand, Aurélie</creatorcontrib><creatorcontrib>Cassir, Nadim</creatorcontrib><creatorcontrib>Aherfi, Sarah</creatorcontrib><creatorcontrib>La Scola, Bernard</creatorcontrib><creatorcontrib>Colson, Philippe</creatorcontrib><title>Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022</title><title>Journal of medical virology</title><addtitle>J Med Virol</addtitle><description>The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next‐generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in‐house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co‐infection. Subsequent HAdV typing for HBoV1‐positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1‐associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.</description><subject>adenovirus</subject><subject>Adenoviruses</subject><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Amino acids</subject><subject>Bacteriology</subject><subject>Cardiology and cardiovascular system</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Cluster analysis</subject><subject>Clustering</subject><subject>Coinfection - epidemiology</subject><subject>Coinfection - virology</subject><subject>coinfections</subject><subject>DNA, Viral - genetics</subject><subject>Emerging diseases</subject><subject>evolution</subject><subject>Female</subject><subject>France - epidemiology</subject><subject>Genetic Variation</subject><subject>genome</subject><subject>Genome, Viral - genetics</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Genotype</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>human bocavirus</subject><subject>Human bocavirus - classification</subject><subject>Human bocavirus - genetics</subject><subject>Human bocavirus - isolation & purification</subject><subject>Human health and pathology</subject><subject>Humans</subject><subject>Infant</subject><subject>Infectious diseases</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Microbiology and Parasitology</subject><subject>Middle Aged</subject><subject>Nasopharynx - virology</subject><subject>Parasitology</subject><subject>Parvoviridae Infections - epidemiology</subject><subject>Parvoviridae Infections - virology</subject><subject>Phylogeny</subject><subject>Principal components analysis</subject><subject>Respiratory diseases</subject><subject>Rhinovirus</subject><subject>Sequence Analysis, DNA</subject><subject>Virology</subject><subject>Young Adult</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>24P</sourceid><sourceid>EIF</sourceid><recordid>eNp10U1rFDEcBvAgit1WD34BCXixh2nzNsnMsZTWKiseql5DJvnPbpaZZE1mtlS_vNlurSCYSyD88uTlQegNJWeUEHa-GXdnrFVEPkMLSlpZtUTR52hBqJCVlLQ-Qsc5bwghTcvYS3TEmzIopQv06xZ-zBCsDytsgsN2bZKxEyT_00w-Bhx7vJ5HE3AXrdn5NGe8ghBHyLhPccTbwiBMGTtvViFmcNgHfBvnaQ0p4OtkggXcwXQHEDAjVD2cwwhjr9CL3gwZXj_OJ-jb9dXXy5tq-eXDx8uLZWV5w2TVCAuOKCN4L2vuHLC-7AYue0oZbxlvOlcX0NWdqLtacGmdpJYr7hohpOAn6PSQuzaD3iY_mnSvo_H65mKp92tESKVaJne02PcHu02xfEye9OizhWEwAeKcNSeKqLZuRVvou3_oJs4plJfsFRONaiX_e7hNMecE_dMNKNH79nRpTz-0V-zbx8S5G8E9yT91FXB-AHd-gPv_J-lPn78fIn8DuGuhww</recordid><startdate>202406</startdate><enddate>202406</enddate><creator>Hikmat, Houmadi</creator><creator>Le Targa, Lorlane</creator><creator>Boschi, Celine</creator><creator>Py, Justine</creator><creator>Bedotto, Marielle</creator><creator>Morand, Aurélie</creator><creator>Cassir, Nadim</creator><creator>Aherfi, Sarah</creator><creator>La Scola, Bernard</creator><creator>Colson, Philippe</creator><general>Wiley Subscription Services, Inc</general><general>Wiley-Blackwell</general><scope>24P</scope><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><scope>1XC</scope><orcidid>https://orcid.org/0000-0001-8006-7704</orcidid><orcidid>https://orcid.org/0000-0001-6285-0308</orcidid></search><sort><creationdate>202406</creationdate><title>Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022</title><author>Hikmat, Houmadi ; 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Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next‐generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in‐house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co‐infection. Subsequent HAdV typing for HBoV1‐positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1‐associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>38888111</pmid><doi>10.1002/jmv.29706</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0001-8006-7704</orcidid><orcidid>https://orcid.org/0000-0001-6285-0308</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | adenovirus Adenoviruses Adolescent Adult Aged Amino acids Bacteriology Cardiology and cardiovascular system Child Child, Preschool Cluster analysis Clustering Coinfection - epidemiology Coinfection - virology coinfections DNA, Viral - genetics Emerging diseases evolution Female France - epidemiology Genetic Variation genome Genome, Viral - genetics Genomes Genomic analysis Genotype High-Throughput Nucleotide Sequencing human bocavirus Human bocavirus - classification Human bocavirus - genetics Human bocavirus - isolation & purification Human health and pathology Humans Infant Infectious diseases Life Sciences Male Microbiology and Parasitology Middle Aged Nasopharynx - virology Parasitology Parvoviridae Infections - epidemiology Parvoviridae Infections - virology Phylogeny Principal components analysis Respiratory diseases Rhinovirus Sequence Analysis, DNA Virology Young Adult |
| title | Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022 |
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