Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region

Autores
Sicilia, Paola; Fantilli, Anabella Clara; Cuba, Facundo; Di Cola Bucciarelli, Guadalupe; Barbas, Maria Gabriela; Poklepovich, Tomás; Ré, Viviana Elizabeth; Castro, Gonzalo; Pisano, María Belén
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Molecular epidemiology of hepatitis A virus (HAV) plays a critical role in identifying outbreak originand conducting surveillance. Although it is mostly carried out using short partial VP1/2A genomicsequences, utilizing whole-genome sequences (WGS) provides more accurate and robust information. We developed an amplicon-based next-generation sequencing (NGS) strategy to obtain complete HAV genomes utilizing the COVIDSeq Test (Illumina). Twenty-five primer pairs were designed and used to amplify partial genomic fragments (400 bp) that comprise the entire HAV genome sequence from previously HAV positive serum and stool samples from Argentina. The DNA library was prepared using the Illumina COVIDSeq Test and sequenced in a MiSeq equipment. Phylogenetic analyses were performed with IQ-Tree using WGS and VP1/2A partial sequences of 1084pb and 422pb. Eleven samples were amplified and sequenced, with coverage between 79.3 and 100% (> 90% in 9 samples). Although phylogenetic analyses of partial sequences allowed genotype and subgenotype identification, WGS analyses yielded more accurate and reliable results for the phylogeny (phylogenetic definition). The amplicon-based NGS WGS tool developed by adapting the COVIDSeq test to HAV proved to be efficient. The study of partial VP1/2A regions (mainly the 1084 bp fragment) would constitute useful alternatives for outbreak investigation and surveillance when WGS could not be performed.
Fil: Sicilia, Paola. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina
Fil: Fantilli, Anabella Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Cuba, Facundo. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Centro Nacional de Genética Médica; Argentina
Fil: Di Cola Bucciarelli, Guadalupe. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Barbas, Maria Gabriela. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina
Fil: Poklepovich, Tomás. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Centro Nacional de Genética Médica; Argentina
Fil: Ré, Viviana Elizabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Castro, Gonzalo. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Pisano, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Materia
HEPATITIS A VIRUS
HAV
NGS
SEQUENCING
WHOLE GENOME SEQUENCING
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/289458
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic regionSicilia, PaolaFantilli, Anabella ClaraCuba, FacundoDi Cola Bucciarelli, GuadalupeBarbas, Maria GabrielaPoklepovich, TomásRé, Viviana ElizabethCastro, GonzaloPisano, María BelénHEPATITIS A VIRUSHAVNGSSEQUENCINGWHOLE GENOME SEQUENCINGhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Molecular epidemiology of hepatitis A virus (HAV) plays a critical role in identifying outbreak originand conducting surveillance. Although it is mostly carried out using short partial VP1/2A genomicsequences, utilizing whole-genome sequences (WGS) provides more accurate and robust information. We developed an amplicon-based next-generation sequencing (NGS) strategy to obtain complete HAV genomes utilizing the COVIDSeq Test (Illumina). Twenty-five primer pairs were designed and used to amplify partial genomic fragments (400 bp) that comprise the entire HAV genome sequence from previously HAV positive serum and stool samples from Argentina. The DNA library was prepared using the Illumina COVIDSeq Test and sequenced in a MiSeq equipment. Phylogenetic analyses were performed with IQ-Tree using WGS and VP1/2A partial sequences of 1084pb and 422pb. Eleven samples were amplified and sequenced, with coverage between 79.3 and 100% (> 90% in 9 samples). Although phylogenetic analyses of partial sequences allowed genotype and subgenotype identification, WGS analyses yielded more accurate and reliable results for the phylogeny (phylogenetic definition). The amplicon-based NGS WGS tool developed by adapting the COVIDSeq test to HAV proved to be efficient. The study of partial VP1/2A regions (mainly the 1084 bp fragment) would constitute useful alternatives for outbreak investigation and surveillance when WGS could not be performed.Fil: Sicilia, Paola. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; ArgentinaFil: Fantilli, Anabella Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; ArgentinaFil: Cuba, Facundo. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Centro Nacional de Genética Médica; ArgentinaFil: Di Cola Bucciarelli, Guadalupe. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; ArgentinaFil: Barbas, Maria Gabriela. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; ArgentinaFil: Poklepovich, Tomás. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Centro Nacional de Genética Médica; ArgentinaFil: Ré, Viviana Elizabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; ArgentinaFil: Castro, Gonzalo. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; ArgentinaFil: Pisano, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; ArgentinaNature Publishing Group2025-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/289458Sicilia, Paola; Fantilli, Anabella Clara; Cuba, Facundo; Di Cola Bucciarelli, Guadalupe; Barbas, Maria Gabriela; et al.; Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region; Nature Publishing Group; Scientific Reports; 15; 1; 2-2025; 1-82045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-025-91116-7info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-025-91116-7info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-08-25T14:30:52Zoai:ri.conicet.gov.ar:11336/289458instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982026-08-25 14:30:53.051CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
title Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
spellingShingle Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
Sicilia, Paola
HEPATITIS A VIRUS
HAV
NGS
SEQUENCING
WHOLE GENOME SEQUENCING
title_short Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
title_full Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
title_fullStr Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
title_full_unstemmed Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
title_sort Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region
dc.creator.none.fl_str_mv Sicilia, Paola
Fantilli, Anabella Clara
Cuba, Facundo
Di Cola Bucciarelli, Guadalupe
Barbas, Maria Gabriela
Poklepovich, Tomás
Ré, Viviana Elizabeth
Castro, Gonzalo
Pisano, María Belén
author Sicilia, Paola
author_facet Sicilia, Paola
Fantilli, Anabella Clara
Cuba, Facundo
Di Cola Bucciarelli, Guadalupe
Barbas, Maria Gabriela
Poklepovich, Tomás
Ré, Viviana Elizabeth
Castro, Gonzalo
Pisano, María Belén
author_role author
author2 Fantilli, Anabella Clara
Cuba, Facundo
Di Cola Bucciarelli, Guadalupe
Barbas, Maria Gabriela
Poklepovich, Tomás
Ré, Viviana Elizabeth
Castro, Gonzalo
Pisano, María Belén
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv HEPATITIS A VIRUS
HAV
NGS
SEQUENCING
WHOLE GENOME SEQUENCING
topic HEPATITIS A VIRUS
HAV
NGS
SEQUENCING
WHOLE GENOME SEQUENCING
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Molecular epidemiology of hepatitis A virus (HAV) plays a critical role in identifying outbreak originand conducting surveillance. Although it is mostly carried out using short partial VP1/2A genomicsequences, utilizing whole-genome sequences (WGS) provides more accurate and robust information. We developed an amplicon-based next-generation sequencing (NGS) strategy to obtain complete HAV genomes utilizing the COVIDSeq Test (Illumina). Twenty-five primer pairs were designed and used to amplify partial genomic fragments (400 bp) that comprise the entire HAV genome sequence from previously HAV positive serum and stool samples from Argentina. The DNA library was prepared using the Illumina COVIDSeq Test and sequenced in a MiSeq equipment. Phylogenetic analyses were performed with IQ-Tree using WGS and VP1/2A partial sequences of 1084pb and 422pb. Eleven samples were amplified and sequenced, with coverage between 79.3 and 100% (> 90% in 9 samples). Although phylogenetic analyses of partial sequences allowed genotype and subgenotype identification, WGS analyses yielded more accurate and reliable results for the phylogeny (phylogenetic definition). The amplicon-based NGS WGS tool developed by adapting the COVIDSeq test to HAV proved to be efficient. The study of partial VP1/2A regions (mainly the 1084 bp fragment) would constitute useful alternatives for outbreak investigation and surveillance when WGS could not be performed.
Fil: Sicilia, Paola. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina
Fil: Fantilli, Anabella Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Cuba, Facundo. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Centro Nacional de Genética Médica; Argentina
Fil: Di Cola Bucciarelli, Guadalupe. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Barbas, Maria Gabriela. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina
Fil: Poklepovich, Tomás. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Centro Nacional de Genética Médica; Argentina
Fil: Ré, Viviana Elizabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Castro, Gonzalo. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Pisano, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
description Molecular epidemiology of hepatitis A virus (HAV) plays a critical role in identifying outbreak originand conducting surveillance. Although it is mostly carried out using short partial VP1/2A genomicsequences, utilizing whole-genome sequences (WGS) provides more accurate and robust information. We developed an amplicon-based next-generation sequencing (NGS) strategy to obtain complete HAV genomes utilizing the COVIDSeq Test (Illumina). Twenty-five primer pairs were designed and used to amplify partial genomic fragments (400 bp) that comprise the entire HAV genome sequence from previously HAV positive serum and stool samples from Argentina. The DNA library was prepared using the Illumina COVIDSeq Test and sequenced in a MiSeq equipment. Phylogenetic analyses were performed with IQ-Tree using WGS and VP1/2A partial sequences of 1084pb and 422pb. Eleven samples were amplified and sequenced, with coverage between 79.3 and 100% (> 90% in 9 samples). Although phylogenetic analyses of partial sequences allowed genotype and subgenotype identification, WGS analyses yielded more accurate and reliable results for the phylogeny (phylogenetic definition). The amplicon-based NGS WGS tool developed by adapting the COVIDSeq test to HAV proved to be efficient. The study of partial VP1/2A regions (mainly the 1084 bp fragment) would constitute useful alternatives for outbreak investigation and surveillance when WGS could not be performed.
publishDate 2025
dc.date.none.fl_str_mv 2025-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/289458
Sicilia, Paola; Fantilli, Anabella Clara; Cuba, Facundo; Di Cola Bucciarelli, Guadalupe; Barbas, Maria Gabriela; et al.; Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region; Nature Publishing Group; Scientific Reports; 15; 1; 2-2025; 1-8
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/289458
identifier_str_mv Sicilia, Paola; Fantilli, Anabella Clara; Cuba, Facundo; Di Cola Bucciarelli, Guadalupe; Barbas, Maria Gabriela; et al.; Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region; Nature Publishing Group; Scientific Reports; 15; 1; 2-2025; 1-8
2045-2322
CONICET Digital
CONICET
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language eng
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info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-025-91116-7
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
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eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
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repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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