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Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program()

Surveillance networks for rotavirus document the burden of the disease using the proportion of children hospitalized with gastroenteritis positive for rotavirus by enzyme immunoassay. They also describe genotypes of circulating viruses by polymerase chain reaction for the VP7 and VP4 genes, which de...

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Autores principales: Babji, Sudhir, Arumugam, Rajesh, Sarvanabhavan, Anuradha, Gentsch, Jon R., Kang, Gagandeep
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934339/
https://www.ncbi.nlm.nih.gov/pubmed/25091686
http://dx.doi.org/10.1016/j.vaccine.2014.04.024
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author Babji, Sudhir
Arumugam, Rajesh
Sarvanabhavan, Anuradha
Gentsch, Jon R.
Kang, Gagandeep
author_facet Babji, Sudhir
Arumugam, Rajesh
Sarvanabhavan, Anuradha
Gentsch, Jon R.
Kang, Gagandeep
author_sort Babji, Sudhir
collection PubMed
description Surveillance networks for rotavirus document the burden of the disease using the proportion of children hospitalized with gastroenteritis positive for rotavirus by enzyme immunoassay. They also describe genotypes of circulating viruses by polymerase chain reaction for the VP7 and VP4 genes, which determine G and P types, respectively. A proportion of samples cannot be genotyped based on initial testing and laboratories need to assess further testing strategies based on resources and feasibility. To 365 samples obtained from an Indian rotavirus strain surveillance program, we applied an approach to determine the G and P types in antigen positive samples that failed to type initially with the standard laboratory protocol. Fifty-eight samples (19%) were negative for the VP6 gene, indicating that the antigen test was likely to have been false positive. Alternative extraction and priming approaches resulted in the identification of G and P types for 264 strains. The identity of one strain was determined by sequencing the first-round amplicons. Thirty-five strains were partially typed and seven strains could not be typed at all. The distribution of G and P types among strains that had initially failed to type, except one strain, did not differ from that in strains that were typed using the standard laboratory protocol.
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spelling pubmed-79343392021-03-05 Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program() Babji, Sudhir Arumugam, Rajesh Sarvanabhavan, Anuradha Gentsch, Jon R. Kang, Gagandeep Vaccine Article Surveillance networks for rotavirus document the burden of the disease using the proportion of children hospitalized with gastroenteritis positive for rotavirus by enzyme immunoassay. They also describe genotypes of circulating viruses by polymerase chain reaction for the VP7 and VP4 genes, which determine G and P types, respectively. A proportion of samples cannot be genotyped based on initial testing and laboratories need to assess further testing strategies based on resources and feasibility. To 365 samples obtained from an Indian rotavirus strain surveillance program, we applied an approach to determine the G and P types in antigen positive samples that failed to type initially with the standard laboratory protocol. Fifty-eight samples (19%) were negative for the VP6 gene, indicating that the antigen test was likely to have been false positive. Alternative extraction and priming approaches resulted in the identification of G and P types for 264 strains. The identity of one strain was determined by sequencing the first-round amplicons. Thirty-five strains were partially typed and seven strains could not be typed at all. The distribution of G and P types among strains that had initially failed to type, except one strain, did not differ from that in strains that were typed using the standard laboratory protocol. 2014-08-11 /pmc/articles/PMC7934339/ /pubmed/25091686 http://dx.doi.org/10.1016/j.vaccine.2014.04.024 Text en This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).
spellingShingle Article
Babji, Sudhir
Arumugam, Rajesh
Sarvanabhavan, Anuradha
Gentsch, Jon R.
Kang, Gagandeep
Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program()
title Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program()
title_full Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program()
title_fullStr Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program()
title_full_unstemmed Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program()
title_short Approach to molecular characterization of partially and completely untyped samples in an Indian rotavirus surveillance program()
title_sort approach to molecular characterization of partially and completely untyped samples in an indian rotavirus surveillance program()
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934339/
https://www.ncbi.nlm.nih.gov/pubmed/25091686
http://dx.doi.org/10.1016/j.vaccine.2014.04.024
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