Nigerian rotavirus serotype G8 could not be typedby PCR due to nucleotide mutation at the 3′ endof the primer binding site

Nigerian rotavirus serotype G8 could not be typedby PCR due to nucleotide mutation at the 3′... A rotavirus strain HMG89 from Nigeria with short electrophoretic pattern was typed G3 by PCR. A cDNA clone from the PCR product which hybridised in Northern blots to RNA segment 9 of the homologous Nigerian rotavirus strain HMG89 and laboratory reference strain 69M but not to other mammalian group A rotaviruses was sequenced. The VP7 gene 9 sequence is 1060 nucleotides long with two base deletions at positions 1034–1035. Sequence analysis of the primer (aAT8) used in the previous PCR serotyping assay revealed a mutation in one of the three nucleotide bases at the 3′ end of the primer binding site accounting for our inability to serotype G8 strains in our samples. These findings demonstrate that PCR analysis can, albeit infrequently, lead to error in typing of rotaviruses due to small numbers of mutations in the primer binding region. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Archives of Virology Springer Journals

Nigerian rotavirus serotype G8 could not be typedby PCR due to nucleotide mutation at the 3′ endof the primer binding site

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Publisher
Springer-Verlag
Copyright
Copyright © Wien by 1997 Springer-Verlag/
Subject
Legacy
ISSN
0304-8608
eISSN
1432-8798
D.O.I.
10.1007/s007050050206
Publisher site
See Article on Publisher Site

Abstract

A rotavirus strain HMG89 from Nigeria with short electrophoretic pattern was typed G3 by PCR. A cDNA clone from the PCR product which hybridised in Northern blots to RNA segment 9 of the homologous Nigerian rotavirus strain HMG89 and laboratory reference strain 69M but not to other mammalian group A rotaviruses was sequenced. The VP7 gene 9 sequence is 1060 nucleotides long with two base deletions at positions 1034–1035. Sequence analysis of the primer (aAT8) used in the previous PCR serotyping assay revealed a mutation in one of the three nucleotide bases at the 3′ end of the primer binding site accounting for our inability to serotype G8 strains in our samples. These findings demonstrate that PCR analysis can, albeit infrequently, lead to error in typing of rotaviruses due to small numbers of mutations in the primer binding region.

Journal

Archives of VirologySpringer Journals

Published: Sep 1, 1997

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