Indian Journal of Medical Research

CORRESPONDENCE
Year
: 2011  |  Volume : 133  |  Issue : 5  |  Page : 548--549

Phylogenetic analysis of swine & human hepatitis E virus


Aditya Narayan Sarangi, Shambhavi Srivastava 
 Department of Biomedical Informatics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226 014 (UP), India

Correspondence Address:
Shambhavi Srivastava
Department of Biomedical Informatics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226 014 (UP)
India




How to cite this article:
Sarangi AN, Srivastava S. Phylogenetic analysis of swine & human hepatitis E virus.Indian J Med Res 2011;133:548-549


How to cite this URL:
Sarangi AN, Srivastava S. Phylogenetic analysis of swine & human hepatitis E virus. Indian J Med Res [serial online] 2011 [cited 2020 Nov 24 ];133:548-549
Available from: https://www.ijmr.org.in/text.asp?2011/133/5/548/81673


Full Text

Sir,

We have read with interest a recent paper published in the journal [1] .The authors amplified genomic material from swine sera using primers based on hepatitis E virus (HEV) genomic sequences, and sequenced the amplicons so obtained. They drew a phylogenetic tree based on the sequences of these Indian swine isolates, and genomic sequences of HEV isolates from humans and animals.

The PCR amplicons which were 246-nucleotide long, included sequences of the primers used for PCR. The primer part of the amplicon is provided from outside. Hence it may not accurately represent the sequence of the target nucleic acid and cannot be used for sequence analysis. Thus, for phylogenetic analysis, only the middle part of the sequence after removing the primer sequences on either side should be used. Removal of the primers in this case would have left a 196-nucleotide long sequence (i.e. 246-nucleotide PCR product minus 22 and 28-nucleotide forward and reverse primers); this would have been the appropriate region for comparison with other sequences.

We have redrawn a phylogenetic tree using only this 196-nucleotide segment after omitting the primer regions from the sequence used. This tree [Figure 1] is though similar to that drawn by the authors [1] shows minor variations in the branching pattern of the branch lengths in same clades. However, we thought that we will take this opportunity to correct this minor error in the published record.{Figure 1}

References

1Begum N, Polipalli SK, Husain SA, Kar P. Molecular analysis of swine hepatitis E virus from north India. Indian J Med Res 2010; 132 : 504-8.