Easy-to-use phylogenetic analysis system for hepatitis B virus infection

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http://onlinelibrary.wiley.com/doi/10.1111/j.1872-034X.2011.00859.x/abstract

Easy-to-use phylogenetic analysis system for hepatitis B virus infection

Masaya Sugiyama1,2,†, Ayano Inui3, Tadasu Shin-I1, Haruki Komatsu3, Motokazu

Mukaide1,4, Naohiko Masaki1, Kazumoto Murata1, Kiyoaki Ito1, Makoto Nakanishi2,

Tomoo Fujisawa3, Masashi Mizokami1,*

Article first published online: 26 AUG 2011

DOI: 10.1111/j.1872-034X.2011.00859.x

© 2011 The Japan Society of Hepatology

Issue

Hepatology Research

Early View (Online Version of Record published before inclusion in an issue)

Abstract

Aim:  The molecular phylogenetic analysis has been broadly applied to clinical

and virological study. However, the appropriate settings and application of

calculation parameters are difficult for non-specialists of molecular genetics.

In the present study, the phylogenetic analysis tool was developed for the easy

determination of genotypes and transmission route.

Methods:  A total of 23 patients of 10 families infected with hepatitis B

virus (HBV) were enrolled and expected to undergo intrafamilial transmission.

The extracted HBV DNA were amplified and sequenced in a region of the S gene.

Results:  The software to automatically classify query sequence was

constructed and installed on the Hepatitis Virus Database (HVDB). Reference

sequences were retrieved from HVDB, which contained major genotypes from A to H.

Multiple-alignments using CLUSTAL W were performed before the genetic distance

matrix was calculated with the six-parameter method. The phylogenetic tree was

output by the neighbor-joining method. User interface using WWW-browser was also

developed for intuitive control. This system was named as the easy-to-use

phylogenetic analysis system (E-PAS). Twenty-three sera of 10 families were

analyzed to evaluate E-PAS. The queries obtained from nine families were

genotype C and were located in one cluster per family. However, one patient of a

family was classified into the cluster different from her family, suggesting

that E-PAS detected the sample distinct from that of her family on the

transmission route.

Conclusions:  The E-PAS to output phylogenetic tree was developed since

requisite material was sequence data only. E-PAS could expand to determine HBV

genotypes as well as transmission routes.