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

• Published in: Hepatology research Vol. 41; no. 10; pp. 936 - 945
• Main Authors: Sugiyama, Masaya, Inui, Ayano, Shin-I, Tadasu, Komatsu, Haruki, Mukaide, Motokazu, Masaki, Naohiko, Murata, Kazumoto, Ito, Kiyoaki, Nakanishi, Makoto, Fujisawa, Tomoo, Mizokami, Masashi
• Format: Journal Article
• Language: English
• Published: Melbourne, Australia Blackwell Publishing Asia 01.10.2011
• Subjects: genotype; Hepatitis B virus; intrafamilial transmission; phylogenetic analysis
• ISSN: 1386-6346; 1872-034X
• DOI: 10.1111/j.1872-034X.2011.00859.x

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.