Computational protocol: Investigation of Occult Hepatitis B Virus Infection in Anti-HBc Positive Patients from a Liver Clinic

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Protocol publication

[…] Four local non-occult samples sourced from SEALS at POWH dating from January 2007 until March 2013 were sequenced and used as local references. These local references had a serological profile of HBsAg positive, anti-HBc positive and HBV DNA positive. Furthermore, HBV genotype C sequences were retrieved from GenBank as references and a consensus sequence was made from seven GenBank references. All sequences were aligned using ClustalW2. Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 5.2. Genetic distances were estimated using the Kimura two-parameter method, and standard errors of distances were computed using a bootstrap method (1,000 replicates). A phylogenetic tree was constructed with the neighbour-joining method, and its statistical significance was tested by the bootstrap method (1,000 replicates). […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Hepatitis B virus, Homo sapiens
Diseases Hepatitis B