“…Phylogenetic tree construction was optimized by nearest neighbour interchange and subtree pruning and regrafting with branch support computed by the approximate likelihood-ratio test based on a Shimodaira-Hasegawa-like procedure [27]. Nucleotide sequence alignments were translated to amino acid in order to determine the presence of mutations affecting susceptibility to antiviral therapies (any variant at reverse transcriptase amino acid sites rtI169, rtV173, rtL180, rtA181, rtT184, rtV191, rtA194, rtS202, rtM204 was noted) and immune recognition of the HBsAg protein (any variant at HBsAg amino acid sites P105, T116, T118, G119, K/R122, S/T123, C124, T/I126, P127, Q129, T/N131, M133, S136, C139, T140, K141, P142, S/T143, D144, G145, E164, P178, Q181, and I195 was noted) [28,29]. The risk of PCR environmental contamination was controlled with spatial and temporal separation of all steps (DNA extraction, PCR reaction pre-mix preparation, PCR amplification, and nested PCR analysis) as well as the inclusion of negative controls at the extraction and amplification steps.…”