Identification of a novel second-generation circulating recombinant form (CRF48-01B) in Malaysia: A descendant of the previously identified CRF33-01B

A molecular epidemiological investigation conducted among injecting drug users in eastern Peninsular Malaysia in 2007 identified a cluster of sequences (n = 3) located outside any known HIV-1 genotype. Analyses of near full-length nucleotide sequences of these strains from individuals with no recognizable linkage revealed that they have an identical subtype structure comprised of CRF01-AE and subtype B′, distinct from any known circulating recombinant forms (CRFs). This novel CRF, designated CRF48-01B, is closely related to CRF33-01B, previously identified in Kuala Lumpur. Phylogenetic analysis of multiple CRF48-01B genome regions showed that CRF48-01B forms a monophyletic cluster within CRF33-01B, suggesting that this new recombinant is very likely a descendant of CRF33-01B. CRF48-01B thus represents one of the first examples of a "second-generation" CRF, generated by additional crossover with pre-existing CRFs. Corroborating these results, Bayesian molecular clock analyses indicated that CRF48-01B emerged in ∼2001, approximately ∼8 years after the emergence of CRF33-01B.