Identification of a Novel Second-Generation Circulating Recombinant Form (CRF48_01B) in Malaysia: A Descendant of the Previously Identified CRF33_01B

• Main Authors: Li, Yue, Tee, Kok Keng, Liao, Huanan, Hase, Saiki, Uenishi, Rie, Li, Xiao-Jie, Tsuchiura, Takayo, Yang, Rongge, Govindasamy, Sumathi, Yong, Yean Kong, Tan, Hong Yien, Pybus, Oliver G., Kamarulzaman, Adeeba, Takebe, Yutaka
• Format: Article
• Published: Lippincott, Williams & Wilkins 2010
• Subjects: R Medicine
• Online Access: http://eprints.um.edu.my/4589/; https://doi.org/10.1097/QAI.0b013e3181d82ce5

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.