Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines

Abstract

The growth rate of new HIV infections in the Philippines was the fastest of any countries in the Asia-Pacific region between 2010 and 2016. To date, HIV-1 subtyping results in the Philippines have been determined by characterizing only partial viral genome sequences. It is not known whether recombination occurs in the majority of unsequenced genome regions. Nearfull-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes from plasma samples collected between 2015 and 2017 from 23 newly diagnosed infected individuals in the Philippines. Phylogenetic analysis showed that the newly characterized sequences were CRF01_AE (14), subtype B (3), CRF01/B recombinants (5) and a CRF01/CRF07/B recombinant (1). All 14 CRF01_AE formed a tight cluster, suggesting that they were derived from a single introduction. The time to the most recent common ancestor (tMRCA) for CRF01_AE in the Philippines was 1995 (1992-1998), about 10-15 years later than that of CRF01_AE in China and Thailand. All five CRF01/B recombinants showed distinct recombination patterns, suggesting ongoing recombination between the two predominant circulating viruses. The identification of partial CRF07_BC sequences in one CRF01/CRF07/B recombinant, not reported previously in the Philippines, indicated that CRF07_BC may have been recently introduced into that country from China, where CRF07_BC is prevalent. Our results show that the major epidemic strains may have shifted to an increased predominance of CRF01_AE and its recombinants, and that other genotypes such as CRF07_BC may have been introduced into the Philippines.

Prevalent subtypes and one-year outcomes of an HIV-cohort from an urban Philippine center

“…It was interesting to see within our data that the proportions of subtypes noted based on pro-RT were revised when the longer LTR-VIF region, which incorporated these pro-RT sequences, was analyzed. A higher proportion of the cohort appeared to carry CRF01_AE/B strains, as well as other recombinants, similar to the trend reported by Chen et al [ 9 ] Hence, it is important to remember when reporting prevalence that the designation of subtype and recombinants may be influenced by the length of the sequence analyzed (i.e., just pro-RT vs partial full length vs near full-length).…”

“…Telan, 2013 [7] Salvana, 2017 [5] Chen, 2019 [9] Current study [24] Region Sequenced Pro-RT 1. The recombinant regions in the POL gene varied in size and position.…”

Multidrug-resistant tuberculosis (MDR-TB) and multidrug-resistant HIV (MDR-HIV) syndemic: challenges in resource limited setting

“…In our setting, ART is currently limited to NRTI (3TC, AZT), NNRTI (EFV, NVP) and PI (LPV/r). The current Philippine HIV epidemic is driven by the predominance of the CRF01_AE subtype29 30 in contrast to the predominance of subtype B in the Americas, Western Europe and Australasia,31 and subtype C in Africa 31. Infection with CRF01_AE has been associated with rapid progression to AIDS and possibly higher mortality,31 32 thus ART classes that rapidly suppress HIV viral load are essential.…”

Diagnostic Applications for RNA-Seq Technology and Transcriptome Analyses in Human Diseases Caused by RNA Viruses

“…that clustered separately from their reference sequences, as determined by the maximum likelihood phylogenetic algorithm [26]. The introduction of circulating recombinant forms (CRF01_AE and CRF02_AG) into the Asian-Pacific region from Continental Asia was identified using similar "half genome" sequencing approach [27]. Another approach, the "switching mechanism at the 5′ end of RNA transcript" (SMART), leverages the templateswitching capability of certain RT enzymes toward full-length template.…”