Origin and evolution of HIV-1 subtype A6

Abstract

Background HIV outbreaks in the Former Soviet Union (FSU) countries were characterized by repeated transmission of the HIV variant AFSU, which is now classified as a distinct subtype A sub-subtype called A6. The current study used phylogenetic/phylodynamic and signature mutation analyses to determine likely evolutionary relationship between subtype A6 and other subtype A sub-subtypes. Methods For this study, an initial Maximum Likelihood phylogenetic analysis was performed using a total of 553 full-length, publicly available, reverse transcriptase sequences, from A1, A2, A3, A4, A5, and A6 sub-subtypes of subtype A. For phylogenetic clustering and signature mutation analysis, a total of 5961 and 3959 pol and env sequences, respectively, were used. Results Phylogenetic and signature mutation analysis showed that HIV-1 sub-subtype A6 likely originated from sub-subtype A1 of African origin. A6 and A1 pol and env genes shared several signature mutations that indicate genetic similarity between the two subtypes. For A6, tMRCA dated to 1975, 15 years later than that of A1. Conclusion The current study provides insights into the evolution and diversification of A6 in the backdrop of FSU countries and indicates that A6 in FSU countries evolved from A1 of African origin and is getting bridged outside the FSU region.

Molecular Epidemiology of HIV-1 in Eastern Europe and Russia

“…The phylogenetic relation of the B subtypes identified in our study to archetypical IDU-B (Eastern European) viruses, that initiated the outbreak in Ukraine, and the Western European B-variant was studied by phylogenetic analysis of a 919 bp fragment of the HIV-1 PR/RT gene, using Western B, Thai B, and IDU-B sequences as references ( Figure 1 C). In contrast to earlier observations [ 5 ], viruses from the different regions included in our study could not be distinguished by phylogeny.…”

“…Although this method is not as accurate as classic epidemiological investigation and is biased by sample size and differences in the observed periods, our conclusions are in line with historical observations. In line with earlier studies, our molecular epidemiology analysis gives support for the view that the A6 epidemic started in Ukraine and spread further in Eastern Europe [ 3 , 4 , 5 , 6 ]. The largest was the one from Ukraine to Moscow.…”

“…Presumably, the HIV epidemic in this region was initiated by two separate introductions of the virus in intravenous drug users (IDUs) in Ukraine in the mid-1990s [ 3 ]. The IDU-A strain, formerly referred to as A-Former Soviet Union (FSU-A) and now classified as sub-subtype A6, led to an HIV-1 outbreak in Odessa [ 4 , 5 , 6 ]; the IDU-B (FSU-B) strain initiated the epidemic in Mykolaiv. IDU-B differs phylogenetically from other widespread subtypes B—Western B or Thai B—and can be reliably distinguished from them [ 7 ].…”

Romania, a Harbour of HIV-1 Subtype F1: Where Are We after 33 Years of HIV-1 Infection?

“…Repeated transmission of the HIV-1 variant A FSU , now identified as a unique subtype A sub-subtype termed A6, was a hallmark of HIV-1 outbreaks in the nations of the Former Soviet Union (FSU) [17]. Sequences from numerous non-FSU nations, including Bulgaria, Cyprus, the Czech Republic, Mongolia, Poland, Slovenia, and Turkey, were also present in the A6 cluster [17].…”

“…Repeated transmission of the HIV-1 variant A FSU , now identified as a unique subtype A sub-subtype termed A6, was a hallmark of HIV-1 outbreaks in the nations of the Former Soviet Union (FSU) [17]. Sequences from numerous non-FSU nations, including Bulgaria, Cyprus, the Czech Republic, Mongolia, Poland, Slovenia, and Turkey, were also present in the A6 cluster [17]. Except for the Czech Republic, where A6 sequences date from 1998 to 2000, most of the A6 sequences from non-FSU countries were discovered more recently, having been deposited between 2002 and 2017 [17].…”