Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences

Abstract

Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIVinfected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.

HIV-1 subtype diversity and transmission strain source among men who have sex with men in Guangxi, China

“…It is well known that phylogenetic analyses have elucidated the origin and spread of the pandemic human immunodeficiency virus type (HIV-1) group M virus, both during the pre-epidemic period and the epidemic phase of spread among humans 4 . Additionally, it is also applied to evaluate small transmission chains between infected individuals, such as some forensic studies 5 – 7 , and to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries, and within geographically restricted communities 8 .…”

HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network

“…This mechanism gives the virus the ability to quickly adapt to the host immune response, acquire resistance to antiretroviral therapy and results in remarkably molecular diversity 1 . Four HIV-1 groups (named M, N, O and P) originated independently from cross-species transmission events between humans and non-human primates around 100 years ago in Central Africa 2 . Among these, group M successfully spread around the world, diversifying into nine subtypes (A–D, F–H, J, and K) and more than 100 circulating recombinant forms (CRFs) (a complete list of HIV-1 CRF is available at: https://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html ).…”