Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of Human Immunodeficiency Virus Type 1

Abstract

With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this study, we investigate the epidemiological characteristics of 5,675 HIV-1 pol gene sequences sampled from distinct infections in the United Kingdom. These sequences were phylogenetically analyzed in conjunction with 976 complete-genome and 3,201 pol gene reference sequences sampled globally and representing the broad range of HIV-1 genetic diversity, allowing us to estimate the probable geographic origins of the various strains present in the United Kingdom. A statistical analysis of phylogenetic clustering in this data set identified several independent transmission chains within the United Kingdom involving recently introduced strains and indicated that strains more commonly associated with infections acquired heterosexually in East Africa are spreading among men who have sex with men. Coalescent approaches were also used and indicated that the transmission chains that we identify originated in the late 1980s to early 1990s. Similar changes in the epidemiological structuring of HIV epidemics are likely to be taking in place in other industrialized nations with large immigrant populations. The framework implemented here takes advantage of the vast amount of routinely generated HIV-1 sequence data and can provide epidemiological insights not readily obtainable through standard surveillance methods.

Changing patterns in HIV‐1 non‐B clade prevalence and diversity in Italy over three decades*

“…A hallmark of the HIV-1 epidemic in Europe is the substantial increase in non-B clade penetration and circulation that has taken place as a result of the migration flows from subSaharan Africa, South-East Asia and Central and South America that have occurred since the early 1990s [6][7][8][9][10][11][12][13]. In addition to migration, travel to areas with high prevalences of HIV-1 infection, in particular those where commercial sex is widely available, is thought to be responsible for the entry of various group M subtypes into previously subtype B-restricted countries.…”

“…In order to monitor the evolution of the global pandemic, it is convenient and effective to assign viral clades, which allow evaluation of the local epidemiological trends that result from social changes and migration flows. [6][7][8][9][10][11][12][13]. The recent epidemiology of HIV-1 infection in Western European countries with large immigrant communities has been characterized by increasing genetic diversity and a marked rise in non-B subtype strains among newly diagnosed individuals [14][15][16][17].…”

Dilemma of concepts and strategies for the prevention of spread of HIV in relation to human behavior, law and human rights

“…(Hale et al, 2001). However, "the key fact about HIV is that it is a nonequilibrium infectious agent" (Baltimore, 1995; see also Gifford et al, 2007). On an evolutionary time scale HIV is in some respects just at the beginning of its invasion of its new host, Homo sapiens.…”

“…Its evolution is further pushed by the spread of different HIV type I subtypes through modern modes of "travel" (Gifford et al, 2007) thereby favoring the forming of CRFs by HIV superinfections with yet unknown sequelae (Thomson and Nájera, 2001;Blackard and Mayer, 2004;French et al, 2006;McCutchan, 2006;de Oliveira et al, 2010).…”

“…The uniqueness of the replication cycle of HIV favors adaptation in its new host with ongoing generation of viral genetic diversity (Gifford et al, 2007):…”