An African HIV-1 sequence from 1959 and implications for the origin of the epidemic

Abstract

There is considerable genetic diversity among viruses of different subtypes (designated A to J) in the major group of human immunodeficiency virus type 1 (HIV-1), the form of HIV that is dominant in the global epidemic. If available, HIV-1 sequences pre-dating the recognition of AIDS could be crucial in defining the time of origin and the subsequent evolution of these viruses in humans. The oldest known case of HIV-1 infection was reported to be that of a sailor from Manchester who died of an AIDS-like illness in 1959; however, the authenticity of this case has not been confirmed. Genetic analysis of sequences from clinical materials obtained from 1971 to 1976 from members of a Norwegian family infected earlier than 1971 showed that they carried viruses of the HIV-1 outlier group, a variant form that is mainly restricted to West Africa. Here we report the amplification and characterization of viral sequences from a 1959 African plasma sample that was previously found to be HIV-1 seropositive. Multiple phylogenetic analyses not only authenticate this case as the oldest known HIV-1 infection, but also place its viral sequence near the ancestral node of subtypes B and D in the major group, indicating that these HIV-1 subtypes, and perhaps all major-group viruses, may have evolved from a single introduction into the African population not long before 1959.

Evolutionary analysis of hepatitis C virus gene sequences from 1953

“…When historical viral sequences are available, they not only prove that an infection must have existed at a certain time in the past, but can also strengthen statistical estimates of parameters of interest, such as rates of molecular evolution, dates and locations of epidemic origin and past rates of transmission [2]. For HIV-1, the utility of historical isolates was demonstrated through the discovery and analysis of two archived strains from the Democratic Republic of Congo, one obtained from a 1959 plasma sample [6,7] and the other from a 1960 paraffin-embedded tissue sample [6]. However, for HCV, there are remarkably few sequences that substantially predate discovery of the virus in 1989.…”

Tropism of human pegivirus (formerly known as GB virus C/hepatitis G virus) and host immunomodulation: insights into a highly successful viral infection

“…There are considerable data suggesting a beneficial effect of HPgV infection on survival in HIVpositive subjects Nunnari et al, 2003;Tillmann et al, 2001;Toyoda et al, 1998;Vahidnia et al, 2012;Williams et al, 2004;Xiang et al, 2001;Zhang et al, 2006). It is unlikely that the relationship between HPgV infection and immune activation was selected for by HIV, as HIV was only introduced into humans during the past century (Zhu et al, 1998). Mechanisms purported to contribute to slower HIV disease progression include the findings of reduced surface expression of the chemokine receptors CCR5 and CXCR4, entry co-receptors for HIV (Nattermann et al, 2003;Schwarze-Zander et al, 2007;Xiang et al, 2001), and high plasma levels of the ligands for these receptors, i.e.…”

CHAT Oral Polio Vaccine Was Not the Source of Human Immunodeficiency Virus Type 1 Group M for Humans

“…Therefore, the majority view of evolutionary virologists is that HIV-1 group M originated well before the use of OPV in the Belgian Congo during 1957-1960. In any case, the fact that HIV-1 infection was present in 1959, and that the virus from that infection had already evolved beyond the B-D clade junction [87], means that evolution would have had to have been enormously fast between 1957 and 1959 to be compatible with introduction by OPV. Other explanations are the evolution of all or most of the clades of HIV-1 group M in a single chimpanzee (which is unlikely) or their introduction into the OPV through the use in manufacture of multiple infected chimpanzee kidneys, each carrying a different clade.…”