U.S. Human Immunodeficiency Virus Type 1 Epidemic: Date of Origin, Population History, and Characterization of Early Strains

The Evolutionary and Epidemiological Dynamics of the Paramyxoviridae

“…4b). Strikingly, in all the viruses studied here our estimates of genetic diversity, measured as N e τ, are between 10 and 100 and, hence, considerably lower than those previously recorded in chronic infections such as HIV (Robbins et al 2003) and hepatitis C (Pybus et al 2001). Such consistently low levels of genetic diversity suggest that recurrent population bottlenecks, a characteristic of paramyxovirus population dynamics, are regularly purging, and hence limiting, genetic variation.…”

Phylodynamics of Infectious Disease Epidemics

“…OALESCENT theory has found wide applications for inference of viral phylogenies (Nee et al 1996;Rosenberg and Nordborg 2002;Drummond et al 2005) and estimation of epidemic prevalence (Yusim et al 2001;Robbins et al 2003;Wilson et al 2005), yet there have been few attempts to formally integrate coalescent theory with standard epidemiological models Goodreau 2006). While epidemiological models such as susceptible-infected-recovered (SIR) consider the dynamics of an entire population going forward in time, the coalescent theory operates on a small sample of an infected subpopulation and models the merging of lineages backward in time until a common ancestor has been reached.…”

Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

“…Such studies have proven to be invaluable to clarify the routes of viral transmission in community settings (Holmes et al. 1995, Brown et al 1997, to establish (Ou et al 1992, Blanchard et al 1998 or rule out (Holmes et al 1993, Jaffe et al 1994) iatrogenic viral transmission, to study the pathways of viral spread among clusters of patients (Leitner et al 1996, Robbins et al 2002, to trace the geographic origin of recently introduced subtypes (Gao et al 1996, Kato et al 1999, Yu et al 2001, CoutoFernandez et al 2006, to infer the demographic history and date of origin of epidemic spread (Robbins et al 2003, Bello et al 2006, to investigate unusual forms of viral transmission (Goujon et al 2000, Andreo et al 2004, and has also found forensic applications (Albert et al 1994, Banaschak et al 2000, Metzker et al 2002, Lemey et al 2005. Phylogenetic analyses of HIV-1 sequences have also been used to provide evidence of a high incidence molecular profile, as evidenced by multiple transmission clusters, low level of sequence diversity and signature amino acid substitutions (Liitsola et al 1998, Oelrichs et al 2000, Shankarappa et al 2001, Nguyen et al 2002, and of an old and mature epidemic pattern, given the high sequence diversity and the absence of transmission clusters (Vidal et al 2000, Trask et al 2002.…”