In this study we date the introduction of HIV-2 into the human population and estimate the epidemic history of HIV-2 subtype A in Guinea-Bissau, the putative geographic origin of HIV-2. The evolutionary history of the simian immunodeficiency virus sooty mangabey͞HIV-2 lineage was reconstructed by using available database sequences with known sampling dates, and a timescale for this history was calculated by using maximum likelihood methods. The date of the most recent common ancestor of HIV-2 subtype A strains was estimated to be 1940 ؎ 16 and that of B strains was estimated to be 1945 ؎ 14. In addition we used coalescent theory to estimate the past population dynamics of HIV-2 subtype A in a rural population of Guinea-Bissau. Parametric and nonparametric estimates of the effective number of infections through time were obtained for an equal sample of gag, pol, and env sequences. Our estimates of the epidemic history of HIV-2 subtype A in Guinea-Bissau show a transition from constant size to rapid exponential growth around 1955-1970. Our analysis provides evidence for a zoonotic transfer of HIV-2 during the first half of the 20th century and an epidemic initiation in Guinea-Bissau that coincides with the independence war (1963)(1964)(1965)(1966)(1967)(1968)(1969)(1970)(1971)(1972)(1973)(1974), suggesting that war-related changes in sociocultural patterns had a major impact on the HIV-2 epidemic.T he AIDS epidemic is clearly recognized as a viral zoonosis (1-3). Phylogenetic analysis indicates that multiple interspecies transmissions from simian species have introduced two genetically distinct types of HIV into the human population: HIV-1, closely related to simian immunodeficiency virus (SIV) from chimpanzees (SIV CPZ ), and HIV-2, closely related to SIV from sooty mangabeys (SIV SM ). Whereas HIV-1 group M subtypes (A-D, F, H, J, and K) are spread globally, HIV-2 subtypes are mainly restricted to West Africa and can be categorized as epidemic subtypes (A and B) and nonepidemic subtypes (C-G) (4-7). Biological reasons have been invoked to explain the difference in global epidemiology between HIV-1 and HIV-2, such as lower HIV-2 viral loads that correlate with a lower transmissibility (8-10). However, attempts to compare the history of the epidemics at their respective geographic origins are still lacking.A useful strategy for investigating the epidemic history of HIV combines molecular clock analysis, to estimate the timescale of the epidemic, and coalescent theory, to infer the demographic history of the virus (11). Various molecular clock calculations have dated the most recent common ancestor (MRCA) of HIV-1 group M around 1930 Ϯ 15 (12-14). HIV-1 group M has subsequently spread globally, generating the pandemic observed today. Here, we investigate the epidemic history of HIV-2 to test previously suggested hypotheses of its origin. We provide the first estimated dates of cross-species transmissions of HIV-2. Our results indicate a transfer of HIV-2 subtypes A and B from sooty mangabeys to humans during the fi...

Background: CCR5-restricted (R5) human immunodeficiency virus type 1 (HIV-1) variants cause CD4+ T-cell loss in the majority of individuals who progress to AIDS, but mechanisms underlying the pathogenicity of R5 strains are poorly understood. To better understand envelope glycoprotein (Env) determinants contributing to pathogenicity of R5 viruses, we characterized 37 full-length R5 Envs from cross-sectional and longitudinal R5 viruses isolated from blood of patients with asymptomatic infection or AIDS, referred to as pre-AIDS (PA) and AIDS (A) R5 Envs, respectively.

The severe acute respiratory syndrome (SARS) epidemic of 2003 was responsible for 774 deaths and caused significant economic damage worldwide. Since July 2003, a number of SARS cases have occurred in China, raising the possibility of future epidemics. We describe here a rapid, sensitive, and highly efficient assay for the detection of SARS coronavirus (SARS-CoV) in cultured material and a small number (n ‫؍‬ 7) of clinical samples. Using rolling circle amplification (RCA), we were able to achieve sensitive detection levels of SARS-CoV RNA in both solid and liquid phases. The main advantage of RCA is that it can be performed under isothermal conditions with minimal reagents and avoids the generation of false-positive results, a problem that is frequently encountered in PCR-based assays. Furthermore, the RCA technology provides a faster, more sensitive, and economical option to currently available PCR-based methods.Severe acute respiratory syndrome (SARS) is an emerging disease caused by the novel SARS coronavirus (SARS-CoV) (2,4,5,14). By the end of the SARS epidemic in July 2003, a total of 8,096 SARS cases had been reported from 30 countries, with 774 deaths. Whether future outbreaks of SARS will occur is unknown at present. However, given the recent SARS cases in southern China arising from an unknown source and a number of laboratory-related infections (12), it is important to be prepared for such a possibility. In the absence of a SARSCoV vaccine or antiviral drugs, the use of strict infection control policies and early diagnosis with rapid, sensitive, and highly specific laboratory methods are essential for the early management of SARS-CoV infection.Apart from epidemiological linkages, the clinical and radiographic features of the disease are not SARS specific, identifying a need for specific laboratory tests that can confirm SARS-CoV infection early in the course of the illness. Detection of SARS-CoV-specific antibodies is a sensitive and specific but is not possible at clinical presentation (6,14).Detection of SARS-CoV by reverse transcription-PCR (RT-PCR) in clinical specimens allows diagnosis in the early stage of the disease. However, in contrast to many other acute respiratory infections, only low levels of SARS-CoV are thought to be present during the early symptomatic phase of infection. On the basis of the results of first-generation RT-PCR assays, SARS-CoV RNA can be detected with a sensitivity of only ca. 30 to 50% in a single respiratory specimen. A higher sensitivity can be achieved if serial samples are collected, particularly during the second week of illness when maximal virus shedding occurs (13,14). The type of clinical sample (e.g., nasopharyngeal aspirate, throat swabs, stool samples, urine, etc.) also affects the sensitivity of .Recently, the utility of circularizable oligonucleotides, or "padlock probes," has been demonstrated for the detection of target nucleic acid sequences; this approach shows greater sensitivity than conventional PCR (3,8,16). Upon hybridization to a target DNA or...