Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania

Mehta, Sanjay R.; Wertheim, Joel O.; Delport, Wayne; Ene, Luminiţa; Țârdei, Grațiela; Duiculescu, Dan; Pond, Sergei L. Kosakovsky; Smith, Davey M.

doi:10.1016/j.meegid.2011.03.009

Cited by 30 publications

(44 citation statements)

References 23 publications

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“…The T MRCA of subtype G clade here estimated (1968: 1956–1976) is also fully consistent to that previously estimated for this subtype (1970: 1960–1978) [58]. This onset date is comparable to that estimated for subtype F (1967: 1956–1976) [59]; but more recent than that of subtypes A1 (1954: 1940–1968), C (1955: 1934–1972), and D (1947: 1938–1955) [58].…”

Section: Discussionsupporting

confidence: 90%

Spatiotemporal Dynamics of the HIV-1 Subtype G Epidemic in West and Central Africa

2014

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The human immunodeficiency virus type 1 (HIV-1) subtype G is the second most prevalent HIV-1 clade in West Africa, accounting for nearly 30% of infections in the region. There is no information about the spatiotemporal dynamics of dissemination of this HIV-1 clade in Africa. To this end, we analyzed a total of 305 HIV-1 subtype G pol sequences isolated from 11 different countries from West and Central Africa over a period of 20 years (1992 to 2011). Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method. Our analyses indicate that subtype G most probably emerged in Central Africa in 1968 (1956–1976). From Central Africa, the virus was disseminated to West and West Central Africa at multiple times from the middle 1970s onwards. Two subtype G strains probably introduced into Nigeria and Togo between the middle and the late 1970s were disseminated locally and to neighboring countries, leading to the origin of two major western African clades (GWA-I and GWA-II). Subtype G clades circulating in western and central African regions displayed an initial phase of exponential growth followed by a decline in growth rate since the early/middle 1990s; but the mean epidemic growth rate of GWA-I (0.75 year−1) and GWA-II (0.95 year−1) clades was about two times higher than that estimated for central African lineages (0.47 year−1). Notably, the overall evolutionary and demographic history of GWA-I and GWA-II clades was very similar to that estimated for the CRF06_cpx clade circulating in the same region. These results support the notion that the spatiotemporal dissemination dynamics of major HIV-1 clades circulating in western Africa have probably been shaped by the same ecological factors.

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Section: Discussionsupporting

confidence: 90%

Spatiotemporal Dynamics of the HIV-1 Subtype G Epidemic in West and Central Africa

2014

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“…Similarly, the overall low prevalence of the CRFs_cpx lineages carrying fragments of those ancient may reflect a later emergence of these variants when compared to more prevalent HIV-1 subtypes and CRFs. The evolutionary analyses performed here, however, support that complex CRFs probably started to circulate in Central Africa between the late 1950s and the late 1960s, which coincides with the estimated onset date of several prevalent HIV-1 group M clades including: subtype A1 (T MRCA ~ 1955) [41], subtype C (T MRCA ~ 1955–1965) [41, 50, 51], subtype F1 (T MRCA ~ 1960–1970) [52, 53], subtype G (T MRCA ~ 1965–1970) [41, 54], the CRF01_AE (T MRCA ~ 1970–1975) [41, 55, 56], and the CRF02_AG (T MRCA ~ 1965–1975) [41, 57, 58]. The estimated T MRCA also overlaps with a period of demographic transition of the HIV-1 group M in the DRC around 1960 (95% HPD: 1952–1968), from an early phase of relatively slow exponential growth to a second phase of faster exponential growth [2].…”

Section: Discussionsupporting

confidence: 52%

Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa

Delatorre

Bello

2016

BMC Evol Biol

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BackgroundSeveral HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Here we reconstruct the evolutionary history of some of these complex CRFs (09_cpx, 11_cpx, 13_cpx and 45_cpx) and further investigate the dissemination dynamic of the CRF11_cpx clade by using a Bayesian coalescent-based method.ResultsThe analysis of two HIV-1 datasets comprising 181 pol (36 CRF09_cpx, 116 CRF11_cpx, 20 CRF13_cpx and 9 CRF45_cpx) and 125 env (12 CRF09_cpx, 67 CRF11_cpx, 17 CRF13_cpx and 29 CRF45_cpx) sequences pointed to quite consistent onset dates for CRF09_cpx (~1966: 1958–1979), CRF11_cpx (~1957: 1950–1966) and CRF13_cpx (~1965: 1958–1973) clades; while some divergence was found for the estimated date of origin of CRF45_cpx clade [pol = 1970 (1964–1976); env = 1960 (1952–1969)]. Phylogeographic reconstructions indicate that the HIV-1 CRF11_cpx clade most probably emerged in Cameroon and from there it was first disseminated to the Central Africa Republic and Chad in the early 1970s and to other central and western African countries from the early 1980s onwards. Demographic reconstructions suggest that the CRF11_cpx epidemic grew between 1960 and 1990 with a median exponential growth rate of 0.27 year−1, and stabilized after.ConclusionsThese results reveal that HIV-1 CRFs_cpx clades have been circulating in Central Africa for a period comparable to other much more prevalent HIV-1 group M lineages. Cameroon was probably the epicenter of dissemination of the CRF11_cpx clade that seems to have experienced a long epidemic growth phase before stabilization. The epidemic growth of the CRF11_cpx clade was roughly comparable to other HIV-1 group M lineages circulating in Central Africa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0824-8) contains supplementary material, which is available to authorized users.

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“…Ten of the 49 HIV participants had previous HIV clade evaluation (due to virological failure); all had F1 HIV subtype. Furthermore, previous molecular demographic and phylogeographic analyses (Mehta et al 2011; Mbisa et al 2012) demonstrated that F subtype was responsible for the Romanian nosocomial pediatric HIV epidemic. Participants were excluded if they were unable to provide informed consent, had a neurocognitive morbidity unrelated to HIV condition (e.g., recent and/or significant traumatic brain injury, color blindness, hearing deficit that appears to affect auditory comprehension, neurosyphilis, stroke, etc.…”

Section: Methodsmentioning

confidence: 90%

Neurocognitive functioning in a Romanian cohort of young adults with parenterally-acquired HIV-infection during childhood

et al. 2014

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The Romanian cohort can provide valuable information about the effect of chronic HIV-infection and exposure to combined antiretroviral therapy (cART) on the developing brain, based on its unique characteristics: young adults infected parenterally with HIV clade F in the late 1980s and exposed to cART for a decade. We conducted a prospective study using a neuropsychological test battery validated in other international HIV cohorts, in order to evaluate the rate and severity of neurocognitive impairment in a group of young Romanian adults. The 49 HIV-infected (HIV+) participants and the 20 HIV negative (HIV−) controls were similar for age and gender, although the HIV− group tended to be more educated. We found higher cognitive impairment prevalence in the HIV+ group (59.1 %) versus the HIV− group (10 %), and the impairment rate remained significantly higher even when the groups were matched based on the educational level (38.7 % for the HIV+ group vs. 10.0 % for the HIV− controls; p=0.025). The nadir CD4 count was <200 in 71.4 % of patients, but at the time of neurocognitive assessment, 89.5 % of patients had normal immunological status and 81.8 % undetectable HIV load. Among the HIV-impaired group, 26 % of the participants had syndromic impairment while the other 74 % had asymptomatic neurocognitive impairment. We found a high prevalence of neurocognitive dysfunction in the Romanian young adults growing-up with HIV. The greatest HIV-related cognitive deficits were in the domains of executive and motor functioning, consistent with a frontosubcortical pattern.

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Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania

Cited by 30 publications

References 23 publications

Spatiotemporal Dynamics of the HIV-1 Subtype G Epidemic in West and Central Africa

Spatiotemporal Dynamics of the HIV-1 Subtype G Epidemic in West and Central Africa

Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa

Neurocognitive functioning in a Romanian cohort of young adults with parenterally-acquired HIV-infection during childhood

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