High GUD incidence in the early 20 century created a particularly permissive time window for the origin and initial spread of epidemic HIV strains

HIV infection

The AIDS epidemic has been a global public health issue for more than 40 years and has resulted in ~40 million deaths. AIDS is caused by the retrovirus, HIV-1, which is transmitted via body fluids and secretions. After infection, the virus invades host cells by attaching to CD4 receptors and thereafter one of two major chemokine coreceptors, CCR5 or CXCR4, destroying the host cell, most often a T lymphocyte, as it replicates. If unchecked this can lead to an immune-deficient state and demise over a period of ~2-10 years. The discovery and global roll-out of rapid diagnostics and effective antiretroviral therapy led to a large reduction in mortality and morbidity and to an expanding group of individuals requiring lifelong viral suppressive therapy. Viral suppression eliminates sexual transmission of the virus and greatly improves health outcomes. HIV infection, although still stigmatized, is now a chronic and manageable condition. Ultimate epidemic control will require prevention and treatment to be made available, affordable and accessible for all. Furthermore, the focus should be heavily oriented towards long-term well-being, care for multimorbidity and good quality of life. Intense research efforts continue for therapeutic and/or preventive vaccines, novel immunotherapies and a cure.

It Was Not the Perfect Storm: The Social History of the HIV-2 Virus in Guinea-Bissau

The perfect storm model that was elaborated for the HIV-1M pandemic has also been used to explain the emergence of HIV-2, a second human immunodeficiency virus-acquired immunodeficiency syndrome (HIV-AIDS) that became an epidemic in Guinea-Bissau, West Africa. The use of this model creates epidemiological generalizations, ecological oversimplifications and historical misunderstandings as its assumptions-an urban center with explosive population growth, a high level of commercial sex and a surge in STDs, a network of mechanical transport and country-wide, en masse mobile campaigns-are absent from the historical record. This model fails to explain how the HIV-2 epidemic actually came about. This is the first study to conduct an exhaustive examination of sociohistorical contextual developments and align them with environmental, virological and epidemiological data. The interdisciplinary dialogue indicates that the emergence of the HIV-2 epidemic piggybacked on local sociopolitical transformations. The war's indirect effects on ecological relations, mobility and sociability were acute in rural areas and are a key to the HIV-2 epidemic. This setting had the natural host of the virus, the population numbers, the mobility trends and the use of technology on a scale needed to foster viral adaptation and amplification. The present analysis suggests new reflections on the processes of zoonotic spillovers and disease emergence.

Urban Scaling of Health Outcomes: a Scoping Review

Urban scaling is a framework that describes how city-level characteristics scale with variations in city size. This scoping review mapped the existing evidence on the urban scaling of health outcomes to identify gaps and inform future research. Using a structured search strategy, we identified and reviewed a total of 102 studies, a majority set in high-income countries using diverse city definitions. We found several historical studies that examined the dynamic relationships between city size and mortality occurring during the nineteenth and early twentieth centuries. In more recent years, we documented heterogeneity in the relation between city size and health. Measles and influenza are influenced by city size in conjunction with other factors like geographic proximity, while STIs, HIV, and dengue tend to occur more frequently in larger cities. NCDs showed a heterogeneous pattern that depends on the specific outcome and context. Homicides and other crimes are more common in larger cities, suicides are more common in smaller cities, and traffic-related injuries show a less clear pattern that differs by context and type of injury. Future research should aim to understand the consequences of urban growth on health outcomes in low- and middle-income countries, capitalize on longitudinal designs, systematically adjust for covariates, and examine the implications of using different city definitions.

Newly Discovered Archival Data Show Coincidence of a Peak of Sexually Transmitted Diseases with the Early Epicenter of Pandemic HIV-1

To which extent STDs facilitated HIV-1 adaptation to humans, sparking the pandemic, is still unknown. We searched colonial medical records from 1906–1958 for Leopoldville, Belgian Congo, which was the initial epicenter of pandemic HIV-1, compiling counts of treated STD cases in both Africans and Europeans. Almost all Europeans were being treated, while for Africans, generalized treatment started only in 1929. Treated STD counts in Europeans thus reflect STD infection rates more accurately compared to counts in Africans. In Africans, the highest recorded STD treatment incidence was in 1929–1935, declining to low levels in the 1950s. In Europeans, the recorded treatment incidences were highest during the period 1910–1920, far exceeding those in Africans. Europeans were overwhelmingly male and had frequent sexual contact with African females. Consequently, high STD incidence among Europeans must have coincided with high prevalence and incidence in the city’s African population. The data strongly suggest the worst STD period was 1910–1920 for both Africans and Europeans, which coincides with the estimated origin of pandemic HIV-1. Given the strong effect of STD coinfections on HIV transmission, these new data support our hypothesis of a causal effect of STDs on the epidemic emergence of HIV-1.

Comparison of two simulators for individual based models in HIV epidemiology in a population with HSV 2 in Yaoundé (Cameroon)

Model comparisons have been widely used to guide intervention strategies to control infectious diseases. Agreement between different models is crucial for providing robust evidence for policy-makers because differences in model properties can influence their predictions. In this study, we compared models implemented by two individual-based model simulators for HIV epidemiology in a heterosexual population with Herpes simplex virus type-2 (HSV-2). For each model simulator, we constructed four models, starting from a simplified basic model and stepwise including more model complexity. For the resulting eight models, the predictions of the impact of behavioural interventions on the HIV epidemic in Yaoundé-Cameroon were compared. The results show that differences in model assumptions and model complexity can influence the size of the predicted impact of the intervention, as well as the predicted qualitative behaviour of the HIV epidemic after the intervention. These differences in predictions of an intervention were also observed for two models that agreed in their predictions of the HIV epidemic in the absence of that intervention. Without additional data, it is impossible to determine which of these two models is the most reliable. These findings highlight the importance of making more data available for the calibration and validation of epidemiological models.

Modelling of HIV prevention and treatment progress in five South African metropolitan districts

Globally, large proportions of HIV-positive populations live in cities. The Fast-Track cities project aims to advance progress toward elimination of HIV as a public health threat by accelerating the response in cities across the world. This study applies a well-established HIV transmission model to provide key HIV estimates for the five largest metropolitan districts in South Africa (SA): Cape Town, Ekurhuleni, eThekwini, Johannesburg and Tshwane. We calibrate the model to metro-specific data sources and estimate progress toward the 90-90-90 targets set by UNAIDS (90% of people living with HIV (PLHIV) diagnosed, 90% of those diagnosed on antiretroviral therapy (ART) and viral suppression in 90% of those on ART). We use the model to predict progress towards similarly defined 95-95-95 targets in 2030. In SA, 90.5% of PLHIV were diagnosed in 2018, with metro estimates ranging from 86% in Johannesburg to 92% in eThekwini. However, only 68.4% of HIV-diagnosed individuals nationally were on ART in 2018, with the proportion ranging from 56% in Tshwane to 73% in eThekwini. Fractions of ART users who were virally suppressed ranged from 77% in Ekurhuleni to 91% in eThekwini, compared to 86% in the whole country. All five metros are making good progress to reach diagnosis targets and all (with the exception of Ekurhuleni) are expected to reach viral suppression targets in 2020. However, the metros and South Africa face severe challenges in reaching the 90% ART treatment target.

Baby pangolins on my plate: possible lessons to learn from the COVID-19 pandemic

The Journal of Ethnobiology and Ethnomedicine (JEET), throughout its 15 years of existence, has tried to provide a respected outlet for scientific knowledge concerning the inextricable links between human societies and nature, food, and health. Ethnobiology and ethnomedicine-centred research has moved at the (partially artificial and fictitious) interface between nature and culture and has investigated human consumption of wild foods and wild animals, as well as the use of wild animals or their parts for medicinal and other purposes, along with the associated knowledge, skills, practices, and beliefs. Little attention has been paid, however, to the complex interplay of social and cultural reasons behind the increasing pressure on wildlife. The available literature suggest that there are two main drivers that enhance the necessary conditions for infectious diseases to cross the species barrier from wild animals to humans: (1) the encroachment of human activities (e.g., logging, mining, agricultural expansion) into wild areas and forests and consequent ecological disruptions; and, connected to the former, (2) the commodification of wild animals (and natural resources in general) and an expanding demand and market for wild meat and live wild animals, particularly in tropical and sub-tropical areas. In particular, a crucial role may have been played by the bushmeat-euphoria and attached elitist gastronomies and conspicuous consumption phenomena. The COVID-19 pandemic will likely require ethnobiologists to reschedule research agendas and to envision new epistemological trajectories aimed at more effectively mitigating the mismanagement of natural resources that ultimately threats our and other beings' existence.

Conflicting Views in Narratives on HIV Transmission via Medical Care

Molecular studies suggest that HIV arose in Africa between 1880 and 1940. During this period, there were campaigns by European colonial governments that involved unsterile injections of large numbers of Africans. That, along with other unsafe therapeutic interventions, may have propelled the evolution of HIV from SIV. Since subtype B in Africa may have been concentrated in white African homosexuals, it is possible that Westerners rather than Haitians introduced the virus to the New World. Amplification of HIV subtype B took place in Haiti, where transmission was facilitated by hazardous medical procedures including plasmapheresis. Representations in the media, however, largely ignore Western contributions to the spread of AIDS. This article focuses on the value of alternative narratives in fostering a balanced view that is less stigmatizing on developing nations.

Post-entry restriction factors of SIVcpz

Pandemic HIV-1, a human lentivirus, is the result of zoonotic transmission of SIV from chimpanzees (SIVcpz). How SIVcpz established spread in humans after spillover is an outstanding question. Lentiviral cross-species transmissions are exceptionally rare events. Nevertheless, the chimpanzee and the gorilla were part of the transmission chains that resulted in sustained infections that evolved into HIV-1. Although many restriction factors can repress the early stages of lentiviral replication, others target replication during the late phases. In some cases, viruses incorporate host proteins that interfere with subsequent rounds of replication. Though limited and small, HIVs and SIVs, including SIVcpz can use their genome products to modulate and escape some of these barriers and thus establish a chronic infection.

SIVcpz closely related to the ancestral HIV-1 is less or non-pathogenic to humans in a hu-BLT mouse model

The HIV-1 pandemic is a consequence of the cross-species transmission of simian immunodeficiency virus in wild chimpanzees (SIVcpz) to humans. Our previous study demonstrated SIVcpz strains that are closely related to the ancestral viruses of HIV-1 groups M (SIVcpzMB897) and N (SIVcpzEK505) and two SIVcpz lineages that are not associated with any known HIV-1 infections in humans (SIVcpzMT145 and SIVcpzBF1167), all can readily infect and robustly replicate in the humanized-BLT mouse model of humans. However, the comparative pathogenicity of different SIVcpz strains remains unknown. Herein, we compared the pathogenicity of the above four SIVcpz strains with HIV-1 using humanized-BLT mice. Unexpectedly, we found that all four SIVcpz strains were significantly less pathogenic or non-pathogenic compared to HIV-1, manifesting lower degrees of CD4+ T-cell depletion and immune activation. Transcriptome analyses of CD4+ T cells from hu-BLT mice infected with SIVcpz versus HIV-1 revealed enhanced expression of genes related to cell survival and reduced inflammation/immune activation in SIVcpz-infected mice. Together, our study results demonstrate for the first time that SIVcpz is significantly less or non-pathogenic to human immune cells compared to HIV-1. Our findings lay the groundwork for a possible new understanding of the evolutionary origins of HIV-1, where the initial SIVcpz cross-species transmission virus may be initially less pathogenic to humans.

Rethinking Human-Nonhuman Primate Contact and Pathogenic Disease Spillover

Zoonotic transmissions are a major global health risk, and human-animal contact is frequently raised as an important driver of transmission. A literature examining zooanthroponosis largely agrees that more human-animal contact leads to more risk. Yet the basis of this proposition, the term contact, has not been rigorously analyzed. To understand how contact is used to explain cross-species spillovers, we conducted a multi-disciplinary review of studies addressing human-nonhuman primate (NHP) engagements and pathogenic transmissions and employing the term contact. We find that although contact is frequently invoked, it is employed inconsistently and imprecisely across these studies, overlooking the range of pathogens and their transmission routes and directions. We also examine a related but more expansive approach focusing on human and NHP habitats and their spatial overlap, which can potentially facilitate pathogenic transmission. Contact and spatial overlap investigations cannot, however, explain the processes that bring together people, animals and pathogens. We therefore examine another approach that enhances our understanding of zoonotic spillovers: anthropological studies identifying such historical, social, environmental processes. Comparable to a One Health approach, our ongoing research in Cameroon draws contact, spatial overlap and anthropological-historical approaches into dialog to suggest where, when and how pathogenic transmissions between people and NHPs may occur. In conclusion, we call for zoonotic disease researchers to specify more precisely the human-animal contacts they investigate and to attend to how broader ecologies, societies and histories shape pathogen-human-animal interactions.

The epidemic emergence of HIV: what novel enabling factors were involved?

Humans acquired retroviruses from simians, mainly through bushmeat handling. All epidemically successful HIV groups started to spread in early 20th century, contrasting with the antiquity of T-cell lymphotropic viruses, implying that novel enabling factors were involved in HIV emergence. Here we review the Parenteral Serial Transmission and the Enhanced Heterosexual Transmission hypotheses for the adaptation and early spread of HIV. Epidemic start roughly coincides in time with peak genital ulcer disease in cities, suggesting a major role for sexual transmission. Only ill-adapted and rare HIV groups emerged after approximately 1950, when injections and transfusions attained their maximal levels, suggesting that if parenteral serial transmission was necessary for HIV adaptation, it had to be complemented by sexual transmission for HIV to reach epidemic potential.

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Male Circumcision and the Epidemic Emergence of HIV-2 in West Africa

BACKGROUND

Epidemic HIV-2 (groups A and B) emerged in humans circa 1930-40. Its closest ancestors are SIVsmm infecting sooty mangabeys from southwestern Côte d'Ivoire. The earliest large-scale serological surveys of HIV-2 in West Africa (1985-91) show a patchy spread. Côte d'Ivoire and Guinea-Bissau had the highest prevalence rates by then, and phylogeographical analysis suggests they were the earliest epicenters. Wars and parenteral transmission have been hypothesized to have promoted HIV-2 spread. Male circumcision (MC) is known to correlate negatively with HIV-1 prevalence in Africa, but studies examining this issue for HIV-2 are lacking.

METHODS

We reviewed published HIV-2 serosurveys for 30 cities of all West African countries and obtained credible estimates of real prevalence through Bayesian estimation. We estimated past MC rates of 218 West African ethnic groups, based on ethnographic literature and fieldwork. We collected demographic tables specifying the ethnic partition in cities. Uncertainty was incorporated by defining plausible ranges of parameters (e.g. timing of introduction, proportion circumcised). We generated 1,000 sets of past MC rates per city using Latin Hypercube Sampling with different parameter combinations, and explored the correlation between HIV-2 prevalence and estimated MC rate (both logit-transformed) in the 1,000 replicates.

RESULTS AND CONCLUSIONS

Our survey reveals that, in the early 20th century, MC was far less common and geographically more variable than nowadays. HIV-2 prevalence in 1985-91 and MC rates in 1950 were negatively correlated (Spearman rho = -0.546, IQR: -0.553--0.546, p≤0.0021). Guinea-Bissau and Côte d'Ivoire cities had markedly lower MC rates. In addition, MC was uncommon in rural southwestern Côte d'Ivoire in 1930.The differential HIV-2 spread in West Africa correlates with different historical MC rates. We suggest HIV-2 only formed early substantial foci in cities with substantial uncircumcised populations. Lack of MC in rural areas exposed to bushmeat may have had a role in successful HIV-2 emergence.

Beyond the Cut Hunter: A Historical Epidemiology of HIV Beginnings in Central Africa

In the absence of direct evidence, an imagined "cut hunter" stands in for the index patient of pandemic HIV/AIDS. During the early years of colonial rule, this explanation goes, a hunter was cut or injured from hunting or butchering a chimpanzee infected with simian immunodeficiency virus, resulting in the first sustained human infection with the virus that would emerge as HIV-1M. We argue here that the "cut hunter" relies on a historical misunderstanding and ecological oversimplification of human-chimpanzee (Pan Troglodytes troglodytes) interactions that facilitated pathogenic transmission. This initial host shift cannot explain the beginnings of the HIV/AIDS pandemic. Instead, we must understand the processes by which the virus became transmissible, possibly between Sangha basin inhabitants and ultimately reached Kinshasa. A historical epidemiology of the late nineteenth and twentieth centuries, provides a much-needed corrective to the major shortcomings of the cut hunter. Based on 62 oral historical interviews conducted in southeastern Cameroon and archival research, we show that HIV emerged from ecological, economic, and socio-political transformations of the late nineteenth and twentieth centuries. The gradual imposition of colonial rule built on and reoriented ecologies and economies, and altered older patterns of mobility and sociality. Certain changes may have contributed to the initial viral host shift, but more importantly, facilitated the adaptation of HIV-1M to human-to-human transmission. Our evidence suggests that the most critical changes occurred after 1920. This argument has important implications for public health policy, underscoring recent work emphasizing alternative pathways for zoonotic spillovers into human beings.

'Deadly gonorrhoea': history, collective memory and early HIV epidemiology in East Central Africa

This article combines local oral reminiscences with recent epidemiological literature to sketch a historical context around the onset and expansion of the HIV-1 epidemic in southern Uganda and north-western Tanzania. The local historical imagination has associated the appearance of AIDS in two ways. First, with specific socio-economic structures and circumstances common in the region since the 1960s and their enhancement during the 1970s due to economic changes at national and global levels. Second, the epidemic is associated with changes in the epidemiological situation. Local perspectives are supported by recent phylogenetic research and circumstantial historical evidence, on the basis of which a hypothesis on the expansion of HIV-1 in East Central Africa (southern Uganda, north-western Tanzania, Rwanda) is presented.

HIV competition dynamics over sexual networks: first comer advantage conserves founder effects

Outside Africa, the global phylogeography of HIV is characterized by compartmentalized local epidemics that are typically dominated by a single subtype, which indicates strong founder effects. We hypothesized that the competition of viral strains at the epidemic level may involve an advantage of the resident strain that was the first to colonize a population. Such an effect would slow down the invasion of new strains, and thus also the diversification of the epidemic. We developed a stochastic modelling framework to simulate HIV epidemics over dynamic contact networks. We simulated epidemics in which the second strain was introduced into a population where the first strain had established a steady-state epidemic, and assessed whether, and on what time scale, the second strain was able to spread in the population. Simulations were parameterized based on empirical data; we tested scenarios with varying levels of overall prevalence. The spread of the second strain occurred on a much slower time scale compared with the initial expansion of the first strain. With strains of equal transmission efficiency, the second strain was unable to invade on a time scale relevant for the history of the HIV pandemic. To become dominant over a time scale of decades, the second strain needed considerable (>25%) advantage in transmission efficiency over the resident strain. The inhibition effect was weaker if the second strain was introduced while the first strain was still in its growth phase. We also tested how possible mechanisms of interference (inhibition of superinfection, depletion of highly connected hubs in the network, one-time acute peak of infectiousness) contribute to the inhibition effect. Our simulations confirmed a strong first comer advantage in the competition dynamics of HIV at the population level, which may explain the global phylogeography of the virus and may influence the future evolution of the pandemic.

The African epicentre of the HIV pandemic is home to a vast array of divergent viruses; however, local epidemics in other parts of the world are typically dominated by a single variant (subtype) of the virus, with different subtypes found in the different regions. This pattern indicates that local epidemics outside Africa have been started by the introduction of single “founder” viruses in the susceptible populations. However, how these patterns persisted over several decades in the face of international migration requires further explanation. By analyzing simulated epidemics, we demonstrated that an epidemic established by the first successful founder strain can inhibit the introduction and slow down the subsequent spread of further virus strains by several mechanisms of interference. Our results have implications for the global evolution of the HIV pandemic: the fast expansion of subtypes benefited from a “first comer advantage,” and founder viruses may have been selected by random sampling, rather than due to superior transmissibility/fitness; the fast expansion of these (possibly) suboptimal virus strains may have considerably delayed the spread of more transmissible HIV variants; however, the future evolution of the pandemic is likely to be characterized by a slow expansion of viral strains with increased transmission potential.

On the early dynamics and spread of HIV-1

Until recently, the origin of the HIV-1 group M pandemic largely remained a scientific mystery. The use of comprehensive evolutionary analyses has revealed a unique story regarding viral migration, starting in the 1920s in Kinshasa, and the social and infrastructural changes associated with the early spread of this deadly virus.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

Origins of HIV and the AIDS pandemic

Acquired immunodeficiency syndrome (AIDS) of humans is caused by two lentiviruses, human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2). Here, we describe the origins and evolution of these viruses, and the circumstances that led to the AIDS pandemic. Both HIVs are the result of multiple cross-species transmissions of simian immunodeficiency viruses (SIVs) naturally infecting African primates. Most of these transfers resulted in viruses that spread in humans to only a limited extent. However, one transmission event, involving SIVcpz from chimpanzees in southeastern Cameroon, gave rise to HIV-1 group M-the principal cause of the AIDS pandemic. We discuss how host restriction factors have shaped the emergence of new SIV zoonoses by imposing adaptive hurdles to cross-species transmission and/or secondary spread. We also show that AIDS has likely afflicted chimpanzees long before the emergence of HIV. Tracing the genetic changes that occurred as SIVs crossed from monkeys to apes and from apes to humans provides a new framework to examine the requirements of successful host switches and to gauge future zoonotic risk.

Evidence for selection at HIV host susceptibility genes in a West Central African human population

Background

HIV-1 derives from multiple independent transfers of simian immunodeficiency virus (SIV) strains from chimpanzees to human populations. We hypothesized that human populations in west central Africa may have been exposed to SIV prior to the pandemic, and that previous outbreaks may have selected for genetic resistance to immunodeficiency viruses. To test this hypothesis, we examined the genomes of Biaka Western Pygmies, who historically resided in communities within the geographic range of the central African chimpanzee subspecies (Pan troglodytes troglodytes) that carries strains of SIV ancestral to HIV-1.

Results

SNP genotypes of the Biaka were compared to those of African human populations who historically resided outside the range of P. t. troglodytes, including the Mbuti Eastern Pygmies. Genomic regions showing signatures of selection were compared to the genomic locations of genes reported to be associated with HIV infection or pathogenesis. In the Biaka, a strong signal of selection was detected at CUL5, which codes for a component of the vif-mediated APOBEC3 degradation pathway. A CUL5 allele protective against AIDS progression was fixed in the Biaka. A signal of selection was detected at TRIM5, which codes for an HIV post-entry restriction factor. A protective mis-sense mutation in TRIM5 had the highest frequency in Biaka compared to other African populations, as did a protective allele for APOBEC3G, which codes for an anti-HIV-1 restriction factor. Alleles protective against HIV-1 for APOBEC3H, CXCR6 and HLA-C were at higher frequencies in the Biaka than in the Mbuti. Biaka genomes showed a strong signal of selection at TSG101, an inhibitor of HIV-1 viral budding.

Conclusions

We found protective alleles or evidence for selection in the Biaka at a number of genes associated with HIV-1 infection or progression. Pygmies have also been reported to carry genotypes protective against HIV-1 for the genes CCR5 and CCL3L1. Our hypothesis that HIV-1 may have shaped the genomes of some human populations in West Central Africa appears to merit further investigation.

Enhanced heterosexual transmission hypothesis for the origin of pandemic HIV-1

HIV-1 M originated from SIVcpz endemic in chimpanzees from southeast Cameroon or neighboring areas, and it started to spread in the early 20th century. Here we examine the factors that may have contributed to simian-to-human transmission, local transmission between humans, and export to a city. The region had intense ape hunting, social disruption, commercial sex work, STDs, and traffic to/from Kinshasa in the period 1899-1923. Injection treatments increased sharply around 1930; however, their frequency among local patients was far lower than among modern groups experiencing parenteral HIV-1 outbreaks. Recent molecular datings of HIV-1 M fit better the period of maximal resource exploitation and trade links than the period of high injection intensity. We conclude that although local parenteral outbreaks might have occurred, these are unlikely to have caused massive transmission. World War I led to additional, and hitherto unrecognized, risks of HIV-1 emergence. We propose an Enhanced Heterosexual Transmission Hypothesis for the origin of HIV-1 M, featuring at the time and place of its origin a coincidence of favorable co-factors (ape hunting, social disruption, STDs, and mobility) for both cross-species transmission and heterosexual spread. Our hypothesis does not exclude a role for parenteral transmission in the initial viral adaptation.

Interdisciplinary approaches to understanding disease emergence: the past, present, and future drivers of Nipah virus emergence

Emerging infectious diseases (EIDs) pose a significant threat to human health, economic stability, and biodiversity. Despite this, the mechanisms underlying disease emergence are still not fully understood, and control measures rely heavily on mitigating the impact of EIDs after they have emerged. Here, we highlight the emergence of a zoonotic Henipavirus, Nipah virus, to demonstrate the interdisciplinary and macroecological approaches necessary to understand EID emergence. Previous work suggests that Nipah virus emerged due to the interaction of the wildlife reservoir (Pteropus spp. fruit bats) with intensively managed livestock. The emergence of this and other henipaviruses involves interactions among a suite of anthropogenic environmental changes, socioeconomic factors, and changes in demography that overlay and interact with the distribution of these pathogens in their wildlife reservoirs. Here, we demonstrate how ecological niche modeling may be used to investigate the potential role of a changing climate on the future risk for Henipavirus emergence. We show that the distribution of Henipavirus reservoirs, and therefore henipaviruses, will likely change under climate change scenarios, a fundamental precondition for disease emergence in humans. We assess the variation among climate models to estimate where Henipavirus host distribution is most likely to expand, contract, or remain stable, presenting new risks for human health. We conclude that there is substantial potential to use this modeling framework to explore the distribution of wildlife hosts under a changing climate. These approaches may directly inform current and future management and surveillance strategies aiming to improve pathogen detection and, ultimately, reduce emergence risk.

Circumcision status and incident herpes simplex virus type 2 infection, genital ulcer disease, and HIV infection

OBJECTIVE

We assessed the protective effect of medical male circumcision (MMC) against HIV, herpes simplex virus type 2 (HSV-2), and genital ulcer disease (GUD) incidence.

DESIGN

Two thousand, seven hundred and eighty-seven men aged 18-24 years living in Kisumu, Kenya were randomly assigned to circumcision (n=1391) or delayed circumcision (n=1393) and assessed by HIV and HSV-2 testing and medical examinations during follow-ups at 1, 3, 6, 12, 18, and 24 months.

METHODS

Cox regression estimated the risk ratio of each outcome (incident HIV, GUD, HSV-2) for circumcision status and multivariable models estimated HIV risk associated with HSV-2, GUD, and circumcision status as time-varying covariates.

RESULTS

HIV incidence was 1.42 per 100 person-years. Circumcision was 62% protective against HIV [risk ratio=0.38; 95% confidence interval (CI) 0.22-0.67] and did not change when controlling for HSV-2 and GUD (risk ratio=0.39; 95% CI 0.23-0.69). GUD incidence was halved among circumcised men (risk ratio=0.52; 95% CI 0.37-0.73). HSV-2 incidence did not differ by circumcision status (risk ratio=0.94; 95% CI 0.70-1.25). In the multivariable model, HIV seroconversions were tripled (risk ratio=3.44; 95% CI 1.52-7.80) among men with incident HSV-2 and seven times greater (risk ratio=6.98; 95% CI 3.50-13.9) for men with GUD.

CONCLUSION

Contrary to findings from the South African and Ugandan trials, the protective effect of MMC against HIV was independent of GUD and HSV-2, and MMC had no effect on HSV-2 incidence. Determining the causes of GUD is necessary to reduce associated HIV risk and to understand how circumcision confers protection against GUD and HIV.

Evolutionary dynamics of HIV at multiple spatial and temporal scales

Infectious diseases remain a formidable challenge to human health, and understanding pathogen evolution is crucial to designing effective therapeutics and control strategies. Here, we review important evolutionary aspects of HIV infection, highlighting the concept of selection at multiple spatial and temporal scales. At the smallest scale, a single cell may be infected by multiple virions competing for intracellular resources. Recombination and phenotypic mixing introduce novel evolutionary dynamics. As the virus spreads between cells in an infected individual, it continually evolves to circumvent the immune system. We discuss evolutionary mechanisms of HIV pathogenesis and progression to AIDS. Viral spread throughout the human population can lead to changes in virulence and the transmission of immune-evading variation. HIV emerged as a human pathogen due to selection occurring between different species, adapting from related viruses of primates. HIV also evolves resistance to antiretroviral drugs within a single infected host, and we explore the possibility for the spread of these strains between hosts, leading to a drug-resistant epidemic. We investigate the role of latency, drug-protected compartments, and direct cell-to-cell transmission on viral evolution. The introduction of an HIV vaccine may select for viral variants that escape vaccine control, both within an individual and throughout the population. Due to the strong selective pressure exerted by HIV-induced morbidity and mortality in many parts of the world, the human population itself may be co-evolving in response to the HIV pandemic. Throughout the paper, we focus on trade-offs between costs and benefits that constrain viral evolution and accentuate how selection pressures differ at different levels of selection.

Cross-species transmission of simian retroviruses: how and why they could lead to the emergence of new diseases in the human population

The HIV-1 group M epidemic illustrates the extraordinary impact and consequences resulting from a single zoonotic transmission. Exposure to blood or other secretions of infected animals, through hunting and butchering of bushmeat, or through bites and scratches inflicted by pet nonhuman primates (NHPs), represent the most plausible source for human infection with simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus (STLV) and simian foamy virus. The chance for cross-species transmissions could increase when frequency of exposure and retrovirus prevalence is high. According to the most recent data, human exposure to SIV or STLV appears heterogeneous across the African countries surveyed. Exposure is not sufficient to trigger disease: viral and host molecular characteristics and compatibility are fundamental factors to establish infection. A successful species jump is achieved when the pathogen becomes transmissible between individuals within the new host population. To spread efficiently, HIV likely required changes in human behavior. Given the increasing exposure to NHP pathogens through hunting and butchering, it is likely that SIV and other simian viruses are still transmitted to the human population. The behavioral and socio-economic context of the twenty-first century provides favorable conditions for the emergence and spread of new epidemics. Therefore, it is important to evaluate which retroviruses the human population is exposed to and to better understand how these viruses enter, infect, adapt and spread to its new host.

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

Evolutionary analyses have revealed an origin of pandemic HIV-1 group M in the Congo River basin in the first part of the XX century, but the patterns of historical viral spread in or around its epicentre remain largely unexplored. Here, we combine epidemiologic and molecular sequence data to investigate the spatiotemporal patterns of the CRF02_AG clade. By explicitly integrating prevalence counts and genetic population size estimates we date the epidemic emergence of CRF02_AG at 1973.1 (1972.1, 1975.3, 95% CI). To infer the phylogeographic signature of this clade at a regional scale, we analyze pol and env time-stamped sequence data from 10 countries using a Bayesian phylogeographic approach based on an asymmetric discretized diffusion model. Our data confirms a spatial origin of CRF02_AG in the Democratic Republic of Congo (DRC) and suggests that viral dissemination to Cameroon occurred at an early stage of the evolutionary history of CRF02_AG. We find considerable support for epidemiological linkage between neighbour countries. Compilation of ethnographic data suggested that well-supported viral migration did not reflect sustained human migratory flows. Finally, using sequence data from 15 locations in Cameroon, we use relaxed random walk models to explore the spatiotemporal dynamics of CRF02_AG at a finer geographical detail. Phylogeographic dispersal in continuous space reveals that at least two distinct CRF02_AG lineages are circulating in overlapping regions that are evolving at different evolutionary and diffusion rates. In conclusion, by combining molecular and epidemiological data, our results provide a time scale for CRF02_AG, early 70s, place its spatial root in the DRC within the putative root of group-M diversity and propose a scenario of chance-exportation events for the spatiotemporal patterns of a successful HIV-1 lineage both at a regional and country-scale.

Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A

Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide. We extend phylogenetic diffusion models that simultaneously draw information from multiple loci to estimate location states throughout distinct phylogenies and explicitly attempt to incorporate human migratory fluxes. Our study highlights that Guinea-Bissau, together with Côte d'Ivoire and Senegal, have acted as the main viral sources in the early stages of the epidemic. We show that convenience sampling can obfuscate the estimation of the spatial root of HIV-2A. We explicitly attempt to circumvent this by incorporating rate priors that reflect the ratio of human flow from and to West Africa. We recover four main routes of HIV-2A dispersal that are laid out along colonial ties: Guinea-Bissau and Cape Verde to Portugal, Côte d'Ivoire and Senegal to France. Within Europe, we find strong support for epidemiological linkage from Portugal to Luxembourg and to the UK. We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus.

Male circumcision for HIV prevention: current evidence and implementation in sub-Saharan Africa

Heterosexual exposure accounts for most HIV transmission in sub-Saharan Africa, and this mode, as a proportion of new infections, is escalating globally. The scientific evidence accumulated over more than 20 years shows that among the strategies advocated during this period for HIV prevention, male circumcision is one of, if not, the most efficacious epidemiologically, as well as cost-wise. Despite this, and recommendation of the procedure by global policy makers, national implementation has been slow. Additionally, some are not convinced of the protective effect of male circumcision and there are also reports, unsupported by evidence, that non-sex-related drivers play a major role in HIV transmission in sub-Saharan Africa. Here, we provide a critical evaluation of the state of the current evidence for male circumcision in reducing HIV infection in light of established transmission drivers, provide an update on programmes now in place in this region, and explain why policies based on established scientific evidence should be prioritized. We conclude that the evidence supports the need to accelerate the implementation of medical male circumcision programmes for HIV prevention in generalized heterosexual epidemics, as well as in countering the growing heterosexual transmission in countries where HIV prevalence is presently low.

Human immunodeficiency virus (HIV) immunopathogenesis and vaccine development: a review

The development of a safe, effective and globally affordable HIV vaccine offers the best hope for the future control of the HIV-1 pandemic. Since 1987, scores of candidate HIV-1 vaccines have been developed which elicited varying degrees of protective responses in nonhuman primate models, including DNA vaccines, subunit vaccines, live vectored recombinant vaccines and various prime-boost combinations. Four of these candidate vaccines have been tested for efficacy in human volunteers, but, to the exception of the recent RV144 Phase III trial in Thailand, which elicited a modest but statistically significant level of protection against infection, none has shown efficacy in preventing HIV-1 infection or in controlling virus replication and delaying progression of disease in humans. Protection against infection was observed in the RV144 trial, but intensive research is needed to try to understand the protective immune mechanisms at stake. Building-up on the results of the RV144 trial and deciphering what possibly are the immune correlates of protection are the top research priorities of the moment, which will certainly accelerate the development of an highly effective vaccine that could be used in conjunction with other HIV prevention and treatment strategies. This article reviews the state of the art of HIV vaccine development and discusses the formidable scientific challenges met in this endeavor, in the context of a better understanding of the immunopathogenesis of the disease.

Semen protects CD4+ target cells from HIV infection but promotes the preferential transmission of R5 tropic HIV

Sexual intercourse is the major means of HIV transmission, yet the impact of semen on HIV infection of CD4(+) T cells remains unclear. To resolve this conundrum, we measured CD4(+) target cell infection with X4 tropic HIV IIIB and HC4 and R5 tropic HIV BaL and SF162 after incubation with centrifuged seminal plasma (SP) from HIV-negative donors and assessed the impact of SP on critical determinants of target cell susceptibility to HIV infection. We found that SP potently protects CD4(+) T cells from infection with X4 and R5 tropic HIV in a dose- and time-dependent manner. SP caused a diminution in CD4(+) T cell surface expression of the HIVR CD4 and enhanced surface expression of the HIV coreceptor CCR5. Consequently, SP protected CD4(+) T cells from infection with R5 tropic HIV less potently than it protected CD4(+) T cells from infection with X4 tropic HIV. SP also reduced CD4(+) T cell activation and proliferation, and the magnitude of SP-mediated suppression of target cell CD4 expression, activation, and proliferation correlated closely with the magnitude of the protection of CD4(+) T cells from infection with HIV. Taken together, these data show that semen protects CD4(+) T cells from HIV infection by restricting critical determinants of CD4(+) target cell susceptibility to HIV infection. Further, semen contributes to the selective transmission of R5 tropic HIV to CD4(+) target cells.

Island biogeography reveals the deep history of SIV

Simian immunodeficiency virus (SIV) lineages have been identified that are endemic to Bioko Island. The time the island formed offers a geological time scale calibration point for dating the most recent common ancestor of SIV. The Bioko viruses cover the whole range of SIV genetic diversity, and each Bioko SIV clade is most closely related to viruses circulating in hosts of the same genus on the African mainland rather than to SIVs of other Bioko species. Our phylogeographic approach establishes that SIV is ancient and at least 32,000 years old. Our conservative calibration point and analyses of gene sequence saturation and dating bias suggest it may be much older.