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Background Biological monitoring of antiretroviral treatment (ART) in human immunodeficiency virus (HIV)-infected pediatric population remains challenging. The aim of the present study was to assess the long-term HIV-1 genetic diversity in pol gene in HIV-1-infected children in virological failure under antiretroviral regimen adapted according to the successive World Health Organization (WHO) guidelines for resource-constrained settings. Methods HIV-1 diversity in pol gene was assessed in HIV-1-infected children and adolescents born from HIV-infected mothers (median age at follow-up: 13.8 years) in virological failure (VF+) despite long-term regimen recommended by the WHO. The numbers of nonsynonymous substitutions per potential nonsynonymous site (dN) and of synonymous substitutions at potential synonymous sites (dS) in HIV-1 pol gene and the dN/dS ratios were used to estimate the selective pressure on circulating HIV-1. Results The immunological responses to ART basically corresponded to: 1) Full therapeutic failure with immunological (I-) and virological nonresponses in one-quarter (24.6%) of study children ((I-, VF+) subgroup); 2) Discordant immunovirological responses with paradoxical high CD4 T cell counts (I+) and high HIV-1 RNA load in the remaining cohort patients (75.4%) ((I+, VF+) subgroup). The mean dS was 1.8-fold higher in (I+, VF+) than (I-, VF+) subgroup (25.9 ± 18.4 vs. 14.3 ± 10.8). In the (I+, VF+) subgroup, the mean dS was 1.6-fold higher than the mean dN. Finally, the mean dN/dS ratio was 2.1-fold lower in (I+, VF+) than (I-, VF+) subgroup (0.6 ± 0.3 vs. 1.3 ± 0.7), indicating purifying selection in the immunovirological discordant (I+, VF+) subgroup and positive selection in the immunovirological failure (I-, VF+) subgroup. Conclusions Children and adolescents in immunovirological therapeutic failure harbor positive selection of HIV-1 strains favoring diversifying in pol-encoded amino acids. In contrast, children with persistent discordant immunovirological responses show accumulation of mutations and purifying selection in pol gene sequences, indicating limited genetic evolution and likely suggesting genetic adaptation of viruses to host functional constraints.

International audience; Mayaro virus (MAYV) is an emergent alphavirus that causes MAYV fever. It is often associated with debilitating symptoms, particularly arthralgia and myalgia. MAYV infection is becoming a considerable health issue that, unfortunately, lacks a specific antiviral treatment. Favipiravir, a broad-spectrum antiviral drug, has recently been shown to exert anti-MAYV activity in vitro. In the present study, the potential of Favipiravir to inhibit MAYV replication in an in vivo model was evaluated. Immunocompetent mice were orally administrated 300 mg/kg/dose of Favipiravir at pre-, concurrent-, or post-MAYV infection. The results showed a significant reduction in infectious viral particles and viral RNA transcripts in the tissues and blood of the pre- and concurrently treated infected mice. A significant reduction in the presence of both viral RNA transcript and infectious viral particles in the tissue and blood of pre- and concurrently treated infected mice was observed. By contrast, Favipiravir treatment post-MAYV infection did not result in a reduction in viral replication. Interestingly, Favipiravir strongly decreased the blood levels of the liver disease markers aspartate- and alanine aminotransferase in the pre- and concurrently treated MAYV-infected mice. Taken together, these results suggest that Favipiravir is a potent antiviral drug when administered in a timely manner.

Aim: This study was undertaken to determine the sero-epidemiological information and associated risk factors, of Hepatitis E virus (HEV) among dromedaries in Sub-sahelian region. Study Design: Cross sectional epidemiological survey. Place and Duration: The study was carried out in three countries of West Africa (Burkina Faso, Mali and Niger), over a two month period from February to March 2015. Methodology: A total of 133 serum samples collected from dromedaries (Camelus dromedarius) were examined for the detection of anti-DcHEV total antibody by a mammals targeted ELISA kit (ID vet, France), using a multispecies conjugate. Results: Eleven of the 133 (8.33%; 95%CI [3.6 – 13.0]) dromedaries were positive for anti-DcHEV antibodies. Positive cases had a random geographic distribution (p˃0.05) and all seropositive dromedaries were in close contact with other domestic animals. Conclusion: This study highlight the circulation of HEV in West African mammals and specifically in dromedaries. This is the first study reporting HEV circulation in dromedaries in West Africa. Further studies is needed to identify the HEV genotype involved in the dromedary camel infection, and evaluation of potential transmission to dromedary’s care keepers.

International audience; Human malaria infection begins with a one-time asymptomatic liver stage followed by a cyclic symptomatic blood stage. For decades, the research for novel antimalarials focused on the high-throughput screening of molecules that only targeted the asexual blood stages. In a search for new effective compounds presenting a triple action against erythrocytic and liver stages in addition to the ability to block the transmission of the disease via the mosquito vector, 2-amino-thienopyrimidinone derivatives were synthesized and tested for their antimalarial activity. One molecule, named gamhepathiopine (denoted as “M1” herein), was active at submicromolar concentrations against both erythrocytic (50% effective concentration [EC50] = 0.045 μM) and liver (EC50 = 0.45 μM) forms of Plasmodium falciparum. Furthermore, gamhepathiopine efficiently blocked the development of the sporogonic cycle in the mosquito vector by inhibiting the exflagellation step. Moreover, M1 was active against artemisinin-resistant forms (EC50 = 0.227 μM), especially at the quiescent stage. Nevertheless, in mice, M1 showed modest activity due to its rapid metabolization by P450 cytochromes into inactive derivatives, calling for the development of new parent compounds with improved metabolic stability and longer half-lives. These results highlight the thienopyrimidinone scaffold as a novel antiplasmodial chemotype of great interest to search for new drug candidates displaying multistage activity and an original mechanism of action with the potential to be used in combination therapies for malaria elimination in the context of artemisinin resistance.IMPORTANCE This work reports a new chemical structure that (i) displays activity against the human malaria parasite Plasmodium falciparum at 3 stages of the parasitic cycle (blood stage, hepatic stage, and sexual stages), (ii) remains active against parasites that are resistant to the first-line treatment recommended by the World Health Organization (WHO) for the treatment of severe malaria (artemisinins), and (iii) reduces transmission of the parasite to the mosquito vector in a mouse model. This new molecule family could open the way to the conception of novel antimalarial drugs with an original multistage mechanism of action to fight against Plasmodium drug resistance and block interhuman transmission of malaria.

The emerging coronavirus called SARS-CoV-2 has spread rapidly around the world. Responsible for severe pneumonitis (Covid-19), there are also doubts concerning a possible mother-to-fetal transmission of this virus. Current data are patchy and obtained from small groups of patients. They tend to support the idea that the mother-to-fetal transmission of SARS-CoV-2 is very rare, but the period between infection and childbirth was often very short and may not allow sufficient replication to consider transplacental passage. Here, we reviewed the existing virological data and those remaining to explore. Thus, the natural history of SARS-CoV-2 infection in pregnant women and the risk of transmission in utero is not yet fully understood and defined. Four months from the emergence of this virus, it is therefore reasonable to wait for the results of specific studies on larger cohorts which, to be conclusive, must meet the best scientific criteria.

While SARS-CoV-2 infection has spread rapidly worldwide, data remains scarce about the natural history of infection in pregnant women and the risk of mother-to-fetal transmission. Current data indicates that viral RNA levels in maternal blood are low and there is no evidence of placental infection with SARS-CoV-2. Published reports to date suggest that perinatal transmission of SARSCoV- 2 can occur but is rare. Among 179 newborns tested for SARS-CoV2 at birth from mothers with COVID-19, transmission was suspected in 8 cases, 5 with positive nasopharyngeal SARS-CoV-2 RT-PCR and 3 with SARS-CoV-2 IgM. However, these cases arise from maternal infection close to childbirth and there are no information about exposition during first or second trimester of pregnancy. Welldesigned prospective cohort studies with rigorous judgement criteria are needed to determine the incidence and risk factors for perinatal transmission of SARS-CoV-2.

Classical dendritic cells (cDCs) play a pivotal role in the early events that tip the immune response toward persistence or viral control. In vitro studies indicate that HIV infection induces the dysregulation of cDCs through binding of the LILRB2 inhibitory receptor to its MHC-I ligands and the strength of this interaction was proposed to drive disease progression. However, the dynamics of the LILRB2/MHC-I inhibitory axis in cDCs during early immune responses against HIV are yet unknown. Here, we show that early HIV-1 infection induces a strong and simultaneous increase of LILRB2 and MHC-I expression on the surface of blood cDCs. We further characterized the early dynamics of LILRB2 and MHC-I expression by showing that SIVmac251 infection of macaques promotes coordinated up-regulation of LILRB2 and MHC-I on cDCs and monocytes/macrophages, from blood and lymph nodes. Orientation towards the LILRB2/MHC-I inhibitory axis starts from the first days of infection and is transiently induced in the entire cDC population in acute phase. Analysis of the factors involved indicates that HIV-1 replication, TLR7/8 triggering, and treatment by IL-10 or type I IFNs increase LILRB2 expression. Finally, enhancement of the LILRB2/MHC-I inhibitory axis is specific to HIV-1 and SIVmac251 infections, as expression of LILRB2 on cDCs decreased in naturally controlled chikungunya virus infection of macaques. Altogether, our data reveal a unique up-regulation of LILRB2 and its MHC-I ligands on cDCs in the early phase of SIV/HIV infection, which may account for immune dysregulation at a critical stage of the anti-viral response.

Infections with the human hepatitis B virus (HBV) and hepatitis D virus (HDV) depend on species-specific host factors like the receptor human sodium taurocholate cotransporting polypeptide (hNTCP). Complementation of mouse hepatocytes with hNTCP confers susceptibility to HDV but not HBV, indicating the requirement of additional HBV-specific factors. As an essential premise toward the establishment of an HBV-susceptible animal model, we investigated the role of hNTCP as a limiting factor of hepatocytes in commonly used laboratory animals. Primary hepatocytes from mice, rats, dogs, pigs, rhesus macaques, and cynomolgus macaques were transduced with adeno-associated viral vectors encoding hNTCP and subsequently infected with HBV. Cells were analyzed for Myrcludex B binding, taurocholate uptake, HBV covalently closed circular DNA formation, and expression of all HBV markers. Sodium taurocholate cotransporting polypeptide (Ntcp) from the respective species was cloned and analyzed for HBV and HDV receptor activity in a permissive hepatoma cell line. Expression of hNTCP in mouse, rat, and dog hepatocytes permits HDV infection but does not allow establishment of HBV infection. Contrarily, hepatocytes from cynomolgus macaques, rhesus macaques, and pigs became fully susceptible to HBV upon hNTCP expression with efficiencies comparable to human hepatocytes. Analysis of cloned Ntcp from all species revealed a pronounced role of the human homologue to support HBV and HDV infection. Conclusion: Ntcp is the key host factor limiting HBV infection in cynomolgus and rhesus macaques and in pigs. In rodents (mouse, rat) and dogs, transfer of hNTCP supports viral entry but additional host factors are required for the establishment of HBV infection. This finding paves the way for the development of macaques and pigs as immunocompetent animal models to study HBV infection in vivo, immunological responses against the virus and viral pathogenesis. (Hepatology 2017;66:703–716).

International audience; Alphaviruses such as Chikungunya and Ross River (RRV) viruses are associated with persistent arthritisand arthralgia in humans. Monocytes and macrophages are believed to play an important role in alphaviralarthritides. In this study, we evaluated RRV permissiveness of the human acute leukemia MM6 cellline. Viral growth analysis showed that RRV infection of MM6 cells resulted in a very low virus progenyproduction with daily output. Using recombinant RRV expressing the reporter gene Renilla luciferase, aweak viral replication level was detected in infected cells at the early stages of infection. The infectionrestriction was not associated with type-I interferon and pro-inflammatory cytokines release. Apoptosishallmarks (i.e. mitochondrial BAX localisation and PARP cleavage) were observed in infected MM6cells indicating that RRV can trigger apoptosis at late infection times. The long-term persistence of RRVgenomic RNA in surviving MM6 cells identifies human monocytic cells as potential cellular reservoirs ofviral material within the infected host.

Chikungunya virus (CHIKV) is an arbovirus, transmitted by Aedes aegypti and Ae. albopictus , which causes epidemics of fever, rash and joint pains. First described in 1952 in Tanzania, CHIKV remained a relatively neglected tropical virus, despite causing sporadic outbreaks in Africa and Asia over the next few decades. However, since 2004, an epidemic lineage of the East/Central/South African (ECSA) genotype has arisen in East Africa and spread to cause unprecedented global outbreaks in the Indian Ocean islands, South and Southeast Asia, as well as autochthonous outbreaks in Europe. This spread was driven by mutations in the virus envelope proteins that improved the vectorial competence of Ae. albopictus , which is widely distributed in the affected areas, and which was previously considered a vector of secondary importance to Ae. aegypti . In 2011, the Asian lineage of CHIKV emerged to cause outbreaks in Pacific islands, before unexpectedly spreading to cause explosive epidemics in the Caribbean and Latin America, mainly via Ae. aegypti . The factors behind the global spread of previously niche arboviruses such as CHIKV and more recently Zika virus are complex, multifactorial and poorly understood. The implications on strained health services and economies are considerable, particularly as CHIKV is associated with long-term rheumatological disorders. However, with the increasing ease of global travel and the growing geographical distributions of Aedes mosquito vectors, we should expect further spread of exotic arboviruses to new populations who remain entirely immunologically naive.

Introduction The worldwide use of yellow fever (YF) live attenuated vaccines came recently under close scrutiny as rare but serious adverse events have been reported. The population identified at major risk for these safety issues were extreme ages and immunocompromised subjects. Study NCT01426243 conducted by the French National Agency for AIDS research is an ongoing interventional study to evaluate the safety of the vaccine and the specific immune responses in HIV-infected patients following 17D-204 vaccination. As a preliminary study, we characterized the molecular diversity from E gene of the single 17D-204 vaccine batch used in this clinical study. Materials and methods Eight vials of lyophilized 17D-204 vaccine (Stamaril®, Sanofi-Pasteur, Lyon, France) of the E5499 batch were reconstituted for viral quantification, cloning and sequencing of C/prM/E region. Results The average rate of virions per vial was 8.68 ± 0.07 log10 genome equivalents with a low coefficient of variation (0.81%). 246 sequences of the C/prM/E region (29–33 per vials) were generated and analyzed for the eight vials, 25 (10%) being defective and excluded from analyses. 95% of sequences had at least one nucleotide mutation. The mutations were observed on 662 variant sites distributed through all over the 1995 nucleotides sequence and were mainly non-synonymous (66%). Genome variability between vaccine vials was highly homogeneous with a nucleotide distance ranging from 0.29% to 0.41%. Average p-distances observed for each vial were also homogeneous, ranging from 0.15% to 0.31%. Conclusion This study showed a homogenous YF virus RNA quantity in vaccine vials within a single lot and a low clonal diversity inter and intra vaccine vials. These results are consistent with a recent study showing that the main mechanism of attenuation resulted in the loss of diversity in the YF virus quasi-species.

To the Editor: The safety of blood product use is continually improving, but blood transfusion remains a challenge in Africa, given the high prevalence of bloodborne pathogens (1). In Africa, the main serologic tests done to reduce blood transfusion risks are for HIV and hepatitis B and C viruses. However, unknown or emerging pathogens among the population of blood donors, such as hepatitis E virus (HEV), may also jeopardize transfusion safety. HEV is emerging as a potential threat to blood safety. High rates of HEV IgG prevalence among blood donors have been found in studies in the United States (7.7%), England (13.5%), France (16.6%), and Spain (19.6%) (2,3). A study in Iran showed a prevalence of 14.3% (4), and a study in China showed rates of up to 22.7% (5). Cases of HEV transmission by transfusion or transplantation have been reported, and recent studies in France and England showed risk for HEV in donated blood ranging from 1/2,218 to 1/2,848 donations (5,6). In Burkina Faso, the prevalence of HEV IgG has been reported as 11.6% among pregnant women during 2012. Prevalence is >70% among butchers, who form a population exposed to pigs, which are a reservoir for HEV (7,8). To determine whether HEV continues to circulate among human populations outside known at-risk populations, we investigated prevalence of HEV IgG and IgM in the blood donor population of Ouagadougou. During June and July 2014, we recruited 1,497 first-time blood donors (398 women, 1,099 men) within the National Blood Transfusion Centre in Ouagadougou. Persons 17–65 years of age who weighed >50 kg were included (Figure, panel A). Candidate donors were excluded if they had previously received blood transfusions, had jaundice or clinical signs of hepatitis, were pregnant, or had sexual contact with multiple partners. Demographic data collection was limited to age and sex, and residual serum specimens were anonymized as approved by the Ethics Committee of the National Blood Transfusion Centre. We used Dia.Pro IgG ELISA (Diagnostic Bioprobe Srl, Sesto San Giovanni, Italy) to detect HEV IgG; this assay uses HEV-specific synthetic antigens derived from open reading frame (ORF) 2 and ORF3 of all 4 HEV subtypes. We used Wantai ELISA (Wantai Biologic Pharmacy Enterprise Co., Ltd., Bejiing, China) to test 92 randomly selected samples for HEV IgG, which showed concordant results (data not shown) (8). We also used the Wantai ELISA for the detection of HEV IgM; this test has a sensitivity of 97.1% (95% CI 94.6%–98.5%) and a specificity ranging from 95.3% in serum samples from patients with acute hepatitis A to 100% in healthy donors (http://www.ystwt.cn/IFU/HEV/HEV-IgM_CE.pdf). The HEV IgM positive samples were tested twice for accuracy. All tests were performed according to the manufacturers’ instructions; positive and negative controls were used in each plate. Figure Age and sex distributions and HEV test results for blood donor population, Ouagadougou, Burkina Faso, 2014. A) All blood donors. Women: mean age 29.62 y, median 27 y, range 17–58 y; men: mean age 29.86 y, median 27 y, range 15–70 y. B) ... The prevalence of HEV IgG was 39.0% (95% CI 36.5%–41.5%) by using Dia.Pro ELISA (Figure, panel B). This prevalence was twice that found in 2012 (8), but such wide variations were commonly found in Africa (9). In France, prevalence ranged widely, from 10% in the north to 52% in the south (6). HEV IgG prevalence increased significantly with age (p

Chikungunya virus (CHIKV) is an arthritogenic alphavirus causing epidemics of acute and chronic arthritic disease. Herein we describe a comprehensive RNA-Seq analysis of feet and lymph nodes at peak viraemia (day 2 post infection), acute arthritis (day 7) and chronic disease (day 30) in the CHIKV adult wild-type mouse model. Genes previously shown to be up-regulated in CHIKV patients were also up-regulated in the mouse model. CHIKV sequence information was also obtained with up to ≈8% of the reads mapping to the viral genome; however, no adaptive viral genome changes were apparent. Although day 2, 7 and 30 represent distinct stages of infection and disease, there was a pronounced overlap in up-regulated host genes and pathways. Type I interferon response genes (IRGs) represented up to ≈50% of up-regulated genes, even after loss of type I interferon induction on days 7 and 30. Bioinformatic analyses suggested a number of interferon response factors were primarily responsible for maintaining type I IRG induction. A group of genes prominent in the RNA-Seq analysis and hitherto unexplored in viral arthropathies were granzymes A, B and K. Granzyme A-/-and to a lesser extent granzyme K-/-, but not granzyme B-/-, mice showed a pronounced reduction in foot swelling and arthritis, with analysis of granzyme A-/-mice showing no reductions in viral loads but reduced NK and T cell infiltrates post CHIKV infection. Treatment with Serpinb6b, a granzyme A inhibitor, also reduced arthritic inflammation in wild-type mice. In non-human primates circulating granzyme A levels were elevated after CHIKV infection, with the increase correlating with viral load. Elevated granzyme A levels were also seen in a small cohort of human CHIKV patients. Taken together these results suggest granzyme A is an important driver of arthritic inflammation and a potential target for therapy. Trial Registration: ClinicalTrials.gov NCT00281294 © 2017 Wilson et al.

Elevated blood CXCL10/IP-10 levels during primary HIV-1 infection (PHI) were described as an independent marker of rapid disease onset, more robust than peak viremia or CD4 cell nadir. IP-10 enhances the recruitment of CXCR3+ cells, which include major HIV-target cells, raising the question if it promotes the establishment of viral reservoirs. We analyzed data from four cohorts of HIV+ patients, allowing us to study IP-10 levels before infection (Amsterdam cohort), as well as during controlled and uncontrolled viremia (ANRS cohorts). We also addressed IP-10 expression levels with regards to lymphoid tissues (LT) and blood viral reservoirs in patients and non-human primates. Pre-existing elevated IP-10 levels but not sCD63 associated with rapid CD4 T-cell loss upon HIV-1 infection. During PHI, IP-10 levels and to a lesser level IL-18 correlated with cell-associated HIV DNA, while 26 other inflammatory soluble markers did not. IP-10 levels tended to differ between HIV controllers with detectable and undetectable viremia. IP-10 was increased in SIV-exposed aviremic macaques with detectable SIV DNA in tissues. IP-10 mRNA was produced at higher levels in the small intestine than in colon or rectum. Jejunal IP-10+ cells corresponded to numerous small and round CD68neg cells as well as to macrophages. Blood IP-10 response negatively correlated with RORC (Th17 marker) gene expression in the small intestine. CXCR3 expression was higher on memory CD4+ T cells than any other immune cells. CD4 T cells from chronically infected animals expressed extremely high levels of intra-cellular CXCR3 suggesting internalization after ligand recognition. Elevated systemic IP-10 levels before infection associated with rapid disease progression. Systemic IP-10 during PHI correlated with HIV DNA. IP-10 production was regionalized in the intestine during early SIV infection and CD68+ and CD68neg haematopoietic cells in the small intestine appeared to be the major source of IP-10., Author Summary Chronic immune activation is a hallmark of HIV infection and contributes in multiple ways to HIV persistence. Here, we gained insights on the association between a pro-inflammatory chemokine, CXCL10/IP-10 and HIV infection in four cohorts of HIV+ individuals, studied at distinct stages of infection (before, primary and chronic stage with spontaneous- and treatment-controlled infection). We further analyzed pathogenic and non-pathogenic SIV infections to address IP-10 levels and the presence of infected cells in tissues (lymph nodes, small and large intestine). We found that elevated systemic IP-10 levels before HIV-1 infection associate with a more rapid disease progression. During primary infection, IP-10 in blood strongly correlated with the amount of infected cells in blood. The animal model showed that IP-10 expression was regionalized in the intestine and highest in the small intestine. Studies of aviremic animals suggest that high IP-10 is indicative of viral replication in lymphoid tissues. Haematopoietic cells rather than epithelial/endothelial cells mainly contributed to the IP-10 production in small intestine (jejunum). The receptor of IP-10 was highly expressed on memory CD4+ T cells, i.e. major target cells for the virus. This study contributes to our understanding of the establishment of HIV reservoirs and why IP-10 associates with HIV/AIDS.

Chikungunya virus (CHIKV) has since it re-emerged 10 years ago continued to spread globally and is now present on all continents causing millions of infections worldwide. There is no licensed vaccine available to combat CHIKV infection and numerous vaccine development programs are being pursued. Vaccine candidates being evaluated include chimeric, attenuated or inactivated viruses, subunit preparations, and virus-like particles (VLPs) as well as plasmid DNA. Although pre-clinical results overall have been promising, only three candidates have been evaluated in clinical trials. Of these the apparently best results were obtained with an attenuated vaccine isolate. A single immunization resulted in strong and durable antibody responses, however, this vaccine candidate had concerns regarding safety and further development of this candidate was discontinued. The other two clinically evaluated vaccine candidates were based on virus-like CHIKV particles (VLPs) and recombinant measles virus expressing the structural proteins of CHIKV. These preparations were immunogenic but required several immunizations to achieve reasonable antibody levels. Collectively, these preliminary findings suggest that there is room for improvement and further developments are needed to obtain a safe and affordable vaccine against CHIKV.

Chikungunya virus (CHIKV) is an arthropod-borne alphavirus that causes acute and chronic arthralgia. The virus re-emerged in the Indian Ocean islands in 2005–2006, and is responsible for the outbreaks in the Caribbean islands and the Americas since late 2013. This chapter describes the clinical manifestations of CHIKV in patients that define the disease and how using various relevant animal models from mice to nonhuman primates complemented studies in human immunology from patient cohorts. Studies from understanding cellular factors in CHIKV infection and the interplay with the immune system with a focus on innate and adaptive immunity are illustrated. These provide a clearer picture of the immunopathogenesis of CHIKV infection that will help develop preventive and therapeutic approaches to combat this painful disease in humans.

Simian immunodeficiency virus (SIV) infection in African nonhuman primate (NHP) natural hosts is usually nonpathogenic, despite high levels of virus replication. We have previously shown that chronic SIV infection in sooty mangabeys (SMs) and African green monkeys (AGMs) is associated with low levels of immune activation and bystander T cell apoptosis. To compare these features with those observed in another natural host, the mandrill (MND), we conducted a cross-sectional survey of the 23 SIV-infected and 25 uninfected MNDs from the only semifree colony of mandrills available worldwide. Viral loads (VLs) were determined and phenotypic and functional analysis of peripheral blood- and lymph node-derived lymphocytes was performed. We found that mandrills chronically infected with SIVmnd-1 or SIVmnd-2 have similar levels of viral replication, and we observed a trend toward lower CD4 + T cell counts in chronically SIVmnd-2-infected MNDs than SIVmnd-1-infected MNDs. No correlation between CD4 + T cell counts and VLs in SIV-infected MNDs could be established. Of note, the levels of T cell activation, proliferation, and apoptosis were comparable between SIVmnd-1- and SIVmnd-2-infected MNDs and to those observed in uninfected animals, with the only exception being an increase in tumor necrosis factor alpha-producing CD8 + T cells in SIVmnd-2-infected MNDs. Overall, these findings recapitulate previous observations in SIV-infected SMs and AGMs and lend further evidence to the hypothesis that low levels of immune activation protect natural SIV hosts from disease progression.

Chikungunya virus (CHIKV) is an Aedes-borne alphavirus, historically found in Africa and Asia, where it caused sporadic outbreaks. In 2004, CHIKV reemerged in East Africa and spread globally to cause epidemics, including, for the first time, autochthonous transmission in Europe, the Middle East, and Oceania. The epidemic strains were of the East/Central/South African genotype. Strains of the Asian genotype of CHIKV continued to cause outbreaks in Asia and spread to Oceania and, in 2013, to the Americas. Acute disease, mainly comprising fever, rash, and arthralgia, was previously regarded as self-limiting; however, there is growing evidence of severe but rare manifestations, such as neurological disease. Furthermore, CHIKV appears to cause a significant burden of long-term morbidity due to persistent arthralgia. Diagnostic assays have advanced greatly in recent years, although there remains a need for simple, accurate, and affordable tests for the developing countries where CHIKV is most prevalent. This review focuses on recent important work on the epidemiology, clinical disease and diagnostics of CHIKV.

Chikungunya virus (CHIKV) is a reemerging, ordinarily mosquito-transmitted, alphavirus that occasionally produces hemorrhagic manifestations, such as nose bleed and bleeding gums, in human patients. Interferon response factor 3 and 7 deficient (IRF3/7-/-) mice, which are deficient for interferon α/β responses, reliably develop hemorrhagic manifestations after CHIKV infection. Here we show that infectious virus was present in the oral cavity of CHIKV infected IRF3/7-/- mice, likely due to hemorrhagic lesions in the olfactory epithelium that allow egress of infected blood into the nasal, and subsequently, oral cavities. In addition. IRF3/7-/- mice were more susceptible to infection with CHIKV via intranasal and oral routes, with IRF3/7-/- mice also able to transmit virus mouse-to-mouse without an arthropod vector. Cynomolgus macaques often show bleeding gums after CHIKV infection, and analysis of saliva from several infected monkeys also revealed the presence of viral RNA and infectious virus. Furthermore, saliva samples collected from several acute CHIKV patients with hemorrhagic manifestations were found to contain viral RNA and infectious virus. Oral fluids can therefore be infectious during acute CHIKV infections, likely due to hemorrhagic manifestations in the oral/nasal cavities. Refereed/Peer-reviewed

International audience; Chikungunya virus (CHIKV) is an arbovirus associated with acute and chronic arthralgia that re-emerged in the Indian Ocean islands in 2005–2006 and is currently responsible for the ongoing outbreaks in the Caribbean islands and the Americas. We describe here the acute and chronic clinical manifestations of CHIKV in patients that define the disease. We also review the various animal models that have been developed to study CHIKV infection and pathology and further strengthened the understanding of the cellular and molecular mechanisms of CHIKV infection and immunity. A complete understanding of the immunopathogenesis of CHIKV infection will help develop the needed preventive and therapeutic approaches to combat this arbovirosis.

International audience; We conducted the first survey of zoonotic risk of Hepatitis E virus (REV) transmissions in Ouagadougou, Burkina Faso, through the direct contact with pork meat during professional activity. Anti-REV antibodies were more prevalent in pork butchers, 76% than in the general population, which was 47.8% in 2013 (odds ratio = 3.46, 95% CI = 2.85-4.21, P < 0.001). Among slaughter-aged swine, REV seroprevalence was of 80%, and REV RNA was detected in 1% of pork livers. Phylogenetic analysis pointed out HEV genotype 3. Thus, in addition to possible HEV contamination through the water source, as in endemic region, zoonotic transmissions of REV probably occur in west Africa.

In contrast to lentiviral infections of humans and macaques, simian immunodeficiency virus (SIV) infection of natural hosts is nonpathogenic despite high levels of viral replication. However, the mechanisms underlying this absence of disease are unknown. Here we report that natural hosts for SIV infection express remarkably low levels of CCR5 on CD4+ T cells isolated from blood, lymph nodes, and mucosal tissues. Given that this immunologic feature is found in 5 different species of natural SIV hosts (sooty mangabeys, African green monkeys, mandrills, sun-tailed monkeys, and chimpanzees) but is absent in 5 nonnatural/recent hosts (humans, rhesus, pigtail, cynomolgus macaques, and baboons), it may represent a key feature of the coevolution between the virus and its natural hosts that led to a nonpathogenic infection. Beneficial effects of low CCR5 expression on CD4+ T cells may include the reduction of target cells for viral replication and a decreased homing of activated CD4+ T cells to inflamed tissue.

SummaryHigh-level immune activation and T cell apoptosis represent a hallmark of HIV-1 infection that is absent from nonpathogenic SIV infections in natural primate hosts. The mechanisms causing these varying levels of immune activation are not understood. Here, we report that nef alleles from the great majority of primate lentiviruses, including HIV-2, downmodulate TCR-CD3 from infected T cells, thereby blocking their responsiveness to activation. In contrast, nef alleles from HIV-1 and a subset of closely related SIVs fail to downregulate TCR-CD3 and to inhibit cell death. Thus, Nef-mediated suppression of T cell activation is a fundamental property of primate lentiviruses that likely evolved to maintain viral persistence in the context of an intact host immune system. This function was lost during viral evolution in a lineage that gave rise to HIV-1 and may have predisposed the simian precursor of HIV-1 for greater pathogenicity in humans.

Mandrills are the only nonhuman primate (NHP) naturally infected by two types of simian immunodeficiency virus (SIV): SIVmnd-1 and SIVmnd-2. We have already reported that the high SIVmnd-1 replication during primary infection contrasts with only transient changes in CD4 + and CD8 + cell counts. Since early virus-host interactions predict viral control and disease progression in human immunodeficiency virus-infected patients, we investigated the dynamics of SIVmnd-2 primary infection in mandrills to examine the impact on immune effectors in blood and lymph nodes (LNs). To avoid in vitro strain selection, all mandrills in this study received plasma from SIVmnd-2-infected mandrills. SIVmnd-2 plasma viremia peaked at 10 7 to 10 8 RNA copies/ml between days 7 and 10. This peak was followed in all four monkeys by a decline in virus replication, with a set point level of 10 5 to 10 6 RNA copies/ml at day 42 postinfection (p.i.). Viral DNA load in PBMC and LNs also peaked between days 7 and 10 (10 5 to 10 6 DNA copies/10 6 cells) and stabilized at 10 3 to 10 4 DNA copies/10 6 cells during the chronic phase. Anti-SIVmnd-2 antibodies were detected starting from days 28 to 32. A transitory decline of CD3 + CD4 + cells in the LNs occurred in animals with high peak VLs. CD4 + and CD8 + T-cell activation in blood and LNs was noted between days 5 and 17 p.i., surrounding the peak of viral replication. This was most significant in the LNs. Activation markers then returned to preinfection values despite continuous and active viral replication during the chronic infection. The dynamics of SIVmnd-2 infection in mandrills showed a pattern similar to that of SIVmnd-1 infection. This might be a general feature of nonpathogenic SIV natural African NHP models.

An hepatitis B virus (HBV) molecular survey was conducted in five remote villages in the equatorial forest in Gabon, Central Africa. Two hundred seventy out of 311 inhabitants (86.8%) were HBV-infected or had evidence of past HBV infection. Chronic hepatitis corresponding to hepatitis B surface antigen (HBsAg) positivity was suspected in 27 (8.6%) of the HBV-infected subjects. High HBV viral loads were detected mainly in children aged 4-7 years. The pre-S/S domains were sequenced in 13 cases and 12 strains belonged to HBV-A genotype. In one case we found evidence for recombination between genotypes A and E. Phylogenetic analysis revealed that Gabonese HBV strains were distinct from HBV-A subgenotypes (A1 and A2). These new HBV strains from Gabon clustered with previously reported HBV-A3 subgenotype strains from Cameroon and Democratic Republic of Congo. The analysis of the pre-S2 domain allowed us to determine two amino acid substitutions (N/152/S and N/174/T) specific to the Central African HBV-A3 subgenotype strains and one amino acid substitution (P/155/Q) unique to these new Gabonese HBV-A3 subgenotype isolates. Two full genome sequences of two new Gabonese HBV isolates are also presented and confirm the distinctive HBV-Gab-A3 cluster.

Non-invasive faecal sampling in the equatorial forest in Gabon allowed the first identification of the hepatitis B virus (HBV-Ch RC170 ) genome in samples collected from wild chimpanzees ( Pan troglodytes troglodytes ). The HBV-Ch RCl70 sequence clustered with 100% bootstrap support with previous viral sequences obtained from Pan troglodytes subspecies. This is the first evidence of HBV infection in wild apes and confirms that the HBV-like strains thus far characterized in captive apes are directly related to those circulating in the wild.

To better understand which factors govern the levels of viral loads in early lentiviral infections of primates, we developed a model that allows distinguishing between the influences of host and viral factors on viremia. Herein we report that two species of African green monkeys ( Chlorocebus sabaeus and C. pygerythrus ) infected with their respective wild-type simian immunodeficiency virus SIVagm viruses (SIVagm.sab92018 and SIVagm.ver644) consistently showed reproducible differences in viremia during primary infection but not at later stages of infection. Cross-infections of SIVagm.sab92018 and SIVagm.ver644 into, respectively, C. pygerythrus and C. sabaeus revealed that the dynamics of viral replication during primary infection were dependent on the viral strain used for the infection but not on the host. Hence, the kinetics of SIVagm.sab92018 and SIVagm.ver644 were similar in both sabaeus and vervet animals, indicating that the difference in viremia levels between the two groups during the early phase of infection was not associated with the host. Coreceptor usage for these two strains showed a larger coreceptor repertoire for SIVagm.sab92018, which is able to efficiently use CXCR4 in addition to CCR5, than for SIVagm.ver644, which showed a classical CCR5 coreceptor usage pattern. These differences could not be explained by different charges of the V3 loop for SIVagm.sab92018 and for SIVagm.ver644. In conclusion, our study showed that the extent of virus replication during the primary infection is primarily dependent on viral determinants.

We used an ELISA to determine the prevalence of IgG antibodies specific for the Zaire subtype of Ebola virus in 790 nonhuman primates, belonging to 20 species, studied between 1985 and 2000 in Cameroon, Gabon, and the Republic of Congo. The seroprevalence rate of Ebola antibody in wild-born chimpanzees was 12.9%, indicating that (1) Ebola virus circulates in the forests of a large region of central Africa, including countries such as Cameroon, where no human cases of Ebola infections have been reported; (2) Ebola virus was present in the area before recent outbreaks in humans; (3) chimpanzees are continuously in contact with the virus; and (4) nonlethal Ebola infection can occur in chimpanzees. These results, together with the unexpected detection of Ebola-specific IgG in other species (5 drills, 1 baboon, 1 mandrill, and 1 Cercopithecus), may help to narrow the search for the reservoir of Ebola virus. They also suggest that future Ebola outbreaks may occur anywhere in the central African forest region.

Objectives To evaluate a phenotype assay based on plasma reverse transcriptase (RT) to assess HIV susceptibility to nonnucleoside RT inhibitors (NNRTIs). To compare RT-based phenotype with recombinant virus assay (RVA) phenotype- and genotype-based analysis. To assess group O and HIV-2 susceptibility to NNRTIs in correlation with genotype polymorphisms. Methods RT activity was quantified and its susceptibility to efavirenz, nevirapine, and delavirdine measured as drug concentration resulting in 50% inhibition. RT phenotype was compared with genotype analysis. Eighteen plasma samples from 14 group M- and culture supernatants from 4 group M-, 9 group O-, and 7 HIV-2-infected patients were investigated. RT-based and RVA-based phenotypes were compared for identical plasma from 9 group M-infected patients. Results RT-based and RVA-based phenotypes were in complete agreement. RT-based phenotype- and genotype-predicted susceptibility were concordant for all but 1 group M samples. One plasma showed susceptibility to 3 NNRTIs by phenotypes, despite the presence of 101E and 106I/V residues. The HIV-2 RTs were totally resistant to the NNRTIs tested. Among HIV-1 group O, 6 were totally resistant to NNRTIs independently of the presence of the 181C mutation and 3 were susceptible to some NNRTIs. Conclusion Plasma RT-based phenotype could be useful as a simple alternative for monitoring resistance to NNRTIs. This assay is suitable for highly divergent strains. It would be particularly useful for large epidemiologic survey of the natural HIV polymorphism and the potential impact in emergence of drug resistance, particularly to nevirapine, widely used to prevent mother-to-child transmission.

The mandrill (Mandrillus sphinx) has been shown to be infected with an STLV-1 closely related to HTLV-1. Two distinct STLV-1 subtypes (D and F) infect wild mandrills with high overall prevalence (27.0%) but are different with respect to their phylogenetic relationship and parallel to the mandrills' geographic range. The clustering of these new STLV-1mnd sequences with HTLV-1 subtype D and F suggests first, past simian-to-human transmissions in Central Africa and second, that species barriers are easier to cross over than geographic barriers.

A recent serological survey of wild-born captive monkeys from Gabon, Central Africa, revealed that 1 of 20 Cercopithecus nictitans tested was infected with a new simian T cell lymphotropic virus type 1 (STLV-1). We investigated the molecular relationship between the STLV-1 strain present in this C. nictitans (CN01) and the other available HTLV/STLV strains. Phylogenetic analysis of the env (gp46 and gp21) region showed that the new STLV(nict) clusters with the HTLV-1/STLV-1 group and not with the other nictitans STLVs belonging to the STLV-3 group. Moreover, our new STLV(nict) is closely related to the molecular subtype D, which presently includes five HTLV-1 and three mandrill STLV-1 strains from Gabon and two from Cameroon. These data show that C. nictitans may be the natural carrier of two different molecular types of STLV, one related to STLV-3 and the other possibly one of the simian STLV type 1 counterparts of HTLV-1 subtype D.

Viral loads were investigated in SIVmnd-1 chronically infected mandrills and the results were compared with those previously observed in other nonpathogenic natural SIV infections. Four naturally and 11 experimentally SIVmnd-1-infected mandrills from a semi-free-ranging colony were studied during the chronic phase of infection. Four SIVmnd-1-infected wild mandrills were also included for comparison. Twelve uninfected mandrills were used as controls. Viral loads in all chronically infected mandrills ranged from 10 5 to 9 × 10 5 copies/ml and antibody titers ranged from 200 to 14,400 and 200 to 12,800 for anti-V3 and anti-gp36, respectively. There were no differences between groups of wild and captive mandrills. Both parameters were stable during the follow-up, and no clinical signs of immune suppression were observed. Chronic SIVmnd-1-infected mandrills presented slight increases in CD20 + and CD28 + /CD8 + cell counts, and a slight decrease in CD4 + /CD3 + cell counts. A slight CD4 + /CD3 + cell depletion was also observed in old uninfected controls. Similar to other nonpathogenic models of lentiviral infection, these results show a persistent high level of SIVmnd-1 replication during chronic infection of mandrills, with minimal effects on T cell subpopulations.

Thus far, simian immunodeficiency virus from chimpanzees (SIVcpz) genomes have been characterized as Pan troglodytes troglodytes and show a strong relation with human immunodeficiency virus (HIV)-1 N in their env genes. We fully characterized another SIVcpz from P. t. troglodytes. This chimpanzee (Cam5) was, as was also the host of SIVcpz-cam3, wild born in Cameroon, a region where all three groups of HIV-1 (M, N and O) co-occur. In contrast to other SIVcpz, SIVcpz-cam5 was isolated immediately after the rescue of the animal. Our data demonstrate that SIVcpz-cam5, like SIVcpz-cam3, grows easily on human peripheral blood mononuclear cells (PBMCs) and uses CCR5 as a co-receptor similar to HIV-1 N YBF30. Phylogenetic analysis based on the entire env gene shows that SIVcpz-cam5 falls into the same unique subcluster as HIV-1 N YBF30, SIVcpz-cam3 and SIVcpz-US. A phylogenetic relationship was also found with the vif gene of HIV-1 N. This study provides proof that HIV-1 N related viruses circulate in wild P. t. troglodytes.

Hepatitis E virus (HEV) is globally distributed, transmitted enterically and between humans and animals. Phylogenetic analysis has identified five distinct HEV genotypes. The first full-length sequence of an African strain (Chad) is presented and compared to 31 complete HEV genomes available, including the fulminant hepatitis strain from India, swine strains and a strain from Morocco. The two African strains are more closely related to genotype 1 than to any other genotypes and together they possibly form a sub-genotype or sixth genotype. The first evidence for recombination between divergent HEV strains is presented.

African nonhuman primates are natural hosts for simian immunodeficiency viruses (SIVs). To date, SIV infections have been detected in 20 distinct species (24). SIVs were shown to cluster in six major, approximately equidistant lineages (17, 53). Human immunodeficiency virus type 1 (HIV-1) and HIV-2 belong to two of these clusters and emerged most likely following zoonotic transmissions of, respectively, SIVcpz from chimpanzees and SIVsm from sooty mangabeys (14, 16, 21). The remaining clusters are formed by SIVs isolated from African green monkeys (AGMs), Syke's monkeys, l'hoest monkeys, and colobus monkeys (4, 17, 20, 27, 39, 60). The phylogeny of many SIVs resembles that of their host species, suggesting a coevolution (1, 21, 39). In contrast to these, some viruses (SIVrcm, SIVagm.sab, SIVmnd-2, and SIVdrl) cluster in different lineages according to the genomic region analyzed (15, 22, 31, 55). These viruses most likely result from recombination events in monkeys dually infected by SIVs of two distinct lineages (15, 22, 31, 55). Such dual infections suppose the existence of cross-species transmissions of SIV in nature. It has indeed been shown that wild patas monkeys and baboons can acquire SIVagm (7, 32, 61). It remains unclear if these two latter species are infected with species-specific SIVs (54). This was also questioned for mandrills (Mandrillus sphinx). The first SIVmnd strain (GB1), now defined as SIVmnd-1, was isolated 13 years ago from a wild-born mandrill (59). This virus was the only representative of the SIVmnd lineage until two Cercopithecinae viruses, from l'hoest (Cercopithecus l'hoesti l'hoesti) and sun-tailed monkeys (Cercopithecus l'hoesti solatus) were shown to cluster in the same lineage as SIVmnd GB1 (4, 29). As the genome of SIVmnd GB1 had the organization of Cercopithecus SIVs and not that of Papionini SIVs, and because the habitat of mandrills and sun-tailed monkeys overlaps in Gabon, it was suggested that SIVmnd GB1 represents a virus cross-transmitted from sun-tailed monkeys to mandrills, and the lineage was renamed the l'hoest lineage (4, 5). It was subsequently demonstrated that SIVmnd GB1-related viruses are commonly present in wild adult mandrills, indicating that the virus is capable, at least today, of efficiently spreading between animals of this species (55). Mandrills infected with SIVmnd-1 are separated by the Ogooue River from mandrills infected with SIVmnd type 2 (55). This latter virus has a genomic organization distinct from those of SIVmnd GB1 and SIVlhoest and identical to that of SIVs of other Papio monkeys, such as SIVsm and SIVdrl (15, 55). It is unknown why SIV infections are generally nonpathogenic in African nonhuman primates. SIVmnd-2 infections in mandrills have not been associated with signs of AIDS. SIVmnd-1 infection, which apparently results from SIV transmission from C. l'hoesti to mandrills, is also considered to be asymptomatic, although a possible exception has been reported (44). SIVlhoest, which is genetically close to SIVmnd-1 and is also associated with asymptomatic infection in its natural host, appears to induce AIDS in macaques (29). In both HIV-1-infected humans and SIVmac-infected macaques, it was shown that early virus-host interactions are predictive of the outcome of infection. Predictive markers are in particular gag-specific T-helper responses and viral load levels in the post-acute phase of infection (36, 50). In macaques, the steady-state level of plasma viremia 5 to 6 weeks after exposure to the virus is an excellent predictor of the subsequent disease course (28, 35, 42, 63). RNA levels in plasma measured early in HIV-1 infection are also highly predictive of subsequent rates of disease progression (36, 37, 43). However, although this observation is broadly acknowledged and used as the main indication for treating HIV-1-infected patients early in the course of the disease (10), little is still known about the driving mechanism(s) directing this phenomenon. Studies of the early events during nonpathogenic infections in natural host species can help to elucidate such mechanisms. So far, studies during the early phase of infection in African nonhuman primates are limited (58). Studies in SIVagm.sab92018-infected AGMs have revealed for the first time an extensive replication during the acute and post-acute phases (18). Many naturally infected AGMs analyzed during the chronic phase also show continuously high levels of viral RNA in plasma (9, 23). Moreover, virus load in the blood and lymph nodes (LN) of mangabeys during chronic infection is at levels equivalent to that in macaques and humans progressing to AIDS, despite the lack of clinical signs of AIDS (49). The absence of AIDS in these monkeys therefore seems to be paradoxical in the presence of such a high viral load. However, it is not clear whether the high viral replication observed is a general feature of nonpathogenic infections in natural host species (3, 23). Moreover, the precise dynamics of CD4+ and CD8+ cells during primary infection have not been reported so far. Our primary objective for the present study was to investigate the acute and post-acute phases of SIVmnd-1 infection in mandrills. SIVmnd-1 is thought to represent the result of an ancient cross-species transmission in the wild (4, 6), and we investigated whether it would represent an intermediate model between the pathogenic and nonpathogenic models of lentiviral infections. We analyzed viral dynamics and corroborated the virological study with the analyses of CD4+- and CD8+-T-cell changes over time in the blood and LN.

We assess the genetic relationships between 49 HIV-1 group O strains from 24 and 25 patients living in Cameroon and France, respectively. Strains were sequenced in four genomic regions: gag (p24) and three env regions (C2-V3, gp41, and for 22 C2-gp41). In each of the genomic regions analyzed, the genetic diversity among the group O strains was higher than that exhibited by group M. We characterize three major group O phylogenetic clusters (O:A, O:B, and O:C) that comprised the same virus strains in each of the genomic regions analyzed. The majority of strains cluster in O:A, a cluster previously identified by analysis of pol and env sequences. Group O recombinants were also identified. Importantly, the distinction between these three major group O clades was weak compared to the strong clustering apparent in the global group M phylogenetic tree that led to the identification of subtypes. Thus, these clusters of group O viruses should not be considered as equivalent to the group M subtypes. This difference between the pattern of group O and the global group M diversity, both taking into account the pandemic status of the group M subtypes and the comparatively small number of group O-infected individuals (the majority being from Cameroon), indicates that the group O phylogeny primarily represents viral divergence in the Cameroon region, analogous to group M viral diversity present in the Democratic Republic of Congo.

HIV-1 variants in breast milk and peripheral blood have been compared in three HIV-1 infected mothers. Analysis of DNA and RNA env C2-V3 sequences showed a differential distribution of HIV variants between the two compartments. The major provirus variant found in breast milk corresponds to a minor variant in the blood of two mothers. In the third mother, the predominant proviral variant detected in breast milk was not represented in the HIV-1 blood population. The major RNA variant in breast milk was not represented in the blood of two mothers. The predominant RNA variant in breast milk and blood was however the same for the third mother. Unexpectedly, the pattern of free virus variants in breast milk of three mothers did not correspond to that of the proviral form, suggesting that free viruses do not derive from infected cells in breast milk. The observation of a compartmentalization of HIV-1 between peripheral blood and breast milk emphasizes that postnatal transmission of HIV occurs with variants that may not be predicted from the analysis of circulating viral populations.

The sensitivity of one ELISA method, six HIV-1/HIV-2 rapid screening tests, and one confirmatory test was evaluated in comparison with a third-generation EIA method (taken as the 'gold standard') and Western blot on well-characterized panels of sera. HIV diversity was represented by 50 HIV-1 group M subtype A to H, nine HIV-1 group O, 12 HIV-2, two HIV1+2 positive and six indeterminate Western blot profiles. Sensitivity during HIV-1 seroconversion was studied on 39 serial samples collected from six patients during early primary infection. Serial samples obtained from two primates during experimental primary SIV infection were used to mimic HIV-2 seroconversion samples. The sensitivity ranged from 100 to 94.6% according to the test. During seroconversion, rapid tests became positive 2-8 days later than the third-generation EIA. This reveals a major limitation of rapid tests, which are being recommended for use in developing countries. The lack of sensitivity seen during early HIV-1 seroconversion and/or limited specificity in some of the evaluated tests present serious limitations to their use in countries with high HIV incidence and variability. It is suggested that, as soon as possible, less sensitive rapid tests for blood bank screening should be abandoned in favor of highly sensitive rapid tests and/or more robust, more sensitive and cheaper ELISAs. These results stress the need for better screening tools and specific local evaluations.

We studied the impact of HIV-1 genetic diversity on antiretroviral susceptibility and the prevalence of primary HIV-1 resistance in a cohort of seroconverters in Abidjan. Despite an extensive variation in the protease and reverse transcriptase genes most of the isolates seemed to conserve a full susceptibility to antiretroviral drugs. Minor variations of nevirapine susceptibility should be investigated in a context of the potential wide use of this drug for preventing mother-to-child transmission. (author’s)

Chikungunya virus (CHIKV) is an alphavirus of the Togaviridae family that causes chronic and incapacitating arthralgia in human populations. Since its discovery in 1952, CHIKV was responsible for sporadic and infrequent outbreaks. However, since 2005, global Chikungunya outbreaks have occurred, inducing some fatalities and associated with severe and chronic morbidity. Chikungunya is thus considered as an important re-emerging public health problem in both tropical and temperate countries, where the distribution of the Aedes mosquito vectors continues to expand. This review highlights the most recent advances in our knowledge and understanding of the epidemiology, biology, treatment and vaccination strategies of CHIKV.

Env C2/V3, gag p17/p24, pol protease, and RT regions of HIV-1 isolates recently obtained from 25 HIV-1 seropositive individuals from Ho Chi Minh City (Vietnam) were studied, and genes subtypes were determined by DNA sequence analyses. Twenty-three isolates out of 25 were identified as belonging to subtype E, now recognized as circulating recombinant form 1 (CRF01_AE). The motif at the top of the V3 loop (generally GPGQ) was then preceded by an isoleucine or a methionine (M) residue; the M residue might be a local signature of Vietnamese E isolates compared to Thai E viruses. Two isolates (8%) were shown to be intersubtype recombinants: one E/B and one CRF02_AG(IBNG)/D. The polymorphism of pol protease was considered only for CRF01_AE isolates and is clearly different from that recorded for B viruses with substitutions at positions 13, 35, 36, 41, 69, and 89.

We developed a simple, rapid, inexpensive, and highly sensitive and specific strategy for the detection and lineage differentiation of primate lentiviruses (PIV-ELISA). It is based on the use of two indirect ELISA methods using synthetic peptides mapping the gp41/36 region (detection component) and the V3 region (differentiation component) of four lentivirus lineages, namely SIVcpz/HIV-1 (groups M, O, N, and SIVcpz-gab), SIVmnd, SIVagm, and SIVsm/SIVmac/HIV-2. This strategy was evaluated with panels of sera originating from both humans and nonhuman primates. The human reference panel consisted of 144 HIV Western blot (WB)-positive sera in which the corresponding virus had been genotyped (HIV-1: 72 group M, 28 group O, and 6 group N; HIV-2: 21 subtype A and 10 subtype B; and 7 HIV-1+2) and 105 HIV WB-negative samples. The nonhuman primate reference panel consisted of 24 sera from monkeys infected by viruses belonging to the four lineages included in the PIV-ELISA strategy (5 chimpanzees, 5 macaques, 8 mandrills, and 6 vervets) and 42 samples from seronegative animals. Additional field evaluation panels consisted of 815 human sera from Gabon, Cameroon, and France and 537 samples from 25 nonhuman primate species. All the samples from the two reference panels were correctly detected and discriminated by PIV-ELISA. In the human field evaluation panel, the gp41/36 component correctly identified all the test samples, with 98% specificity. The V3 component discriminated 206 HIV-1 group M, 98 group O, 12 group M+O, and 128 HIV-2 sera. In the primate field evaluation panel, both gp41/36 and V3 detected and discriminated all the WB-positive samples originating from monkeys infected with SIVcpz, SIVagm-ver, SIVmnd-1, SIVmnd-2, SIVdrl, or SIVsun. These results were confirmed by genotyping in every case. Four SIV-infected red-capped mangabeys (confirmed by PCR) were correctly identified by gp41/36, but only two reacted with the V3 peptides in the absence of a specific SIVrcm V3 peptide. Addition of a V3 SIVrcm peptide discriminated all the SIVrcm-positive samples. Fourteen Papio papio samples were positive for SIVsm gp 36 and by WB, but negative by PCR, whereas three Papio cynocephalus samples were positive by gp41/36 but indeterminate by WB and negative by PCR. This combined ELISA system is thus highly sensitive and specific for antibodies directed against HIV and SIV. In addition, the V3-based serotyping results always agreed with genotyping results. This method should prove useful for studies of lentivirus prevalence and diversity in human and nonhuman primates, and may also have the potential to detect previously undescribed SIVs.

Infections by human and simian immunodeficiency viruses (HIV and SIV) are independent of host cell division since the preintegration complex (PIC), containing the viral DNA, is able to undergo active nuclear import after viral entry. In order to clarify the mechanisms responsible for nuclear import of the PIC, we have analyzed the subcellular distribution and the karyophilic properties of its viral components, matrix protein (MA), integrase (IN), Vpr, and Vpx. Although MA has been reported to contain a nuclear localization signal, the MA/GFP fusions are excluded from the nucleus and associated with cellular membranes. In contrast, both HIV-1 and SIV IN and Vpr localize in the nucleus of transfected cells. Interestingly, only Vpx from SIVsm virus accumulate in the nucleus while SIVsm Vpr is uniformly distributed throughout nucleus and cytoplasm. Coexpression of MA, Vpr, and IN does not induce any change in their respective intracellular localizations. Finally, we confirm the karyophilic properties of HIV-1 IN and Vpr using an in vitro nuclear import assay. These results indicate that the viral proteins IN and Vpr, which are strongly associated with the viral DNA within PIC, may participate in the nuclear import of the HIV PIC.

SUMMARY We examined CD4 and major HIV-1 co-receptor expression by trophoblast cells (TC) from early placentas, and the permissiveness of TC for infection by several natural HIV-1 isolates in vitro. Ten early placentas (4–6 weeks of gestation) from HIV−women were obtained after elective abortion. CD4 and HIV-1 co-receptor expression by TC was examined in terms of both mRNA and protein. The same TC were then challenged with three clinical HIV isolates of known phenotype, two originating from mothers who transmitted the virus to their child and one from a vertically infected newborn. TC infection was detected by polymerase chain reaction. CD4 expression was detected in five of the 10 placentas, while membrane protein expression of CCR3, CXCR4 and CCR5 was detected in every case, despite quantitative differences among individuals. Bonzo, GPR1 and ChemR23 mRNAs were detected in all TC preparations. TC from seven out of eight placentas were permissive to HIV entry, but no productive viral replication was detected (reverse transcriptase activity in culture supernatants). Interestingly, the addition of chemokine(s) or a CD4-blocking antibody to the cultures failed to inhibit TC virus entry. These data point to marked interindividual variability in HIV co-receptor expression by trophoblast cells and show that TC from early placentas can be infected in vitro by clinical HIV-1 isolates. They also suggest that viral entry in vitro might occur through a mechanism independent of both CD4 and chemokine receptors.

Objective To study the distribution of HIV-1 subtypes in France and to describe the characteristics of patients infected with non-B subtypes. Methods All adults who tested HIV-1 positive on Western blot for the first time in one of the participating laboratories between September 1996 and March 1998 were eligible, whether or not they had been diagnosed previously elsewhere. Data on age, sex, country of birth, HIV-transmission group, dates of the last negative and first positive HIV test and clinical stage were collected. Serotyping was performed with a peptide subtype-specific enzyme immunoassay on each plasma sample and genotyping with heteroduplex mobility assay on each non-B serotype-infected patient. Patients characteristics were compared in B and non-B subtypes. Results Of the 2168 HIV-positive patients included by 32 laboratories, subtype,results were available for 2042. Among those, 73.4% were men, 12.2% born in sub-Saharan Africa, 41.5% infected through heterosexual contact and 67.6% in CDC stage A. Among the 2042 patients, 1 725 (84.5%) were infected with B subtype. Among the 317 non-B subtypes, subtype A was predominant (66.9%); all other subtypes (C, D, E, F, G, H, O) were present. Factors independently associated with a non-B subtype were to be included in the Paris area [adjusted odds ratio (aOR), 1.6; 95% confidence interval (CI), 1.1-2.3], to be born in sub-Saharan Africa (aOR, 26.0; 95% CI, 17.5-37.8) and to be infected through heterosexual contact (aOR, 4.2; 95% CI, 2.8-6.4). Conclusions In France, although B subtype is still predominant, all non-B subtypes are now present. The diversity of HIV strains may affect diagnostic tests and clinical practice, especially viral load measurements. Moreover, the decreased susceptibility of non-B subtypes to antiretroviral drugs emphasizes the importance of surveillance of HIV diversity.

The critical functions of the HIV-1 nucleocapsid protein NCp7 in genomic RNA packaging and reverse transcription, essentially rely on interactions with nucleic acids. A significant progress in the knowledge of these interactions has been recently achieved with the NMR-derived structures of NCp7 derivatives in complex with two short sequences of the HIV-1 psi packaging signal, namely ACGCC and the stem-loop 3 (SL3) motif. To further identify the key nucleotides in the formation of both NCp7-d(ACGCC) and NCp7-SL3 complexes, we quantitatively analyzed by steady-state and time-resolved fluorescence, the interaction of NCp7 with d(ACGCC) and SL3 mutants where each nucleotide in interaction with the protein has been systematically substituted. Moreover, by using several NCp7 derivatives, we investigated the contributions of Phe16, Trp37, and Trp61, and the various NCp7 domains, in the binding process. The binding of NCp7 appeared essentially driven by the interaction of the zinc finger domain and notably Trp37 with a G residue, irrespective of its location in the oligonucleotide. The involvement of Trp37 in the binding process depended on its location in the C-terminal finger motif and the proper folding of this motif. Phe16 in the N-terminal finger motif also strongly contributed to the binding energy, while in contrast, Trp61 in the C-terminal domain only marginally interacted with the oligonucleotides. The stem-loop structure of SL3 stabilized the binding of NCp7 by about -7 kJ/mol (at 0.1 M NaCl) by favoring the electrostatic binding of both N- and C-terminal domains. Finally, we found that NCp7 bound to nucleic acid single-stranded regions with the following preference: X(i)()TGX(j)() > X(i)()GXGX(j)() approximately X(i)()TXGX(j)() > X(i)()GX(j)() >> X(i)()X(j)(), where X corresponds to either A or C. This implies that recognition of nucleic acids by NCp7 may be achieved by a limited number of sites, and hence, no strong affinities are required in order to get a selective binding.