Peramivir binding affinity with influenza A neuraminidase and research on its mutations using an induced-fit docking approach.

Influenza A virus (IAV) has caused epidemic infections worldwide, with many strains resistant to inhibitors of a surface protein, neuraminidase (NA), due to point mutations on its structure. A novel NA inhibitor named peramivir was recently approved, but no exhaustive computational research regarding its binding affinity with wild-type and mutant NA has been conducted. In this study, a thorough investigation of IAV-NA PDB entries of 9 subtypes is described, providing a list of residues constituting the protein-ligand binding sites. The results of induced-fit docking approach point out key residues of wild-type NA participating in hydrogen bonds and/or ionic interactions with peramivir, among which Arg 368 is responsible for a peramivir-NA ionic interaction. Mutations on this residue greatly reduced the binding affinity of peramivir with NA, with 3 mutations R378Q, R378K and R378L (NA6) capable of deteriorating the docking performance of peramivir by over 50%. 200 compounds from 6-scaffolds were docked into these 3 mutant versions, revealing 18 compounds giving the most promising results. Among them, CMC-2012-7-1527-56 (benzoic acid scaffold, IC50 = 32 nM in inhibitory assays with IAV) is deemed the most potential inhibitor of mutant NA resisting both peramivir and zanamivir, and should be further investigated.

Does smallpox vaccination modify HIV disease progression among ART-naive people living with HIV in Africa?

We examined the association between a history of smallpox vaccination and immune activation (IA) in a population of antiretroviral therapy-naïve people living with HIV (PLHIV). A cross-sectional study was conducted in Senegal from July 2015 to March 2017. Smallpox vaccination was ascertained by the presence of smallpox vaccine scar and IA by the plasma level of ß-2-microglobulin (ß2m). The association was analysed using logistic regression and linear regression models. The study population comprised 101 PLHIV born before 1980 with a median age of 47 years (interquartile range (IQR) = 42-55); 57·4% were women. Smallpox vaccine scar was present in 65·3% and the median ß2m level was 2·59 mg/l (IQR = 2·06-3·86). After adjustment, the presence of smallpox vaccine scar was not associated with a ß2m level ⩾2·59 mg/l (adjusted odds ratio 0·94; 95% confidence interval 0·32-2·77). This result was confirmed by the linear regression model. Our study does not find any association between the presence of smallpox vaccine scar and the ß2m level and does not support any association between a previous smallpox vaccination and HIV disease progression. In this study, IA is not a significant determinant of the reported non-targeted effect of smallpox vaccination in PLHIV.

When private actors matter: Information-sharing network and surveillance of Highly Pathogenic Avian Influenza in Vietnam.

The effectiveness of animal health surveillance systems depends on their capacity to gather sanitary information from the animal production sector. In order to assess this capacity we analyzed the flow of sanitary information regarding Highly Pathogenic Avian Influenza (HPAI) suspicions in poultry in Vietnam. Participatory methods were applied to assess the type of actors and likelihood of information sharing between actors in case of HPAI suspicion in poultry. While the reporting of HPAI suspicions is mandatory, private actors had more access to information than public actors. Actors of the upstream sector (medicine and feed sellers) played a key role in the diffusion of information. The central role of these actors and the influence of the information flow on the adoption by poultry production stakeholders of behaviors limiting (e.g. prevention measures) or promoting disease transmission (e.g. increased animal movements) should be accounted for in the design of surveillance and control programs.

High acceptability of HIV voluntary counselling and testing among female sex workers: impact of individual and social factors.

OBJECTIVES: Voluntary counselling and testing (VCT) for HIV infection is an important tool for prevention of HIV infection and AIDS in high-risk groups. Our goal was to describe the acceptability and consequences of VCT among a stigmatized and vulnerable group, female sex workers (FSWs), in Conakry, Guinea. METHODS: Acceptance of the test and return for test results at baseline and consequences of testing 1 year later were described. The perceived risk of HIV infection and perceived benefits and barriers to testing were examined using quantitative and qualitative methods. RESULTS: All 421 FSW participants agreed to undergo VCT and most participants (92%) returned for their results. The main reason cited for VCT acceptance was the wish to know their HIV status. However, some managers of FSW worksites urged FSWs to be tested, curtailing FSWs' free decision-making. One year later, status disclosure was common (90% of the 198 individuals who knew their results among those who participated in the follow-up part of the study). Positive consequences of testing were far more frequently reported than negative consequences (98% vs. 2%, respectively). Negative life events included banishment from the worksite (one case) and verbal abuse (two cases). CONCLUSION: Acceptability of VCT appears high in the FSW population in Conakry as a consequence of both perceptions of high individual risk and social pressures.

Socio-demographic correlates of late treatment initiation in a cohort of patients starting antiretroviral treatment in Mali, West Africa.

The objective of this study was to investigate factors correlated with late treatment initiation in a cohort of patients starting treatment in Mali, West Africa, while focusing on the role of sex/gender. This study consisted of a cross-sectional analysis of baseline data from a prospective, observational cohort of patients initiating antiretroviral treatment in Mali. Patient data were analyzed with a gender perspective to examine factors correlated with late treatment initiation, defined as having a CD4 count below 100 cells/µl. Aday and Andersen's conceptual framework of access to medical care was used to classify baseline participant characteristics associated with late treatment initiation. Logistic regression was used to evaluate the modifying effect of sex/gender. Results show that 39% of patients initiated treatment late; significantly more of these were men than women. Sex/gender, marital status, and education were associated with late treatment initiation. Unmarried men and uneducated women were significantly more likely to initiate treatment late. Programs need to target unmarried men while being cognizant that uneducated women are arriving late as well.

High level of primary drug resistance in Mali.

BACKGROUND: As access to antiretroviral drugs increases in developing countries, it will become increasingly important to monitor the emergence of resistance and to define the molecular pathways involved to identify optimal therapeutic regimens. METHODS: We performed genotypic resistance testing on plasma obtained from 101 HIV-infected treatment-naïve individuals from Mali. Genotyping was carried out using the Virco protocols and HXB2 was used as the reference strain. RESULTS: CRF02_AG was the most common subtype, present in 71.3% of our patient population. Other subtypes included B, C, G, CRF06_CPX, CRF09_CPX, CRF01_AE, A2/CRF16_A2D, A1 and CRF13_CPX. A total of 9.9% [95% confidence interval (CI) 6.9-12.9%] of patients had at least one resistance mutation. The prevalences of mutations conferring resistance to nucleoside reverse transcriptase inhibitors (NRTIs), nonnucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) were 5% (95% CI 0.7-9.2%), 6% (95% CI 1.3-10.6%) and 0%, respectively. The most frequent mutations were T215A/Y for NRTIs and K103N/T for NNRTIs. One patient harboured three NRTI resistance mutations and one NNRTI mutation. This is the first reported case of multi-drug-resistant viral transmission in Mali. Polymorphisms at protease codons 10I/V and 33F potentially associated with resistance were observed in 18.8% and 1% of patients, respectively. Several polymorphisms in the C-terminal domain of reverse transcriptase were observed: A371V (in 63.4% of patients), G335D (76.2%), E399D (10.9%) and G333E (1%). CONCLUSION: Primary resistance was seen in 9.9% of subjects, which is higher than previously reported in Mali. Taking into consideration other polymorphisms in protease such as L10I/V and 33F, primary resistance could reach 28.7% (95% CI 19.9-37.5%). Our study reflects the need to monitor the evolution of resistance on a regular basis and trends of transmitted resistance.

MHC haplotype and susceptibility to experimental infections (Salmonella Enteritidis, Pasteurella multocida or Ascaridia galli) in a commercial and an indigenous chicken breed.

In three independent experimental infection studies, the susceptibility and course of infection of three pathogens considered of importance in most poultry production systems, Ascaridia galli, Salmonella Enteritidis and Pasteurella multocida were compared in two chicken breeds, the indigenous Vietnamese Ri and the commercial Luong Phuong. Furthermore, the association of the Major Histocompatibility Complex (MHC) with disease-related parameters was evaluated, using alleles of the LEI0258 microsatellite as markers for MHC haplotypes. The Ri chickens were found to be more resistant to A. galli and S. Enteritidis than commercial Luong Phuong chickens. In contrast, the Ri chickens were more susceptible to P. multocida, although production parameters were more affected in the Luong Phuong chickens. Furthermore, it was shown that the individual variations observed in response to the infections were influenced by the MHC. Using marker alleles of the microsatellite LEI0258, which is located within the MHC region, several MHC haplotypes were identified as being associated with infection intensity of A. galli. An association of the MHC with the specific antibody response to S. Enteritidis was also found where four MHC haplotypes were shown to be associated with high specific antibody response. Finally, one MHC haplotype was identified as being associated with pathological lesions and mortality in the P. multocida experiment. Although not statistically significant, our analysis suggested that this haplotype might be associated with resistance. These results demonstrate the presence of local genetic resources in Vietnamese chickens, which could be utilized in breeding programmes aiming at improving disease resistance.

Impact of a modified directly administered antiretroviral treatment intervention on virological outcome in HIV-infected patients treated in Burkina Faso and Mali.

OBJECTIVE: This study explores whether viral load measurements can be used in resource-limited settings to target those in need of adherence assistance. It was hypothesized that high plasma viral loads (pVLs) (>/=500 HIV-1 RNA copies/mL) were the result of poor antiretroviral therapy adherence and amenable to improvement with adherence assistance. DESIGN: A single-arm, multicentre pilot study was conducted from November 2003 to March 2004 on 606 treatment-experienced patients who had initiated an antiretroviral regimen in Mali and Burkina Faso >/=6 months before study enrolment. In these patients, those whose pVL was >/=500 copies/mL were offered 1 month of modified directly administered antiretroviral treatment (mDAART) with weekly follow-up visits from pharmacists or adherence counsellors. METHODS: An adherence questionnaire was given to all cohort patients and viral load was used to screen for patients with >/=500 copies/mL. mDAART participants included cohort patients with >/=500 copies/mL, who completed the adherence questionnaire. Genotypic analyses were conducted on samples taken prior to and after the intervention. The intervention was considered effective when there was a decrease of >/=1 log(10) in pVL. RESULTS: mDAART was effective in over one-third of the intervention participants, while in two-thirds no decrease in pVL was observed. The majority of mDAART participants had major resistance mutations. CONCLUSIONS: pVL measurement was useful to identify patients who needed adherence assistance. However, because it was performed >/=6 months after starting treatment, mDAART came too late for most participants, as they had already developed important resistance mutations that might have been avoided with better laboratory monitoring.

Camelid immunoglobulins and nanobody technology.

It is well established that all camelids have unique antibodies circulating in their blood. Unlike antibodies from other species, these special antibodies are devoid of light chains and are composed of a heavy-chain homodimer. These so-called heavy-chain antibodies (HCAbs) are expressed after a V-D-J rearrangement and require dedicated constant gamma-genes. An immune response is raised in these so-called heavy-chain antibodies following classical immunization protocols. These HCAbs are easily purified from serum, and the antigen-binding fragment interacts with parts of the target that are less antigenic to conventional antibodies. Since the antigen-binding site of the dromedary HCAb is comprised in one single domain, referred to as variable domain of heavy chain of HCAb (VHH) or nanobody (Nb), we designed a strategy to clone the Nb repertoire of an immunized dromedary and to select the Nbs with specificity for our target antigens. The monoclonal Nbs are well produced in bacteria, are very stable and highly soluble, and bind their cognate antigen with high affinity and specificity. We have successfully developed recombinant Nbs for research purposes, as probe in biosensors, to diagnose infections, and to treat diseases like cancer or trypanosomosis.

Gender-related factors influencing HIV serostatus disclosure in patients receiving HAART in West Africa.

Disclosure of HIV serostatus remains an important tool for the prevention of new infections and early initiation of treatment for HIV-positive individuals' regular sexual partners. Our aim is to identify factors associated with disclosure to partner in patients taking antiretroviral treatment, with a gender- and sex-based approach. In this study conducted in Mali and Burkina Faso, men (154) and women (164) who reported being in a marital or cohabitating relationship were included. Sex-specific bivariate analyses and multivariate logistic regression were performed to identify determinants of disclosure. Disclosure to partner was 72.1% in men and 79.9% in women. Results of bivariate and multivariate analyses indicated that cohabiting with partner was strongly associated with disclosure in both men and women. In men only, older age, literacy and having good communication with the treating doctor were significantly associated with disclosure. Among women, disclosure was associated with having children and high self-reported importance of religion. Future research and interventions promoting disclosure should take into account these differences reflecting the social construction of gender roles in these settings.

Inadequate adherence to antiretroviral treatment and prevention in hospital and community sites in Burkina Faso and Mali: a study by the ATARAO group.

Our objective was to determine the prevalence and identify the factors that influence antiretroviral therapy (ART) adherence among patients in Bamako and Ouagadougou. A cross-sectional study was conducted among 94 men and 176 women receiving ART. Data were collected through questionnaires and chart reviews. Logistic regressions were performed to isolate determinants of adherence. Overall, 58% of the patients were adherent, but there were differences in the levels of adherence according to country and treatment site. Sociodemographic factors were not associated with adherence. However, social characteristics such as having children, in Ouagadougou, or being a housewife and not planning to have a child in the next year, in Bamako were associated with adherence. Time on ART was negatively associated with adherence in both countries with decline occurring later in Bamako. Levels of adherence are inadequate particularly among more experienced patients. Further adherence research and monitoring using longitudinal designs are warranted to assess the extent to which adherence is declining with time on treatment.

Prevalence of multiresistant Gram-negative organisms in a surgical hospital in Ho Chi Minh City, Vietnam.

OBJECTIVE: To determine resistance patterns of multiresistant Gram-negative organisms at a surgical hospital in Ho Chi Minh City, Vietnam, in order to guide appropriate antibiotic prescribing and improve infection control procedures. METHOD: All samples sent in for microbiological analysis over a 3-month period were included. A resource neutral double disc-diffusion test was introduced to detect the presence of extended-spectrum beta-lactamase (ESBL) production. RESULTS: We obtained 350 bacterial isolates from clinical specimens; 87.4% were Gram-negative bacteria (GNB). Of these, 88.9% were Enterobacteriaceae, of which 14.7% produced ESBL. Fifteen (37.5%) of these were isolated within 48 h of admission. Resistance to gentamicin and ciprofloxacin occurred in 70.0% and 72.5% of those organisms that produced ESBL and in 39.5% and 38.7% of those that did not. Resistance to third-generation cephalosporins was common: 36.7% of all GNB were resistant to ceftriaxone, 34.0% to cefotaxime, 19.6% to ceftazidime and 36.7% to cefoperazone. CONCLUSION: Multiresistant Gram-negative organisms are common and pose a challenge to antibiotic therapy. Successful implementation of a simple test to detect ESBL production allowed reporting of these organisms, appropriate antibiotic prescribing and infection control interventions. Development of antibiotic-prescribing guidelines must take into account these resistance patterns.

Effects of drug resistance on viral load in patients failing antiretroviral therapy.

Previous studies on patients who develop drug resistant HIV-1 variants have shown that continued use of failing regimens might provide clinical benefit. However, the effect of long-term exposure to drug resistant variants may lead to emergence of compensatory mutations that may jeopardize this effect. In this study, we assess associations among type and number of drug resistant mutations, viral load and disease progression in patients with long-term follow up. Patients with genotypic testing performed at the time of treatment failure were enrolled. Comparison of viral load and CD4 cell count between different resistance groups was performed using analysis of variance. Multiple linear regression analysis was performed to assess the simultaneous effects of the presence of particular mutations and their accumulation on viral load. Data from 475 patients who were followed for a median of 43 months from October 1999 to July 2005 were studied. A "V shape" relationship was observed between the number of mutations and viral load. Specifically, in patients harboring up to five mutations, viral load was reduced by 0.8 log/copies when compared to wild-type variants. However, with more than six mutations viral load progressively increased. Certain reverse transcriptase mutations such as M184V/I, K70R, V108I, and protease mutations such as L33FIV, M84V, and M36I were associated with reduced viral load. Together, these findings suggest that long-term maintenance of a sub-optimal antiretroviral regimen may have deleterious consequences for the patient.

A longitudinal study to identify constraints to dairy cattle health and production in rural smallholder communities in Northern Vietnam.

The objective of the study was to investigate constraints to dairy cattle health and production in rural smallholder communities in northern Vietnam, one of the target areas of the Vietnam government's dairy development programme. A total of 99 dairy farms (11 per commune) were recruited from 9 of 32 communes in Ba Vi District, using random two-stage cluster sampling. After the initial questionnaire interviews were conducted, farms were visited at three monthly intervals over a period of 1 year. Information on several health and production parameters relating to the study cattle was collected. Using multiple indicator modelling, it was found that Fasciola infestation, farmers who had been involved in dairying for longer (not indicative of better management skills), larger herd size, and cattle being kept in a shed were linked to reduced reproductive performances.

Taenia solium taeniasis and cysticercosis in three communities in north Vietnam.

OBJECTIVES: (1) To investigate the response to a serum antigen-detecting ELISA for cysticercosis and a stool coproantigen test for taeniasis in two rural communities (mountainous and coastal areas) and one group of (peri-)urban factory workers; and (2) to examine clinical features of human cysticercosis in northern Vietnam. METHODS: Villagers and factory workers and their families were informed and invited to participate in the study. Blood and faecal samples were collected from the participants and a simple questionnaire on taeniasis/cysticercosis completed. Serum was examined for the presence of circulating cysticercus antigen by a monoclonal-based sandwich ELISA. Ag-ELISA positive persons underwent a clinical examination and a computed tomography (CT) scan. Stool samples were examined microscopically for the presence of Taenia eggs and for copro-antigens. Tapeworms were identified following therapeutic expulsion using morphology and PCR-RFLP. RESULTS: Circulating cysticercus antigens, suggesting active infection, were detected in 5.3% (16/303), 0.6% (1/175) and 0.0% (0/229) of the sampled individuals from the mountainous, coastal and urban regions, respectively. Clinical examination and CT scan of the cysticercus antigen positive persons showed that active cysticercosis did not cause severe disease in most cases. Taenia copro-antigens were found in 0.3% (1/297), 1.8% (3/166) and 0.0% (0/228) of the stool samples from the mountainous, coastal and urban communities, respectively. Three tapeworms were expelled after treatment: two Taenia solium and one Taenia saginata. CONCLUSION: This survey points to a focal distribution of taeniasis/cysticercosis and suggests that human cysticercosis is rather acquired due to close contact with a T. solium carrier and self-infection, than through infection from the environment.

Emergence and evolution of functional heavy-chain antibodies in Camelidae.

Antibodies of jawed-vertebrates are composed of paired heavy (H) and light (L) polypeptide chains. Surprisingly, the sera of camelids, nurse shark and wobbegong shark, and possibly ratfish contain antibodies that lack L-chains. In camelids, these Heavy-chain antibodies (HCAbs) are gamma-isotypes, and are functional in antigen binding. In this review we focus on the dedicated immunoglobulin (Ig) genes that encode the HCAb in Camelidae (camels, dromedaries and llamas), about their origin, and how these camel immunoglobulins evolved and acquire a large and diverse repertoire of antigen binding sites in absence of the H-L combinatorial diversity.

Rational materials design of sorbent coatings for explosives: applications with chemical sensors.

A series of chemoselective polymers had been designed and synthesized to enhance the sorption properties of polymer coated chemical sensors for polynitroaromatic analytes. To evaluate the effectiveness of the chemoselective coatings, a polynitroaromatic vapor test bed was utilized to challenge polymer coated surface acoustic wave (SAW) devices with different explosive vapors. Dinitrotoluene detection limits were determined to be in the <100 parts per trillion ranges. ATR-FTIR studies were used to determine the nature of the polymer-polynitroaromatic analyte interactions, and confirm the presence of hydrogen-bonding between polymer pendant groups and the nitro functional groups of polynitroaromatic explosive materials.

Camel heavy-chain antibodies: diverse germline V(H)H and specific mechanisms enlarge the antigen-binding repertoire.

The antigen-binding site of the camel heavy-chain antibodies devoid of light chain consists of a single variable domain (V(H)H) that obviously lacks the V(H)-V(L) combinatorial diversity. To evaluate the extent of the V(H)H antigen-binding repertoire, a germline database was constructed from PCR-amplified V(H)H/V(H) segments of a single specimen of Camelus dromedarius. A total of 33 V(H)H and 39 V()H unique sequences were identified, encoded by 42 and 50 different genes, respectively. Sequence comparison indicates that the V(H)Hs evolved within the V(H) subgroup III. Nevertheless, the V(H)H germline segments are highly diverse, leading to a broad structural repertoire of the antigen-binding loops. Seven V(H)H subfamilies were recognized, of which five were confirmed to be expressed in vivo. Comparison of germline and cDNA sequences demonstrates that the rearranged V(H)Hs are extensively diversified by somatic mutation processes, leading to an additional hypervariable region and a high incidence of nucleotide insertions or deletions. These diversification processes are driven by hypermutation and recombination hotspots embedded in the V(H)H germline genes at the regions affecting the structure of the antigen-binding loops.

Loss of splice consensus signal is responsible for the removal of the entire C(H)1 domain of the functional camel IGG2A heavy-chain antibodies.

The molecular basis for the absence of the C(H)1 domain in naturally occurring heavy-chain antibodies of the camelids was assessed by determining the entire Camelus dromedarius gamma2a heavy-chain constant gene. The organization of the camel gamma2a constant heavy-chain gene obtained from a liver genomic library appears to be typical of all other mammalian gamma genes sequenced to date. It contains the switch, CH1, hinge, CH2, CH3, M1 and M2 exons. In contrast to the case in mouse and human heavy chain diseases, the camel gamma2a gene shows no major structural defect, and its equivalent CHI exon is intact. However, sequence analysis has revealed that the splicing site, immediately after the CH1 exon, is defective due to point mutations, especially the G(+1) to A(+1) transversion seems to be detrimental. It is concluded that the loss of the splice consensus signal is responsible for the removal of the entire CH1 domain in camel gamma2a heavy-chain immunoglobulins. Additionally, a closer analysis of the hinge exon suggests the possible involvement of transposons in the genetic variation of mammalian Cgamma hinges.