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Background Influenza serologic diagnosis is mainly based on hemagglutination inhibition and microneutralization methods, both methods require handling living viruses under an enhanced biosafety level. Aim The current study was performed for developing an ELISA using synthetic peptides to detect influenza A H1N1 virus 2009 specific antibodies in serum and saliva. Methods Alignments were made with H1N1 hemagglutinin and neuraminidase (HA and NA, respectively) sequences; only conserved sites were used for antigenicity prediction. Two synthetic peptides were assayed; one of neuraminidase (NA15) and one of hemagglutinin (HA-15) and used in ELISA for detecting IgG and IgA antibodies. A cross-sectional study was performed in three municipalities of Mexico City, using negative samples collected before the 2009 influenza outbreak, samples of people who became ill during the outbreak, and samples of the participants in the epidemiological study with or without symptoms. Results The determination of serum IgG antibodies with both peptides allowed differentiating between the post outbreak groups with respect to all others. No differences were found in IgA determination in saliva against both peptides. The frequency of positive participants for NA-15 was 9.5 and 8.8% for HA-15 in serum IgG; whereas the frequency of positive participants for NA-15 was 11%, and for HA-15 was 8.6% for saliva IgA. Conclusions Synthetic peptides of the neuraminidase and hemagglutinin proteins can be used in ELISA for the determination of IgG and IgA antibodies against the influenza A H1N1 virus 2009.

Acinetobacter baumannii is an opportunistic infectious agent that affects primarily immunocompromised individuals. A. baumannii is highly prevalent in hospital settings being commonly associated with nosocomial transmission and drug resistance. Here, we report the identification and genetic characterization of A. baumannii strains among patients in a tertiary level hospital in Mexico. Whole genome sequencing analysis was performed to establish their genetic relationship and drug resistance mutations profile. Ten genetically different, extensively drug resistant strains were identified circulating among seven wards. The genetic profiles showed resistance primarily against aminoglycosides and beta-lactam antibiotics. Importantly, no mutants conferring resistance to colistin were observed. The results highlight the importance of implementing robust classification schemes for advanced genetic characterization of A. baumannii clinical isolates and simultaneous detection of drug resistance markers for adequate patient's management in clinical settings.

Single-nucleotide polymorphisms (SNPs) occurring in immune-related genes have been associated with risk or protection for development of dengue, depending on ethnicity. Here, we genotyped seven SNPs located in immune response-related genes to identify their association with severe forms of dengue in patients from an endemic region in Mexico. One hundred and thirty-eight patients with dengue fever (DF), thirty-one dengue hemorrhagic fever (DHF) patients, as well as 304 healthy donors were genotyped by using a TaqMan-based approach. SNP analysis, including rs1800629 (TNF), rs4804803 (CD209), rs2780831 (JAK1), rs1801274 (FCGR2A), rs231775 (CTLA4), rs12979860, and rs8099917 (IFNL3), was performed. The rs1800629 A-allele in the TNF gene was associated with an increased risk of DHF (OR = 3.4, CI = 1.235-9.284 p = 0.0212) whereas SNPs rs4804803, rs2780831, rs1801274, rs231775, rs12979860, and rs8099917 showed no association in this cohort. These results show that allelic variations in TNF can play an important role in the development of DHF. However, the lack of association between all remaining SNPs and DHF suggests that the genetic background might directly modify the role of these immune-related molecules, leading to the milder illness often observed in a Mexican population.

Despite the significant public health problems associated with hepatitis B virus (HBV) in sub-Saharan Africa, many countries in this region do not have systematic HBV surveillance or genetic information on HBV circulating locally. Here, we report on the genetic characterization of 772 HBV strains from Tanzania. Phylogenetic analysis of the S-gene sequences showed prevalence of HBV genotype A (HBV/A, n=671, 86.9 %), followed by genotypes D (HBV/D, n=95, 12.3 %) and E (HBV/E, n=6, 0.8 %). All HBV/A sequences were further classified into subtype A1, while the HBV/D sequences were assigned to a new cluster. Among the Tanzanian sequences, 84 % of HBV/A1 and 94 % of HBV/D were unique. The Tanzanian and global HBV/A1 sequences were compared and were completely intermixed in the phylogenetic tree, with the Tanzanian sequences frequently generating long terminal branches, indicating a long history of HBV/A1 infections in the country. The time to the most recent common ancestor was estimated to be 188 years ago [95 % highest posterior density (HPD): 132 to 265 years] for HBV/A1 and 127 years ago (95 % HPD: 79 to 192 years) for HBV/D. The Bayesian skyline plot showed that the number of transmissions ‘exploded’ exponentially between 1960–1970 for HBV/A1 and 1970–1990 for HBV/D, with the effective population of HBV/A1 having expanded twice as much as that of HBV/D. The data suggest that Tanzania is at least a part of the geographic origin of the HBV/A1 subtype. A recent increase in the transmission rate and significant HBV genetic diversity should be taken into consideration when devising public health interventions to control HBV infections in Tanzania.

OBJECTIVE Ulcerative colitis and Crohn's disease are the two clinical forms of inflammatory bowel disease (IBD). Diverse studies have shown the association of single nucleotide polymorphism (SNP) in molecules of the immune system and the occurrence of IBD. Here, several SNPs of the immune system with controversial results for their association with UC and CD were evaluated in a Mexican population. METHODS SNPs rs1800896, rs3024505 (IL-10); rs11209026 (IL23R); rs2066844, rs2066845 (NOD-2), and rs2241880 (ATG16L1) were assessed in 93 patients with IBD and 200 healthy controls by hybridization probes and quantitative PCR. RESULTS The AG genotype for rs1800896 was associated with an increased risk for both UC and CD (P = 0.005 and P = 0.026, respectively); whereas the AA genotype presents a negative association (P = 0.011 for UC, and 0.0038 for CD). For this SNP, G allele was associated with risk of UC (P = 0-043) but not for CD. For the rs3024505 in IL-10, T allele was associated with UC (P = 0.011). Moreover, this allele was associated with early onset of UC (P = 0.033) and with the use of steroid treatment (P = 0.019). No significant differences for NOD2 (rs2066844T and rs2066845C), IL23R (rs11209026), and ATG16L1 (rs22411880) were found between cases and controls and the homozygous TT genotype for rs2066844 and CC for rs2066845 were not observed. CONCLUSION Our results show both genotypic and phenotypic associations of IL-10 SNPs with IBD but not with the other immune-related SNPs studied in this Mexican cohort.

Identifying the Mycobacterium tuberculosis resistance mutation patterns is of the utmost importance to assure proper patient’s management and devising of control programs aimed to limit spread of disease. Zoonotic Mycobacterium bovis infection still represents a threat to human health, particularly in dairy production regions. Routinary, molecular characterization of M. bovis is performed primarily by spoligotyping and mycobacterial interspersed repetitive units (MIRU) while next generation sequencing (NGS) approaches are often performed by reference laboratories. However, spoligotyping and MIRU methodologies lack the resolution required for the fine characterization of tuberculosis isolates, particularly in outbreak settings. In conjunction with sophisticated bioinformatic algorithms, whole genome sequencing (WGS) analysis is becoming the method of choice for advanced genetic characterization of tuberculosis isolates. WGS provides valuable information on drug resistance and compensatory mutations that other technologies cannot assess. Here, we performed an analysis of the most frequently identified mutations associated with tuberculosis drug resistance and their genetic relationship among 2,074 Mycobacterium bovis WGS recovered primarily from non-human hosts. Full-length gene sequences harboring drug resistant associated mutations and their phylogenetic relationships were analyzed. The results showed that M. bovis isolates harbor mutations conferring resistance to both first- and second-line antibiotics. Mutations conferring resistance for isoniazid, fluoroquinolones, streptomycin, and aminoglycosides were identified among animal strains. Our findings highlight the importance of molecular surveillance to monitor the emergence of mutations associated with multi and extensive drug resistance in livestock and other non-human mammals., Author summary Here we describe the identification of high confidence mutations among Mycobacterium bovis lineages associated with resistance to first- and second-line antituberculosis drugs. Resistance to isoniazid, aminoglycosides and fluoroquinolones among non-human hosts is of importance because of the risk of emergence of multi- and extensively-drug resistance. Further research is warranted for the identification of the mechanisms responsible for acquisition of such mutations as well as the routes of transmissions involved in this process, including selective use of antibiotics or anthroponotic transmission. Our findings highlight the importance of molecular surveillance to monitor the emergence or introduction of strains carrying mutations related to MDR and XDR. This could potentially help to limit the transmission of pathogenic and difficult to treat TB.

Background & Aims: The host genetic environment contributes significantly to the outcomes of hepatitis C virus (HCV) infection and therapy response, but little is known about any effects of HCV infection on the host beyond any changes related to adaptive immune responses. HCV persistence is associated strongly with mitochondrial dysfunction, with liver mitochondrial DNA (mtDNA) genetic diversity linked to disease progression. Methods: We evaluated the genetic diversity of 2 mtDNA genomic regions (hypervariable segments 1 and 2) obtained from sera of 116 persons using next-generation sequencing. Results: Results were as follows: (1) the average diversity among cases with seronegative acute HCV infection was 4.2 times higher than among uninfected controls; (2) the diversity level among cases with chronic HCV infection was 96.1 times higher than among uninfected controls; and (3) the diversity was 23.1 times higher among chronic than acute cases. In 2 patients who were followed up during combined interferon and ribavirin therapy, mtDNA nucleotide diversity decreased dramatically after the completion of therapy in both patients: by 100% in patient A after 54 days and by 70.51% in patient B after 76 days. Conclusions: HCV infection strongly affects mtDNA genetic diversity. A rapid decrease in mtDNA genetic diversity observed after therapy-induced HCV clearance suggests that the effect is reversible, emphasizing dynamic genetic relationships between HCV and mitochondria. The level of mtDNA nucleotide diversity can be used to discriminate recent from past infections, which should facilitate the detection of recent transmission events and thus help identify modes of transmission. Keywords: Disease Biomarkers, mtDNA, Noninvasive

Hepatitis C virus (HCV) genotype 3a accounts for ∼80% of HCV infections in Pakistan, where ∼10 million people are HCV-infected. Here, we report analysis of the genetic heterogeneity of HCV NS3 and NS5b subgenomic regions from genotype 3a variants obtained from Pakistan. Phylogenetic analyses showed that Pakistani genotype 3a variants were as genetically diverse as global variants, with extensive intermixing. Bayesian estimates showed that the most recent ancestor for genotype 3a in Pakistan was last extant in ∼1896–1914 C.E. (range: 1851–1932). This genotype experienced a population expansion starting from ∼1905 to ∼1970 after which the effective population leveled. Death/birth models suggest that HCV 3a has reached saturating diversity with decreasing turnover rate and positive extinction. Taken together, these observations are consistent with a long and complex history of HCV 3a infection in Pakistan.

The establishment of Taenia solium adult parasite in the human intestine causes taeniosis. Importantly, the immunological mechanisms occurring at the interface between the parasite and its host are not fully known. The development of experimental animal models has facilitated the understanding of the host–parasite relationship. In this study we standardized a quantitative RT-PCR method for analyzing hamster messenger RNA for interferon-gamma (IFN-γ) and interleukins (IL): IL-4 IL-10, IL-12 and IL-13. This method was then used to evaluate the local cytokine response elicited against the adult parasite at the attachment site in the intestine of infected hamsters. The results showed an intense IFN-γ response, as well as an up-regulation of IL-4 as early as three days post-infection, permanence of IL-10 until the end of the experiment and down regulation of IL-12. These data are in agreement with a bias toward a Th-2 response as the infection progresses.

Hepatitis C virus (HCV) infection presents an important, but underappreciated public health problem in Africa. In Cote d'Ivoire, very little is known about the molecular dynamics of HCV infection. Plasma samples (n ¼608) from preg- nant women collected in 1995 from Cote d'Ivoire were analyzed in this study. Only 18 specimens (� 3%) were found to be HCV PCR-positive. Phylogenetic analysis of the HCV NS5b sequen- ces showed that the HCV variants belong to genotype 1 (HCV1) (n ¼12, 67%) and genotype 2 (HCV2) (n ¼6, 33%), with a maximum genetic diversity among HCV variants in each genotype being 20.7% and 24.0%, respectively. Although all HCV2 variants were genetically distant from each other, six HCV1 variants formed two tight sub-clusters belonging to HCV1a and HCV1b. Analysis of molecular variance (AMOVA) showed that the genetic structure of HCV iso- lates from West Africa with Cote d'Ivoire includ- ed were significantly different from Central African strains (P ¼0.0001). Examination of intra- host viral populations using next-generation sequencing of the HCV HVR1 showed a signifi- cant variation in intra-host genetic diversity among infected individuals, with some strains composed of sub-populations as distant from each other as viral populations from different hosts. Collectively, the results indicate a com- plex HCV evolution in Cote d'Ivoire, similar to the rest of West Africa, and suggest a unique HCV epidemic history in the country. J. Med. Virol. 2014. Published 2014. This article is a U. S. Government work and is in the public domain in the USA.

There has been a great progress in the development of antiviral agents licensed for treatment of Human immunodeficiency virus (HIV), Herpesviruses, Hepatitis viruses and respiratory viruses1. The emergence of HIV as a major human pathogen and the intensive use of antiretroviral compounds have also provided a better understanding of the genesis of antiviral resistance2. However, there is not a simple method for measuring directly the effect a drug has over a viral population and its individual intra-host variants. Such measure could help screen promising drugs that affect the viral population and also detect the individual variants that are naturally more resistant. In this paper, we use the effects of Interferon (IFN) on HCV as a proof of concept, finding that our drug-resistance estimates, calculated during the first 48 hour after IFN injection, are strongly associated with outcome of therapy at week 12. Hepatitis C virus (HCV) infects nearly 3% of the world's population and is a major cause of liver disease worldwide3. There is no vaccine against HCV and up to recently the standard-of-care therapy involved the combined use of pegylated interferon (peg-IFN) and ribavirin (RBV). This combination therapy is expensive, effective in only 50%-60% of patients, and can be associated with frequent and serious adverse side effects in more than 75% of patients4, 5 In order to improve cost-effectiveness and ameliorate patient hardship, it would be desirable to predict the response at early onset of therapy. IFNs are crucial components of the innate immune system. IFN-α acts by inducing production of interferon stimulating genes (ISGs) to establish a non-specific antiviral state within the cell with direct inhibition of viral replication. It is also known to exert immunomodulatory effects that enhance immune response and accelerate clearance of infected cells6. When exogenously administered as a single injection, IFN-α induces a decline of HCV RNA in two phases: a rapid phase lasting for 24-48 hours, followed by a slower phase of decline over the ensuing weeks. The initial rapid decline is defined by the rate of viral clearance and the effectiveness of IFN in blocking viral production. Successful treatment results in sustained undetectable HCV RNA after completion of therapy. Treatment failure results either from nonresponse (minimal declines in viral titer during therapy) or relapse (robust initial responses followed by rebounds of viral titers after therapy)6. Several independent predictors of a sustained virologic response (SVR) to IFN/RBV therapy have been identified. These include HCV genotypes 2 and 3, low pretreatment viral load, Asian or Caucasian ethnicity, younger age, absence of advanced fibrosis or cirrhosis, and absence of steatosis7. More recently, Genome Wide Association Studies have identified single-nucleotide polymorphisms near the IL28B gene (encoding IFN-λ3) as being particularly associated with spontaneous and treatment-induced clearance of HCV infection8, 9. However, IL28B variations may account for only ∼15% of inter-individual variability of SVR10. The interaction of these host factors determines the therapy effect on the virus, which is directly evidenced by a decline in viral titer, the reason why the rate and magnitude of decline in the first weeks of treatment can predict the outcome of therapy6. HCV exists in infected patients as a large viral population of intra-host variants, which may be differentially resistant to IFN treatment and, therefore, likely to display variable temporal patterns during the first phase of decline following IFN injection. Assessing the spectrum of HCV variants and measuring the IFN resistance of individual variants could be critical for understanding the variability in therapy outcomes. Next-generation sequencing (NGS) technologies in conjunction with computational analysis allow for quantitative assessment of viral intra-host variants, providing data on the intra-host dynamics of individual HCV variants and an opportunity for measuring their resistance to IFN. The HVR1 region of HCV is used here as a tag or marker of individual intra-host viral strains for estimating their relative frequencies over a short period of time. Since the model is based solely on changes in viral titer or the relative frequency of intra-host viral variants persisting during antiviral therapy, without consideration of other viral factors, host factors or type of drug administered, it may be applicable to measure and predict HCV treatment response with other drug regimens, including the newly available direct acting antiviral (DAA) agents. In addition, the presented analytical framework should be applicable to drug resistance of other viral infections.

Clinical infection by hepatitis A virus (HAV) is generally self-limited but in some cases can progress to liver failure. Here, an HAV outbreak investigation among children with acute liver failure in a highly endemic country is presented. In addition, a sensitive method for HAV whole genome amplification and sequencing suitable for analysis of clinical samples is described. In this setting, two fatal cases attributed to acute liver failure and two asymptomatic cases living in the same household were identified. In a second household, one HAV case was observed with jaundice which resolved spontaneously. Partial molecular characterization showed that both households were infected by HAV subtype IA; however, the infecting strains in the two households were different. The HAV outbreak strains recovered from all cases grouped together within cluster IA1, which contains closely related HAV strains from the United States commonly associated with international travelers. Full-genome HAV sequences obtained from the household with the acute liver failure cases were related (genetic distances ranging from 0.01% to 0.04%), indicating a common-source infection. Interestingly, the strain recovered from the asymptomatic household contact was nearly identical to the strain causing acute liver failure. The whole genome sequence from the case in the second household was distinctly different from the strains associated with acute liver failure. Thus, infection with almost identical HAV strains resulted in drastically different clinical outcomes. J. Med. Virol.

Tuberculosis is an important public health problem in Mexico. However, limited information about the genetic diversity of Mycobacterium tuberculosis strains circulating in the country is available. In this work, 109 multidrug-resistant (MDR) M. tuberculosis isolates collected in 23 different states of Mexico in 2003 were retrospectively characterized by spoligotyping and MIRU-VNTRs. All isolates, except for a single cluster containing two strains (subcluster E1), were split when information from the 12-loci MIRUs and spoligo-pattern was simultaneously analyzed. The discriminative power of 12-loci MIRU-VNTR and spoligotyping, by the Hunter-Gaston index, were 0.9998 and 0.9011, respectively. These findings suggest that almost all cases were epidemiologically unrelated. Instead, the genetic variations observed among these strains are suggestive of emergence of acquired drug-resistance during the course of treatment. The results suggest a high degree of genetic variability and a high frequency of SIT53 (T1 family) spoligotype among the MDR M. tuberculosis isolates included in the study.

Viral hepatitis refers to inflammation of the liver caused by several viral agents, including hepatitis A (HAV), B (HBV), C (HCV), D (HDV), and E (HEV) viruses. Generally, HAV and HEV are associated with acute, self-limited infection; however, severe and protracted disease can develop. These nonenveloped viruses have independently evolved interesting mechanisms aimed at evading the immune response and guaranteeing survival in the host. These viruses are phylogenetically unrelated but share several similarities. The genomes from both viruses are single-stranded, positive-polarity RNA. The viruses primarily infect the liver, cause acute infection, and are shed in feces. Moreover, the clinical manifestations from HAV and HEV infection are undistinguishable and require specific laboratory tests for each virus. Despite the similarities exhibited by these viruses, differences in the epidemiology of the respective diseases result in distinctive distribution patterns worldwide.

Oral immunization with functional recombinant Taenia solium calreticulin (rTsCRT) induces 37% reduction in tapeworm burden in the experimental model of intestinal taeniosis in hamsters. Furthermore, tapeworms recovered from vaccinated animals exhibit diminished length, being frequently found in more posterior parts of the small intestine. The aim of this study was to analyze the immunological mechanisms involved in protection in response to rTsCRT oral immunization. Hamsters were orally immunized with rTsCRT using cholera toxin (CT) as adjuvant, weekly for 4 weeks. Fifteen days after the last boost animals were challenged with four T. solium cysticerci. Reduction in the adult worm recovery and increased transcription of mRNA for IL-4 and IFN-γ in the mucosa of rTsCRT+CT immunized animals were observed. Immunization also induced goblet cell hyperplasia in the mucosa surrounding the implantation site of the parasite. Specific IgG and IgA antibodies in serum and fecal supernatants were detected after the second immunization, being more pronounced after challenge. Our data suggest that oral vaccination with rTsCRT+CT regulates a local expression of IL-4 and IFN-γ, stimulating secretion of IgA that, together with the increase of goblet cells and mucin production, could result in an unfavorable environment for T. solium promoting an impaired tapeworm development.

The bovine respiratory syncytial virus (BRSV) is an enveloped, negative sense, single-stranded RNA virus belonging to the pneumovirus genus within the family Paramyxoviridae. BRSV has been recognized as a major cause of respiratory disease in young calves since the early 1970s. The analysis of BRSV infection was originally hampered by its characteristic lability and poor growth in vitro. However, the advent of numerous immunological and molecular methods has facilitated the study of BRSV enormously. The knowledge gained from these studies has also provided the opportunity to develop safe, stable, attenuated virus vaccine candidates. Nonetheless, many aspects of the epidemiology, molecular epidemiology and evolution of the virus are still not fully understood. The natural course of infection is rather complex and further complicates diagnosis, treatment and the implementation of preventive measures aimed to control the disease. Therefore, understanding the mechanisms by which BRSV is able to establish infection is needed to prevent viral and disease spread. This review discusses important information regarding the epidemiology and molecular epidemiology of BRSV worldwide, and it highlights the importance of viral evolution in virus transmission.

Dengue virus (DENV) is the most important arthropod-borne viral infection in humans. Here, the genetic relatedness among autochthonous DENV Mexican isolates was assessed. Phylogenetic and median-joining network analyses showed that viral strains recovered from different geographic locations are genetically related and relatively homogeneous, exhibiting limited nucleotide diversity.

Background Different studies regarding VZV genotype distribution worldwide have demonstrated that genetic diversity and epidemiology of infection significantly vary from region to region. In Mexico, VZV genotype distribution is largely unknown mostly due to the lack of a surveillance system that monitors accurately the presence of viral strains circulating in the country. Objective To identify the main VZV genotypes circulating in the metropolitan area of Mexico City. Study design In this study, 127 different VZV isolates, obtained from residents of the Mexico City Metropolitan area from 2005 to 2008, were identified and genotyped. Viral detection and preliminary genotyping was performed by amplification of the VZV ORF-38 and -54 and RFLP analysis using PstI and BglI endonuclease restriction patterns, respectively. Genotype was confirmed by nucleotide sequence variation along the ORF-22. Results RFLP analysis classified 121 viral strains as European and 6 as mosaic genotype. Genotyping scheme based on the ORF-22 sequence variation identified 120 viral strains belonging to the E genotype, 6 M1 and 1 M4 genotype strains. Conclusions VZV European genotype appears to predominate in Mexico City. This is the first study addressing VZV genotype distribution in Mexico. The information reported in this paper may be useful for future epidemiological studies conducted in the country and also contributes to understand better the molecular epidemiology of VZV in the Americas.

Hepatitis C is a liver disease caused by infection with hepatitis C virus (HCV). The number of people infected with HCV is estimated at ∼130 million word-wide. Approximately, 70%–80% of HCV-infected patients fail to clear the virus and develop chronic hepatitis C (CHC), which is a well-known risk factor for development of liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). At the present time, there are no preventive vaccines against HCV. In spite of the different strategies used for vaccine development against HCV, the development of a successful vaccine remains elusive. The HCV genome exhibits high degree of genetic diversity and divergence, which, in addition to HCV's rapid rate of mutation and capacity to escape from the host immune response, has hindered efforts towards the formulation of a broadly protective vaccine. For the study of humoral immunity responses to HCV infection, synthetic peptides derived from the HVR1 of the envelope protein 2 (E2) of HCV genome have been used as immunogens in small animals and non-human primates. HVR 1 peptides contain a neutralizing epitope and are typically very immunogenic in mice and non-human primates although the pattern of reactivity varies significantly depending on the HCV strain. The challenge of developing an efficacious vaccine(s) is finding immunogens capable of eliciting a humoral response that leads the immune system of the host to produce antibodies (Ab's) which broadly and strongly cross-immunoreact against all HCV strains circulating in human populations. The immune-reactivity properties of HCV proteins can be modeled in quantitative-structure-activity-relationship (QSAR) models. Polynomial neural networks, as non-parametric algorithms offer an ideal approach to QSAR studies. In this study, we built polynomial neural networks (PNN) to model the immune-reactivity properties of synthetic HCV HVR1 peptides and examined PNN performance to predict cross-immunoreactive patterns using amino-acid (aa)-based physicochemical parameters. We implemented a non-linear regression PNN algorithm to correlate aa-based physicochemical properties of HVR1 peptides to their corresponding cross-immunoreactivity patterns. PNN models were synthesized from a dataset of hyper-immune sera tested against 326 HVR1 peptide variants (representative of 6 genotypes of HCV). Synthesis of PNN models was constrained to 20 iterations and degree= x*y. The residual sum of squares (RSS) criterion was used for selection of the best PNN model. Evaluation of PNN models was conducted using the reliability rate (RR) criterion on two external validation datasets (n=4 and n=10). The statistics of training evaluation of the best PNN models was: R^2=0.771, q^2=0.771, RMSE=1.7776, var=0.229 and MAE=1.305, where R^2 is the square of correlation coefficient; q^2, the squared correlation coefficient of predictions; var, the variation accuracy criterion; RMSE, the Root Mean Squared Error as and MAE, the Mean Absolute Error. The statistics of performance evaluations on validation set (n=4) was: R^2=0.937, q^2= 0.748, RMSE=1.8316, var=0.252, MAE=1.294, and for validation set (n=10): R^2=0.632, q^2=0.565, RMSE=2.7244, var=0.435, MAE=2.059. Furthermore, linear projection (LP) mappings indicate differential spatial distribution between cross-reactive and non-cross-reactive HVR1 peptides with high sensitivity and specificity (classification accuracy = 0.9967, sensitivity = 1.0; specificity = 0.9383; F score = 0.9983; Brier score = 0.0036). In addition, several HVR1 features relevant for accurate performance of models were identified. Our findings indicate that the immune-reactivity property of the HCV HVR1 is associated to the physicochemical profile of peptide sequences. Such association can be modeled by mathematical and computational means. Predictive models generated in this study may provide useful aid for selection of potentially efficacious HCV HVR1 vaccine candidates.

Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections are associated with unsafe injection practices, drug diversion, and other exposures to blood and are difficult to detect and investigate. Here, we developed and validated a simple approach for molecular detection of HCV transmissions in outbreak settings. We obtained sequences from the HCV hypervariable region 1 (HVR1), using end-point limiting-dilution (EPLD) technique, from 127 cases involved in 32 epidemiologically defined HCV outbreaks and 193 individuals with unrelated HCV strains. We compared several types of genetic distances and calculated a threshold, using minimal Hamming distances, that identifies transmission clusters in all tested outbreaks with 100% accuracy. The approach was also validated on sequences obtained using next-generation sequencing from HCV strains recovered from 239 individuals, and findings showed the same accuracy as that for EPLD. On average, the nucleotide diversity of the intrahost population was 6.2 times greater in the source case than in any incident case, allowing the correct detection of transmission direction in 8 outbreaks for which source cases were known. A simple and accurate distance-based approach developed here for detecting HCV transmissions streamlines molecular investigation of outbreaks, thus improving the public health capacity for rapid and effective control of hepatitis C.

Taenia solium causes two diseases in humans, cysticercosis and taeniosis. Tapeworm carriers are the main risk factor for neurocysticercosis. Limited information is available about the immune response elicited by the adult parasite, particularly the induction of Th2 responses, frequently associated to helminth infections. Calreticulin is a ubiquitous, multifunctional protein involved in cellular calcium homeostasis, which has been suggested to play a role in the regulation of immune responses. In this work, we assessed the effect of recombinant T. solium calreticulin (rTsCRT) on the cytokine, humoral and cellular responses upon experimental infection in Syrian Golden hamsters (Mesocricetus auratus). Animals were infected with T. solium cysticerci and euthanized at different times after infection. Specific serum antibodies, proliferative responses in mesenteric lymph nodes and spleen cells, as well as cytokines messenger RNA (mRNA) were analyzed. The results showed that one third of the infected animals elicited anti-rTsCRT IgG antibodies. Interestingly, mesenteric lymph node (MLN) cells from either infected or non-infected animals did not proliferate upon in vitro stimulation with rTsCRT. Additionally, stimulation with a tapeworm crude extract resulted in increased expression of IL-4 and IL-5 mRNA. Upon stimulation, rTsCRT increased the expression levels of IL-10 in spleen and MLN cells from uninfected and infected hamsters. The results showed that rTsCRT favors a Th2-biased immune response characterized by the induction of IL-10 in mucosal and systemic lymphoid organs. Here we provide the first data on the cytokine, antibody and cellular responses to rTsCRT upon in vitro stimulation during taeniasis.

International audience; Here, we describe the molecular characterization of six human Mycobacterium bovis clinical isolates, including three multidrug resistant (MDR) strains, collected in Mexico through the National Survey on Tuberculosis Drug Resistance (ENTB-2008), a nationally representative survey conducted during 2008-2009 in nine states with a stratified cluster sampling design. The genetic background of bovine M. bovis strains identified in three different states of Mexico was studied in parallel to assess molecular relatedness of bovine and human strains. Additionally, resistance to first and second line anti-tuberculosis (TB) drugs and molecular identification of mutations conferring drug resistance was also performed. All strains were characterized by spoligotyping and 24-loci MIRU-VNTRs, and analyzed using the SITVIT2 (n = 112,000 strains) and SITVITBovis (n = 25,000 strains) proprietary databases of Institut Pasteur de la Guadeloupe. Furthermore, data from this study (n = 55 isolates), were also compared with genotypes recorded for M. bovis from USA (n = 203), Argentina (n = 726), as well as other isolates from Mexico (independent from the present study; n = 147), to determine any evidence for genetic relatedness between circulating M. bovis strains. The results showed that all human M. bovis cases were not genetically related between them or to any bovine strain. Interestingly, a high degree of genetic variability was observed among bovine strains. Several autochthonous and presumably imported strains were identified. The emergence of drug-resistant M. bovis is an important public health problem that jeopardizes the success of TB control programs in the region.

Made available in DSpace on 2022-04-28T19:00:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-01-01 Emergence of Extensively Drug-Resistant (XDR) Tuberculosis (TB) is an important public health problem worldwide. In Mexico, the extent of circulation of XDR-TB strains is unknown. Here, the drug-resistance patterns of TB isolates collected in Mexico between 2006 and 2008 were analyzed. Among 137 TB isolates, (58%) were classified as MDR exclusively, (33%) were Pre-XDR and (9%) were assigned as XDR. The results confirmed the circulation of Pre-XDR and XDR-TB in Mexico. Surveillance and drug-susceptibility testing should be improved in Mexico to monitor the circulation of XDR strains. Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaría de Salud Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Department of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University Unidad de Investigación Multidisciplinaria, Universidad Nacional Autónoma de México, Estado de México Department of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University

Globally, hepatitis C Virus (HCV) infection is responsible for a large proportion of persons with liver disease, including cancer. The infection is highly prevalent in sub-Saharan Africa. West Africa was identified as a geographic origin of two HCV genotypes. However, little is known about the genetic composition of HCV populations in many countries of the region. Using conventional and next-generation sequencing (NGS), we identified and genetically characterized 65 HCV strains circulating among HCV-positive blood donors in Kumasi, Ghana. Phylogenetic analysis using consensus sequences derived from 3 genomic regions of the HCV genome, 5'-untranslated region, hypervariable region 1 (HVR1) and NS5B gene, consistently classified the HCV variants (n = 65) into genotypes 1 (HCV-1, 15%) and genotype 2 (HCV-2, 85%). The Ghanaian and West African HCV-2 NS5B sequences were found completely intermixed in the phylogenetic tree, indicating a substantial genetic heterogeneity of HCV-2 in Ghana. Analysis of HVR1 sequences from intra-host HCV variants obtained by NGS showed that three donors were infected with >1 HCV strain, including infections with 2 genotypes. Two other donors share an HCV strain, indicating HCV transmission between them. The HCV-2 strain sampled from one donor was replaced with another HCV-2 strain after only 2 months of observation, indicating rapid strain switching. Bayesian analysis estimated that the HCV-2 strains in Ghana were expanding since the 16th century. The blood donors in Kumasi, Ghana, are infected with a very heterogeneous HCV population of HCV-1 and HCV-2, with HCV-2 being prevalent. The detection of three cases of co- or super-infections and transmission linkage between 2 cases suggests frequent opportunities for HCV exposure among the blood donors and is consistent with the reported high HCV prevalence. The conditions for effective HCV-2 transmission existed for ~ 3–4 centuries, indicating a long epidemic history of HCV-2 in Ghana.

Dengue virus (DV) infections are serious causes of morbidity and mortality worldwide, and adaptive (secondary) immune response appears to influence the severity of this arboviral disease (Morens 1994; Halstead & O'Rourke 1977; Rigau-Perez et al. 1998). There are an estimated 50–100 million cases of dengue fever and 250,000-500,000 cases of dengue haemorrhagic fever (DHF) annually in the world (WHO 1997). The dengue shock syndrome (DSS), the most severe and potentially fatal form of the disease, especially in developing countries, is less frequent. In the model proposed here, we have chosen to examine DV2, because it is the prevalent serotype (Gomez-Dantes et al. 2004). The high seroprevalence together with the co-circulation of multiple serotypes indicates that Mexico could be in risk of an important DHF outbreak (Gomez-Dantes et al. 2004). The exact pathogenic mechanisms following DV infection are not well understood, especially in the severe forms of the infection (DHF and DSS). The immune response to DV seems at least partially involved in the process (Halstead 1988; Avirutnan et al. 1998; Diamond et al. 2000). Several theories have been advanced including facilitation of DV infection by non-neutralizing antibodies (Halstead & O'Rourke 1977; Halstead et al. 1977; Morens 1994), the potential differential virulence of each infecting serotype (Leitmeyer et al. 1999; Kawaguchi et al. 2003), CD4-CD8 T-cell cross-reactivity and host factors such as a particular, but yet undefined susceptibility (Klenerman & Zinkernagel 1998; Mongkolsapaya et al. 2003). While there is an excellent research on dengue about the molecular structure and epidemiology of this virus, the basic mechanisms of the immunopathology still remain obscure (Haywood 1994; Kuhn et al. 2002). For instance, until very recently (Johnston et al. 2000; Wu et al. 2000), it was unknown whether DV was able to replicate in cutaneous cells. Likewise, there are two other features largely unexplored regarding DV infection: (i) the very early stages of the infection, because, by necessity, patients are examined when disease is almost over, when the patients are under recovery or when they have entered into DSS and (ii) which type of responses, if any, occur cutaneously, in situ, following DV inoculation when mosquitoes feed. We wanted to develop an in situ approach that would enable us to study the early immune pathology of the cellular events regarding the infectious process and the first reactions of the peripheral immune system, the dendritic cells (DCs). DCs constitute a system of highly dynamic sentinel cells, whose most studied element in peripheral non-lymphoid tissues is the epidermal Langerhans cells (LCs). It is now known that LCs perform multiple tasks including antigen capturing and processing, antigen ferrying to regional lymphoid tissues, and ultimately, cognate antigen presentation to naive lymphocytes, once in secondary lymphoid organs (Flores-Romo 2001). Under the influence of a variety of stimuli such as cytokines, antigens or microbial products, LCs become activated, start to migrate into the dermis and concomitantly to up-regulate antigen-presenting molecules and to express co-stimulatory and maturation markers (Cumberbatch & Kimber 1992; Cumberbatch et al. 1997). Nevertheless, despite that LCs as sensors of the external antigenic world are the most exposed cells of the immune system during mosquito feeding, and the initial virus inoculation through skin, the interactions of these cells with DV and the outcome of such potential interplay regarding both the virus and the LC have received little attention in situ (Wu et al. 2000). We attempted to address some of these issues by establishing a model with fresh, healthy, non-cadaveric human skin explants exposed to DV, to analyse whether local infection and viral replication are feasible experimentally, to assess the most early phases of the initiation of the immune responses in situ and the immediate local repercussions of viral inoculation upon local antigen-presenting cells (APCs), particularly on the DCs, the sentinel posts of the immune system in the skin.

Made available in DSpace on 2015-03-18T15:55:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-07-14Bitstream added on 2015-03-18T16:28:35Z : No. of bitstreams: 1 WOS000345682800004.pdf: 1403582 bytes, checksum: 52ae6747619aa45c91860ded91be58cb (MD5) Centers for Disease Control and Prevention Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance. Ctr Dis Control & Prevent, Div Viral Hepatitis, Atlanta, GA 30333 USA UNESP Sao Paulo State Univ, Dept Biol, Lab Genom Studies, Sao Paulo, Brazil Harvard Univ, Beth Israel Deaconess Med Ctr, Sch Med, Liver Ctr,Div Gastroenterol, Cambridge, MA 02138 USA UNESP Sao Paulo State Univ, Dept Biol, Lab Genom Studies, Sao Paulo, Brazil

Hepatitis C virus (HCV) infection presents an important, but underappreciated public health problem in Africa. In Côte d’Ivoire, very little is known about the molecular dynamics of HCV infection. Plasma samples (n = 608) from pregnant women collected in 1995 from Côte d’Ivoire were analyzed in this study. Only 18 specimens (~3%) were found to be HCV PCR-positive. Phylogenetic analysis of the HCV NS5b sequences showed that the HCV variants belong to genotype 1 (HCV1) (n = 12, 67%) and genotype 2 (HCV2) (n = 6, 33%), with a maximum genetic diversity among HCV variants in each genotype being 20.7% and 24.0%, respectively. Although all HCV2 variants were genetically distant from each other, six HCV1 variants formed two tight sub-clusters belonging to HCV1a and HCV1b. Analysis of molecular variance (AMOVA) showed that the genetic structure of HCV isolates from West Africa with Côte d’Ivoire included were significantly different from Central African strains (P = 0.0001). Examination of intra-host viral populations using next-generation sequencing of the HCV HVR1 showed a significant variation in intra-host genetic diversity among infected individuals, with some strains composed of sub-populations as distant from each other as viral populations from different hosts. Collectively, the results indicate a complex HCV evolution in Côte d’Ivoire, similar to the rest of West Africa, and suggest a unique HCV epidemic history in the country.

Uncontrolled and intricate production of inflammatory factors is the characteristic feature of dengue infection. The triggering receptor expressed in myeloid cells-1 (TREM-1), expressed on the surface of monocytes and neutrophils, is capable of enhancing and regulating the inflammatory response via the production of different mediators in bacterial and viral infections. Here, both the expression of TREM-1 on human monocytes and neutrophils from peripheral blood of dengue infected individuals, as well as the levels of the soluble form of TREM-1 (sTREM-1) in the sera of these patients were compared against healthy controls. A significant reduction of TREM-1 expression was observed in neutrophils during the first days of infection, followed by a gradual recovery throughout the course of infection. Also, sera from DENV-infected patients exhibited significantly higher sTREM-1 levels than healthy individuals. The difference was more pronounced during the first 5 days after the onset of symptoms. These findings highlight the dynamic process of TREM-1 expression during DENV infection. We hypothesized that increment of free sTREM-1 could be a compensatory mechanism aiming to counteract the inflammatory process elicited during DENV infection.

Clinical infection by hepatitis A virus (HAV) is generally self-limited but in some cases can progress to liver failure. Here, an HAV outbreak investigation among children with acute liver failure in a highly endemic country is presented. In addition, a sensitive method for HAV whole genome amplification and sequencing suitable for analysis of clinical samples is described. In this setting, two fatal cases attributed to acute liver failure and two asymptomatic cases living in the same household were identified. In a second household, one HAV case was observed with jaundice which resolved spontaneously. Partial molecular characterization showed that both households were infected by HAV subtype IA; however, the infecting strains in the two households were different. The HAV outbreak strains recovered from all cases grouped together within cluster IA1, which contains closely related HAV strains from the United States commonly associated with international travelers. Full-genome HAV sequences obtained from the household with the acute liver failure cases were related (genetic distances ranging from 0.01% to 0.04%), indicating a common-source infection. Interestingly, the strain recovered from the asymptomatic household contact was nearly identical to the strain causing acute liver failure. The whole genome sequence from the case in the second household was distinctly different from the strains associated with acute liver failure. Thus, infection with almost identical HAV strains resulted in drastically different clinical outcomes.

Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions.

In virology, molecular epidemiology is defined as the applica-tion of molecular methods to study the causation and dynamicsof viral diseases in a population. In the study of viral diseases,this is determined by the transmission of the corresponding eti-ological agent on its host, and how this phenomenon affects thespread of the disease within the population. Molecular epidemi-ology uses information about genetic variation to investigate theevolution, transmissionandpathogenesisofviralagents.Molecularepidemiological toolshaveprovidedimportantinsightsinthestudyof viral diseases, improving significantly our understanding aboutthe history of infection, virus evolution, spread and disease trans-mission that have helped to implement public health policies.

Hepatitis B virus (HBV) places a substantial health burden on Africa. Here, we investigated genetic diversity of HBV variants circulating in 4 countries of sub-Saharan Africa using archived samples. In total, 1492 plasma samples were tested from HIV-infected individuals and pregnant women, among which 143 (9.6%) were PCR-positive for HBV DNA (Côte d'Ivoire, 70/608 [11.5%]; Ghana, 13/444 [2.9%]; Cameroon, 33/303 [10.9%]; and Uganda, 27/137 [19.7%]).Phylogenetic analysis of the S-gene sequences identified HBV genotypes E (HBV/E, n=96) and A (HBV/A, n=47) distributed as follows: 87% of HBV/E and 13% of HBV/A in Côte d'Ivoire; 100% of HBV/E in Ghana; 67% of HBV/E and 33% of HBV/A in Cameroon; and 100% of HBV/A in Uganda. The average and maximal nucleotide distances among HBV/E sequences were 1.9% and 6.4%, respectively, suggesting a greater genetic diversity for this genotype than previously reported (p0.001). HBV/A strains were classified into subgenotypes HBV/A1, HBV/A2 and HBV/A3. In Uganda, 93% of HBV/A strains belonged to HBV/A1 whereas HBV/A3 was the only subgenotype of HBV/A found in Cameroon. In Côte d'Ivoire, HBV/A strains were classified as HBV/A1 (11.1%), HBV/A2 (33.3%) and HBV/A3 (55.6%). Phylogeographic analysis of the sequences available from Africa supported earlier suggestions on the origin of HBV/A1, HBV/A2 and HBV/A3 in East, South and West/Central Africa, respectively. Using predicted amino acid sequences, hepatitis B surface antigen (HBsAg) was classified into serotype ayw4 in 93% of HBV/E strains and adw2 in 68% of HBV/A strains. Also, 7.7% of the sequences carried substitutions in HBsAg associated with immune escape.The observations of pan-African and global dissemination of HBV/A1 and HBV/A2, and the circulation of HBV/E and HBV/A3 almost exclusively in West and Central Africa suggest a more recent increase in prevalence in Africa of HBV/E and HBV/A3 compared to HBV/A1 and HBV/A2. The broad genetic heterogeneity of HBsAg detected here may impact the efficacy of prevention and control efforts in sub-Saharan Africa.