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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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Here, we analyze the viral divergence among hepatitis C virus (HCV) chronic cases infected with genotype 1. The intrahost viral evolution was assessed by deep sequencing using the 454 Genome Sequencer platform. The results showed a rapid nucleotide sequence divergence. This notorious short-term viral evolution is of the utmost importance for the study of HCV transmission, because direct links between related samples were virtually lost. Thus, rapid divergence of HCV significantly affects genetic relatedness studies and outbreak investigations.

The genetic characterization of hepatitis A virus (HAV) strains is commonly accomplished by sequencing subgenomic regions, such as the VP1/P2B junction. HAV genome is not extensively variable, thus presenting opportunity for sharing sequences of subgenomic regions among genetically unrelated isolates. The degree of misrepresentation of phylogenetic relationships by subgenomic regions is especially important for tracking transmissions. Here, we analyzed whole-genome (WG) sequences of 101 HAV strains identified from 4 major multi-state, food-borne outbreaks of hepatitis A in the Unites States and from 14 non-outbreak-related HAV strains that shared identical VP1/P2B sequences with the outbreak strains. Although HAV strains with an identical VP1/P2B sequence were specific to each outbreak, WG were different, with genetic diversity reaching 0.31% (mean 0.09%). Evaluation of different subgenomic regions did not identify any other section of the HAV genome that could accurately represent phylogenetic relationships observed using WG sequences. The identification of 2–3 dominant HAV strains in 3 out of 4 outbreaks indicates contamination of the implicated food items with a heterogeneous HAV population. However, analysis of intra-host HAV variants from eight patients involved in one outbreak showed that only a single sequence variant established infection in each patient. Four non-outbreak strains were found closely related to strains from 2 outbreaks, whereas ten were genetically different from the outbreak strains. Thus, accurate tracking of HAV strains can be accomplished using HAV WG sequences, while short subgenomic regions are useful for identification of transmissions only among cases with known epidemiological association.

Here, we describe a transmission event of hepatitis C virus (HCV) among injection drug users. Next-generation sequencing (NGS) was used to assess the intrahost viral genetic variation. Deep amplicon sequencing of HCV hypervariable region 1 allowed for a detailed analysis of the structure of the viral population. Establishment of the genetic relatedness between cases was accomplished by phylogenetic analysis. NGS is a powerful tool with applications in molecular epidemiology studies and outbreak investigations.

We investigated the molecular epidemiology and population dynamics of HCV infection among indigenes of two semi-isolated communities in North-Central Nigeria. Despite remoteness and isolation, ~15 % of the population had serological or molecular markers of hepatitis C virus (HCV) infection. Phylogenetic analysis of the NS5b sequences obtained from 60 HCV-infected residents showed that HCV variants belonged to genotype 1 (n = 51; 85 %) and genotype 2 (n = 9; 15 %). All sequences were unique and intermixed in the phylogenetic tree with HCV sequences from people infected from other West African countries. The high-throughput 454 pyrosequencing of the HCV hypervariable region 1 and an empirical threshold error correction algorithm were used to evaluate intra-host heterogeneity of HCV strains of genotype 1 (n = 43) and genotype 2 (n = 6) from residents of the communities. Analysis revealed a rare detectable intermixing of HCV intra-host variants among residents. Identification of genetically close HCV variants among all known groups of relatives suggests a common intra-familial HCV transmission in the communities. Applying Bayesian coalescent analysis to the NS5b sequences, the most recent common ancestors for genotype 1 and 2 variants were estimated to have existed 675 and 286 years ago, respectively. Bayesian skyline plots suggest that HCV lineages of both genotypes identified in the Nigerian communities experienced epidemic growth for 200–300 years until the mid-20th century. The data suggest a massive introduction of numerous HCV variants to the communities during the 20th century in the background of a dynamic evolutionary history of the hepatitis C epidemic in Nigeria over the past three centuries.

Little is known about the characteristics of acute viral hepatitis cases in the United States (US)–Mexico border region. We analyzed characteristics of acute viral hepatitis cases collected from the Border Infectious Disease Surveillance Project from January 2000–December 2009. Over the study period, 1,437 acute hepatitis A, 311 acute hepatitis B, and 362 acute hepatitis C cases were reported from 5 Mexico and 2 US sites. Mexican hepatitis A cases most frequently reported close personal contact with a known case, whereas, US cases most often reported cross-border travel. Injection drug use was common among Mexican and US acute hepatitis B and C cases. Cross-border travel during the incubation period was common among acute viral hepatitis cases in both countries. Assiduous adherence to vaccination and prevention guidelines in the US is needed and strategic implementation of hepatitis vaccination and prevention programs south of the border should be considered.

The use of telaprevir and boceprevir, both protease inhibitors (PI), as part of the specifically targeted antiviral therapy for hepatitis C (STAT-C) has significantly improved sustained virologic response (SVR) rates. However, different clinical studies have also identified several mutations associated with viral resistance to both PIs. In the absence of selective pressure, drug-resistant hepatitis C virus (HCV) mutants are generally present at low frequency, making mutation detection challenging. Here, we describe a mismatch amplification mutation assay (MAMA) PCR method for the specific detection of naturally occurring drug-resistant HCV mutants. MAMA PCR successfully identified the corresponding HCV variants, while conventional methods such as direct sequencing, endpoint limiting dilution (EPLD), and bacterial cloning were not sensitive enough to detect circulating drug-resistant mutants in clinical specimens. Ultradeep pyrosequencing was used to confirm the presence of the corresponding HCV mutants. In treatment-naïve patients, the frequency of all resistant variants was below 1%. Deep amplicon sequencing allowed a detailed analysis of the structure of the viral population among these patients, showing that the evolution of the NS3 is limited to a rather small sequence space. Monitoring of HCV drug resistance before and during treatment is likely to provide important information for management of patients undergoing anti-HCV therapy.

Dengue virus replication involves synthesis of a replicative intermediate RNA (RI-RNA), whose presence reveals an actual infection. We report on a simple and rapid reverse transcription-PCR for the detection of viral RI-RNA in infected cells. The product is demonstrated at 20 min postinfection. This method is useful for the study of virus-cell tropism.

Background Varicella (chickenpox) exhibits a characteristic epidemiological pattern which is associated with climate. In general, primary infections in tropical regions are comparatively less frequent among children than in temperate regions. This peculiarity regarding varicella-zoster virus (VZV) infection among certain age groups in tropical regions results in increased susceptibility during adulthood in these regions. Moreover, this disease shows a cyclic behavior in which the number of cases increases significantly during winter and spring. This observation further supports the participation of environmental factors in global epidemiology of chickenpox. However, the underlying mechanisms responsible for this distinctive disease behavior are not understood completely. In a recent publication, Philip S. Rice has put forward an interesting hypothesis suggesting that ultra-violet (UV) radiation is the major environmental factor driving the molecular evolution of VZV. Discussion While we welcomed the attempt to explain the mechanisms controlling VZV transmission and distribution, we argue that Rice's hypothesis takes lightly the circulation of the so called "temperate VZV genotypes" in tropical regions and, to certain degree, overlooks the predominance of such lineages in certain non-temperate areas. Here, we further discuss and present new information about the overwhelming dominance of temperate VZV genotypes in Mexico regardless of geographical location and climate. Summary UV radiation does not satisfactorily explain the distribution of VZV genotypes in different tropical and temperate regions of Mexico. Additionally, the cyclic behavior of varicella does not shown significant differences between regions with different climates in the country. More studies should be conducted to identify the factors directly involved in viral spreading. A better understanding of the modes of transmissions exploited by VZV and their effect on viral fitness is likely to facilitate the implementation of preventive measures for disease control.

The reason(s) that hepatitis A virus (HAV) infection may progress infrequently to acute liver failure are poorly understood. We examined host and viral factors in 29 consecutive adult patients with HAV-associated acute liver failure enrolled at 10 sites participating in the US ALF Study Group. Eighteen of twenty-four acute liver failure sera were PCR positive while six had no detectable virus. HAV genotype was determined using phylogenetic analysis and the full-length genome sequences of the HAV from a cute liver failure sera were compared to those from self-limited acute HAV cases selected from the CDC database. We found that rates of nucleotide substitution did not vary significantly between the liver failure and non-liver failure cases and there was no significant variation in amino acid sequences between the two groups. Four of 18 HAV isolates were sub-genotype IB, acquired from the same study site over a 3.5-year period. Sub-genotype IB was found more frequently among acute liver failure cases compared to the non-liver failure cases (chi-square test, P

BACKGROUND: In Nigeria, hepatitis B virus (HBV) infection has reached hyperendemic levels and its nature and origin have been described as a puzzle. In this study, we investigated the molecular epidemiology and epidemic history of HBV infection in two semi-isolated rural communities in North/Central Nigeria. It was expected that only a few, if any, HBV strains could have been introduced and effectively transmitted among these residents, reflecting limited contacts of these communities with the general population in the country. METHODS AND FINDINGS: Despite remoteness and isolation, approximately 11% of the entire population in these communities was HBV-DNA seropositive. Analyses of the S-gene sequences obtained from 55 HBV-seropositive individuals showed the circulation of 37 distinct HBV variants. These HBV isolates belong predominantly to genotype E (HBV/E) (n=53, 96.4%), with only 2 classified as sub-genotype A3 (HBV/A3). Phylogenetic analysis showed extensive intermixing between HBV/E variants identified in these communities and different countries in Africa. Quasispecies analysis of 22 HBV/E strains using end-point limiting-dilution real-time PCR, sequencing and median joining networks showed extensive intra-host heterogeneity and inter-host variant sharing. To investigate events that resulted in such remarkable HBV/E diversity, HBV full-size genome sequences were obtained from 47 HBV/E infected persons and P gene was subjected to Bayesian coalescent analysis. The time to the most recent common ancestor (tMRCA) for these HBV/E variants was estimated to be year 1952 (95% highest posterior density (95% HPD): 1927-1970). Using additional HBV/E sequences from other African countries, the tMRCA was estimated to be year 1948 (95% HPD: 1924-1966), indicating that HBV/E in these remote communities has a similar time of origin with multiple HBV/E variants broadly circulating in West/Central Africa. Phylogenetic analysis and statistical neutrality tests suggested rapid HBV/E population expansion. Additionally, skyline plot analysis showed an increase in the size of the HBV/E-infected population over the last approximately 30-40 years. CONCLUSIONS: Our data suggest a massive introduction and relatively recent HBV/E expansion in the human population in Africa. Collectively, these data show a significant shift in the HBV/E epidemic dynamics in Africa over the last century.

Full-length genome analysis of varicella-zoster virus (VZV) has shown that viral strains can be classified into seven different genotypes: European (E), Mosaic (M), and Japanese (J), and the E and M genotypes can be further subclassified into E1, E2, and M1 through 4, respectively. The distribution of the main VZV genotypes in Mexico was described earlier, demonstrating the predominance of E genotype, although other genotypes (M1 and M4) were also identified. However, no information regarding the circulation of either E genotype in the country is available. In the present study, we confirm the presence of both E1 and E2 genotypes in the country and explore the possibility of coinfection as the triggering factor for increased virulence among severe cases. A total of 61 different European VZV isolates collected in the Mexico City metropolitan area from 2005 to 2006 were typed by using a PCR method based on genotype-specific primer amplification. Fifty isolates belonged to the E1 genotype, and the eleven remaining samples were classified as E2 genotypes. No coinfection with both E genotypes was identified among these specimens. We provide here new information on the distribution of VZV genotypes circulating in Mexico City.

Scarce information on the seroprevalence of Trypanosoma cruzi among Amerindians is available, and the distribution of this disease in Mexican Indian populations is unknown. In this study, the presence of specific antibodies against T. cruzi among Teenek Amerindians in nine different communities located in San Luis Potosi State was analyzed. An average seroprevalence of 6.5% was found in these populations, suggesting that active transmission of disease occurs in this relatively isolated population in Mexico, and therefore, further studies should be conducted to identify risk factor associated to Chagas disease in other isolated populations across the country to determine the prevalence of Chagas disease in Mexican Amerindians.

The 39 oyster consumption-related cases of hepatitis A reported in 2005 represent the first large outbreak of hepatitis A associated with shellfish consumption in the United States in >15 years. This is the first outbreak investigation in which an identical hepatitis A virus sequence was obtained from both the implicated food product and case patients.

SUMMARYCurrent serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.

Background Molecular epidemiologic investigations can link geographically separate foodborne hepatitis A outbreaks but have not been used while field investigations are in progress. In 2003, outbreaks of foodborne hepatitis A were reported in multiple states. Methods Case-control studies were conducted in 3 states. Hepatitis A virus was sequenced from serologic specimens from individuals associated with outbreaks and from individuals concurrently ill with hepatitis A in non-outbreak settings in the United States and Mexico. Results Case-control studies in Tennessee (TN), North Carolina (NC), and Georgia (GA) found green onions to be associated with illness among restaurant patrons (TN: odds ratio [OR], 65.5 [95% confidence interval {CI}, 8.9-482.5; NC: OR, 2.4 [95% CI, 0.3-21.9]; GA: OR, 20.9 [95% CI, 3.9-110.3]). Viral sequences from TN case patients differed by 2 nt, compared with those from case patients in NC and GA. A third sequence, differing from the TN and GA/NC sequences by 1 nt, was identified among case patients in a subsequent outbreak in Pennsylvania. Each outbreak sequence was identical to > or =1 sequence isolated from northern Mexican resident(s) with hepatitis A. The sources of green onions served in restaurants in TN and GA were 3 farms in northern Mexico. Conclusions Ongoing viral strain surveillance facilitated the rapid implementation of control measures. Incorporation of molecular epidemiologic methods into routine hepatitis A surveillance would improve the detection of hepatitis A outbreaks and increase our understanding of hepatitis A epidemiology in the United States.

Background Invariant NKT cells (or type 1 NKT cells) co-express CD3 marker and NK receptors (CD56, CD161) and use a single type of TCRα chain (Vα24Jα18 for humans), comprising CD4-CD8-, CD4+ and CD8+ subsets. Participation of these cells and their cytokines in asthmatic children, in stable conditions and under exacerbation, was studied. Methods Three groups on children (6–12 years old) were selected: 1) asthmatics under exacerbation attack (AE) within the first 24 hours after the attack and before starting any treatment; 2) asthmatics with stable asthma (SA), without symptoms for at least a month before bleeding; and 3) healthy controls (HC) without history of asthma, atopy and with normal lung function were selected in the Allergy and Clinical Immunology Service, Hospital Infantil de Mexico. Invariant NKT cells and subset levels as well as intracellular cytokines were evaluated in whole blood by 4-color flow cytometry (antibodies against CD3, CD4, CD8, CD161, Va24, IL-4 and IFN-g). Results Proportion of iNKT cells among total CD3+ cells in HC group was 0.9%, while in SA patients they were increased up to 2.6%; interestingly, during exacerbation such cells were dimished (1.8%). Concerning iNKT CD4+ cells were 0.6% in HC, 1.8% in SA, and 0.7% in AE, while iNKT CD8+ cells were 0.1% in HC, 0.7% in SA, and 0.4% in AE. Both iNKT cell subsets expressed intracellular IFN-g and IL-4 cytokines in AE, SA and HC but predominantly IFN-g in iNKT CD8+ cells from AE patients. Conclusions iNKT cells participation in asthma pathogenesis was confirmed. Increase of IFN-g production in patients with exacerbations, may provide a regulatory environment to stabilize the condition.

Viral population evolution dynamics of influenza A is crucial for surveillance and control. In this paper we analyzed viral genetic features during the recent pandemic caused by the new influenza human virus A H1N1, using a conventional population genetics approach based on 4689 hemagglutinin (HA) and neuraminidase (NA) sequences available in GenBank submitted between March and December of 2009. This analysis showed several relevant aspects: a) a scarce initial genetic variability within the viral isolates from some countries that increased along 2009 when influenza was dispersed around the world; b) a worldwide virus polarized behavior identified when comparing paired countries, low differentiation and high gene flow were found in some pairs and high differentiation and moderate or scarce gene flow in others, independently of their geographical closeness, c) lack of positive selection in HA and NA due to increase of the population size of virus variants, d) HA and NA variants spread in a few months all over the world being identified in the same countries in different months along 2009, and e) containment of viral variants in Mexico at the beginning of the outbreak, probably due to the control measures applied by the government.