Rapid hepatitis C virus divergence among chronically infected individuals.

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.

Identification of hepatitis C virus transmission using a next-generation sequencing approach.

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.

Specific detection of naturally occurring hepatitis C virus mutants with resistance to telaprevir and boceprevir (protease inhibitors) among treatment-naïve infected individuals.

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.

Molecular epidemiology of autochthonous dengue virus strains circulating in Mexico.

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.

Is ultra-violet radiation the main force shaping molecular evolution of varicella-zoster virus?

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.

Serotipos de dengue en México durante 2009 y 2010 / Dengue serotypes in México during 2009-2010

Introducción. El dengue en México es un problema prioritario de salud pública. Desde el 2008 el Departamento para la Vigilancia Epidemiológica y Virológica del InDRE implementó un nuevo algoritmo de diagnóstico del dengue, que utiliza la Red de Laboratorios Estatales de Salud Pública, para favorecer la representatividad geográfica, la oportunidad, la sensibilidad y la especificidad de la información que se obtiene. Métodos. La identificación de serotipos se realizó a partir de muestras positivas a la proteína NS1 por ensayo inmunoenzimático (ELISA). Las técnicas que se utilizaron fueron: aislamiento viral, PCR punto final y, desde 2009, RT-PCR en tiempo real (qRT-PCR). Resultados. En 2009 se analizaron 6,336 muestras; en 2,944 de éstas (46.6%) se identificó el serotipo DENV-1 que predominó sobre el serotipo DENV-2; el serotipo DENV-3 sólo se identificó en dos casos en Guerrero y el serotipo DENV-4 en un caso en Chiapas. En 2010 se analizaron 2,013 muestras. Se identificó algún serotipo en 1,607 muestras (79.88%) y, nuevamente, el serotipo DENV-1 predominó en todo el país. En Chiapas se identificaron los serotipos DENV-1, 2 y 4 y en Jalisco los serotipos DENV-1 y 3. Además, se identificó la circulación del serotipo DENV-3 en Guerrero y apareció el serotipo DENV-4 en San Luis Potosí. Conclusiones. Por la selección de muestras para vigilancia virológica de dengue mediante la positividad a la proteína NS1 y por la introducción de la técnica de qRT-PCR se optimizó la identificación de serotipos circulantes. La alta endemia, los brotes en nuevas regiones, el predominio del serotipo DENV-1 por varios años y la introducción lenta de otros serotipos, principalmente DENV-3, pueden favorecer la aparición de formas clínicas graves de dengue. La vigilancia epidemiológica inteligente del dengue brindará información para un mejor entendimiento de la enfermedad y promoverá acciones para su control y prevención.

Background. Dengue is a public health priority in Mexico. Since 2008, the dengue diagnostic algorithm for epidemiological and virological surveillance has been improved at InDRE and the public health laboratory network (RLESP) to optimize geographic representation, opportunity, sensitivity and specificity of the produced information. Methods. Dengue serotype identification is based on ELISA NS1 positive samples. Methods used are viral isolation, endpoint PCR and, since August 2009, real-time PCR (qRT-PCR). Results. In 2009, 6,336 serum samples were analyzed and 2,944 (46.6%) were positive for serotype identification. DENV-1 was detected in greater proportion followed by DENV-2, and DENV-3 4 was only identified in two cases in Guerrero and DENV-4 in one case in Chiapas. In 2010, 2,013 serum samples were analyzed and 1,607 (78.8%) were positive for serotype identification. DENV-1 was predominant throughout the country. In Chiapas, DENV-1, 2 and 4 were identified and in Jalisco DENV-1 and 3. DENV-3 was identified in Guerrero again and DENV-4 was detected in San Luis Potosí. Conclusions. The selection samples through NS1 positive samples and the introduction of qRT-PCR optimized serotype identification. Hyperendemicity, outbreaks in new geographic areas, the predominant circulation of DENV-1 for several years and the slow reintroduction of the other serotypes, mainly DENV-3, could increase clinical cases of severe dengue. An ¡intelligentí epidemiological surveillance program would offer information for a better understanding of the disease and promote action for its control and prevention.