There is no comprehensive study available on the natural hepatitis C virus (HCV) polymorphism in sites associated with resistance including all viral genotypes which may present variable susceptibilities to particular direct-acting antivirals (DAAs). This study aimed to analyze the frequencies, genetic barriers, and evolutionary histories of naturally occurring resistance-associated variants (RAVs) in the six main HCV genotypes. A comprehensive analysis of up to 103 RAVs was performed in 2,901, 2,216, and 1,344 HCV isolates for the NS3, NS5A, and NS5B genes, respectively. We report significant intergenotypic differences in the frequencies of natural RAVs for these three HCV genes. In addition, we found a low genetic barrier for the generation of new RAVs, irrespective of the viral genotype. Furthermore, in 1,126 HCV genomes, including sequences spanning the three genes, haplotype analysis revealed a remarkably high frequency of viruses carrying more than one natural RAV to DAAs (53% of HCV-1a, 28.5% of HCV-1b, 67.1% of HCV-6, and 100% of genotype 2, 3, 4, and 5 haplotypes). With the exception of HCV-1a, the most prevalent haplotypes showed RAVs in at least two different viral genes. Finally, evolutionary analyses revealed that, while most natural RAVs appeared recently, others have been efficiently transmitted over time and cluster in well-supported clades. In summary, and despite the observed high efficacy of DAA-based regimens, we show that naturally occurring RAVs are common in all HCV genotypes and that there is an overall low genetic barrier for the selection of resistance mutations. There is a need for natural DAA resistance profiling specific for each HCV genotype.

Until very recently, treatment for chronic hepatitis C virus (HCV) infection has been based on the combination of two non-viral specific drugs: pegylated interferon-α and ribavirin, which is effective in, overall, about 40%-50% of cases. To improve the response to treatment, novel drugs have been designed to specifically block viral proteins. Multiple compounds are under development, and the approval for clinical use of the first of such direct-acting antivirals in 2011 (Telaprevir and Boceprevir), represents a milestone in HCV treatment. HCV therapeutics is entering a new expanding era, and a highly-effective cure is envisioned for the first time since the discovery of the virus in 1989. However, any antiviral treatment may be limited by the capacity of the virus to overcome the selective pressure of new drugs, generating antiviral resistance. Here, we try to provide a basic overview of new treatments, HCV resistance to new antivirals and some considerations derived from a Public Health perspective, using HCV resistance to protease and polymerase inhibitors as examples.

Continuous surveillance for genetic changes in circulating influenza viruses is needed to guide influenza prevention and control. To compare intra-seasonal influenza genetic diversity of hemagglutinin in influenza A strains isolated from influenza hospital admissions collected at two distinct sites during the same season. Comparative phylogenetic analysis of full-length hemagglutinin genes from 77 isolated influenza A viruses from the St. Petersburg, Russian Federation and Valencia, Spain sites of the Global Influenza Hospital Surveillance Network (GIHSN) during the 2013/14 season. We found significant variability in A(H3N2) and A(H1N1)pdm09 viruses between the two sites, with nucleotide variation at antigenic positions much lower for A(H1N1)pdm09 than for A(H3N2) viruses. For A(H1N1)pdm09, antigenic sites differed by three to four amino acids from the vaccine strain, two of them common to all tested isolates. For A(H3N2) viruses, antigenic sites differed by six to nine amino acids from the vaccine strain, four of them common to all tested isolates. A fifth amino acid substitution in the antigenic sites of A(H3N2) defined a new clade, 3C.2. For both influenza A subtypes, pairwise amino acid distances between circulating viruses and vaccine strains were significantly higher at antigenic than at non-antigenic sites. Whereas A(H1N1)pdm09 viruses clustered with clade 6B and 94% of A(H3N2) with clade 3C.3, at both study sites A(H3N2) clade 3C.2 viruses emerged towards the end of the season, showing greater pairwise amino acid distances from the vaccine strain compared to the predominant clade 3C.3. Influenza A antigenic variants differed between St. Petersburg and Valencia, and A(H3N2) clade 3C.2 viruses were characterized by more amino acid differences from the vaccine strain, especially at the antigenic sites.

ResumenIntroducciónLos pacientes con insuficiencia renal crónica en tratamiento con hemodiálisis constituyen un grupo de riesgo para la infección con el virus de la hepatitis C. La infección por este virus representa la causa más frecuente de enfermedad hepática crónica en los hemodializados.ObjetivoEvaluar la prevalencia y realizar la caracterización de la infección por el virus de la hepatitis C en un grupo de pacientes en hemodiálisis de la ciudad de Posadas (Argentina).Materiales y métodosSe evaluó la presencia del virus de la hepatitis C mediante enzimoinmunoanálisis en 113 muestras de sangre total obtenidas por venopunción de pacientes con insuficiencia renal crónica en tratamiento con hemodiálisis. En los casos positivos se confirmó la presencia de genoma viral por medio de una RT-PCR anidada de la región 5′ no codificante del virus de la hepatitis C y se determinó el genotipo y subtipo viral mediante análisis del polimorfismo de longitud de fragmentos de restricción.ResultadosDe una población de 113 pacientes con insuficiencia renal crónica en tratamiento con hemodiálisis, el 89,4% (n=101) de los casos fueron no reactivos para anticuerpos contra el virus de la hepatitis C mediante enzimoinmunoanálisis, mientras que el 10,6% (n=12) de los casos fueron reactivos. Se confirmó el resultado reactivo en los 12 casos por RT-PCR, y se determinó la infección por genotipo 1a (7/12) y genotipo 2a (5/12).ConclusiónLa prevalencia de la infección por el virus de la hepatitis C en este grupo de pacientes en hemodiálisis fue del 10,6%, y los genotipos virales del virus de la hepatitis C encontrados (1a y 2a) coinciden con los genotipos que prevalecen en la población infectada de Argentina.AbstractIntroductionPatients with chronic renal failure on hemodialysis comprise a risk group for infection with hepatitis C. This viral infection is the most common cause of chronic liver disease in hemodialysis.ObjectiveTo evaluate the prevalence and to characterise hepatitis C virus infection in a group of patients from the city Posadas (Argentina) who are on hemodialysis.Materials and methodsThe presence of the virus of hepatitis C was evaluated by enzyme immunoassay of 113 samples of whole blood obtained from patients with chronic renal failure undergoing hemodialysis. In positive cases, the presence of the viral genome was confirmed by RT-nested PCR of the 5’-noncoding region of the hepatitis C virus, and the viral genotype and subtype were determined by restricted fragment length polymorphism analysis.ResultsOf a population of 113 patients with chronic renal failure on hemodialysis, the detection of hepatitis C virus infection was performed by enzyme immunoassay, of which 89.4% (n=101) of the cases were non-reactive, and 10.6% (n=12) of cases were reactive. We confirmed the reactive results in 12 cases by RT-PCR, and we determined that these cases were genotype 1a (7/12) and genotype 2a (5/12).ConclusionThe prevalence of infection with hepatitis C virus in this group of patients on hemodialysis was 10.6%, and the hepatitis C virus genotypes found (1a and 2a) were the same as the prevalent genotypes in the infected population of Argentina

Rotavirus alphagastroenteritidis is the major causative agent of acute gastroenteritis in both children under the age of 5 and young mammals and birds globally. RVAs are non-enveloped viruses with a genome comprising 11 double-stranded RNA segments. In 2008, the Rotavirus Classification Working Group pioneered a comprehensive and complete RVA genome classification system, establishing a specific threshold, which measures the genetic distances between homologous genes. The aim of this study was to perform an updated systematic analysis of the genetic variability across all RVA genes. Our investigation involved assessing the established cutoff values for each RVA genome segment and determining the need for any updates. To achieve this objective, multiple sequence alignments were constructed for all 11 genes and one for each genotype with discrepancies. Also, pairwise distances along with their cutoff values were evaluated. The analyses provided insights into the current relevance of cutoff values, which remain applicable for the majority of genotypes. In conclusion, this study fortifies the current classification system by highlighting its robustness and accurate genotyping of Rotavirus alphagastroenteritidis.

Introduction The chikungunya virus (CHIKV) is an arbovirus vectored by Aedes mosquitoes that infects humans in tropical and sub-tropical areas of Asia and Africa. Recently, outbreaks have been reported in tropical and sub-tropical areas of countries that were previously unaffected (e.g., Brazil, Colombia). Currently, the following geographical genotypes have been identified through phylogenetic analysis of CHIKV E1 gene sequences: the West African (WAf), East/Central/South African (ECSA), and Asian genotypes. Outbreaks in a geographical area can happen with the same or different genotypes. Determining which genotypes are circulating in an outbreak is important for public health management. Objectives To create a computer-based system available online that is suitable for detecting changes in CHIKV nucleotide and amino acid sequences and identifying their corresponding geographical genotype. Methods We used several computer frameworks, tools, programming languages, algorithms, and infrastructure systems to build a software tool that analyzes changes in nucleotide and amino acid sequences and identifies different geographical genotypes through phylogenetic analysis. Results We have built an online software tool called Pathogen Sequence Signature Analysis (PSSA) that allows researchers to analyze nucleotide and amino acid sequence variations between sample CHIKV sequences taken from infected patients and obtained through conventional Sanger sequencing, to identify their corresponding geographical genotype. Conclusion PSSA is able to analyze sequences in a simple and effective manner, and includes proper documentation (i.e., UML diagrams) and also basic examples that serve to test the algorithm. Furthermore, PSSA provides various ways to visualize the data in order to aid understanding and interpretation of results. Results provided by PSSA will be useful for the identification of circulating CHIKV genotypes and public health surveillance. PSSA is available at: http://pssa.itiud.org.