Recombination in Hepatitis C Virus

Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high levels of genetic diversity which have been used to differentiate six major genotypes and about 80 subtypes. Although the different genotypes and subtypes share basic biological and pathogenic features they differ in clinical outcomes, response to treatment and epidemiology. The first HCV recombinant strain, in which different genome segments derived from parentals of different genotypes, was described in St. Petersburg (Russia) in 2002. Since then, there have been only a few more than a dozen reports including descriptions of HCV recombinants at all levels: between genotypes, between subtypes of the same genotype and even between strains of the same subtype. Here, we review the literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it. Finally, we analyze the potential consequences, especially in clinical practice, of HCV recombination in light of the coming new therapeutic approaches against this virus

A transcriptomic approach highlights induction of secondary metabolism in citrus fruit in response to Penicillium digitatum infection

<p>Abstract</p> <p>Background</p> <p>Postharvest losses of citrus fruit due to green mold decay, caused by the fungus <it>Penicillium digitaum</it>, have a considerable economic impact. However, little is known about the molecular processes underlying the response of citrus fruit to <it>P. digitatum</it>.</p> <p>Results</p> <p>Here we describe the construction of a subtracted cDNA library enriched in citrus genes preferentially expressed in response to pathogen infection followed by cDNA macroarray hybridization to investigate gene expression during the early stages of colonization of the fruit's peel by <it>P. digitatum</it>. Sequence annotation of clones from the subtracted cDNA library revealed that induction of secondary and amino acid metabolisms constitutes the major response of citrus fruits to <it>P. digitatum </it>infection. Macroarray hybridization analysis was conducted with RNA from either control, wounded, ethylene treated or <it>P. digitatum </it>infected fruit. Results indicate an extensive overlap in the response triggered by the three treatments, but also demonstrated specific patterns of gene expression in response to each stimulus. Collectively our data indicate a significant presence of isoprenoid, alkaloid and phenylpropanoid biosynthetic genes in the transcriptomic response of citrus fruits to <it>P. digitatum </it>infection. About half of the genes that are up-regulated in response to pathogen infection are also induced by ethylene, but many examples of ethylene-independent gene regulation were also found. Two notable examples of this regulation pattern are the genes showing homology to a caffeine synthase and a berberine bridge enzyme, two proteins involved in alkaloid biosynthesis, which are among the most induced genes upon <it>P. digitatum </it>infection but are not responsive to ethylene.</p> <p>Conclusions</p> <p>This study provided the first global picture of the gene expression changes in citrus fruit in response to <it>P. digitatum </it>infection, emphasizing differences and commonalities with those triggered by wounding or exogenous ethylene treatment. Interpretation of the differentially expressed genes revealed that metabolism is redirected to the synthesis of isoprenes, alkaloids and phenylpropanoids.</p

Comparative analysis of the sensitivity to distinct antimicrobials among Penicillium spp. causing fruit postharvest decay

The postharvest fungal pathogens Penicillium digitatum, P. italicum and P. expansum are an increasing problem for the Mediterranean orchards and fruit industry. This study was designed to gain knowledge on factors affecting susceptibility of Penicillium spp. to antimicrobial peptides (AMPs) as new antifungal compounds for plant protection. The previously characterized PAF26 is a novel penetratin-type AMP with activity against phytopathogenic fungi. Comparative analyses were conducted on the sensitivity of Penicillium spp. to PAF26, to the cytolytic peptide melittin and to other antimicrobials. The research included microscopic observations, chitin quantification, virulence assays on citrus and apple fruits, and molecular phylogenetic relationships within Penicillium isolates from citrus fruit. Virulence analysis and phylogenetic reconstruction confirmed the host specificity and monophyletic origin for P. digitatum, contrary to the closely-related species P. expansum and P. italicum. A parallelism was found between sensitivity to PAF26 of Penicillium isolates and to the chitin dye calcofluor white (CFW). No such correlation was found between sensitivity to PAF26 and to the membrane perturbing compound SDS or the oxidizing agent H2O2. Microscopy studies showed that mycelium and conidia from the PAF26-sensitive fungi were also prone to CFW staining, but no direct correlation with the mycelial chitin content was found. The data are consistent with the fact that fungal cell walls influence the outcome of the interaction of AMPs with fungi, and that PAF26 is more active towards Penicillium citrus fruit pathogens. In this context, CFW could help both to elucidate AMPs mode of action and in studies of the mechanisms of virulence and host specificity within Penicillium spp

Relating the outcome of HCV infection and different host SNP polymorphisms in a Majorcan population coinfected with HCV–HIV and treated with pegIFN-RBV

Hepatitis C virus (HCV) is one of the major causes of chronic hepatitis, cirrhosis, and hepatocellular carcinoma, and the development of HCV-related disease is accelerated in individuals coinfected with human immunodeficiency-1 virus (HIV). In the present study, we correlated different host single-nucleotide polymorphisms (SNPs) in the IL28B, CTLA4, LDLr, and HFE genes and mitochondrial DNA (mtDNA) haplogroups with the outcome of HCV infection and the response to pegylated-interferon plus ribavirin (pegIFN-RBV) treatment. Our study population consisted of 63 Majorcan patients coinfected with HCV and HIV and 59 anonymous unrelated controls. Whereas the population frequency of IL28B alleles was similar to that found in a North-American cohort of European descent, the frequency of the rs12979860 C allele was lower than that determined in other cohorts from Spain. The frequencies of CTLA4 and LDLr polymorphisms were comparable to those reported in other populations. Significant differences between cases and control cohorts occurred only for the H63D mutation of the HFE gene. There were no other differences in the frequencies of other polymorphisms or mtDNA haplogroups. The IL28B rs12979860 CC genotype was shown to be associated with a rapid virological response, and the spontaneous viral clearance rate for HCV was higher in patients with the CTLA4+49 G allele. There was no relationship between SNPs in the LDLr and HFE genes and mtDNA haplogroups and the response to treatment. Our results suggest that the host genetic background plays a significant role in the pegIFN-RBV response of patients coinfected with HCV and HIV. [Int Microbiol 2014; 17(1):11-20]Keywords: HCV&ndash;HIV co-infection &middot; mtDNA haplogroups &middot; SNP polymorphism

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.Peer reviewe

Evolutionary and phenotypic characterization of two spike mutations in European lineage 20E of SARS-CoV-2.

We have detected two mutations in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at amino acid positions 1163 and 1167 that appeared independently in multiple transmission clusters and different genetic backgrounds. Furthermore, both mutations appeared together in a cluster of 1,627 sequences belonging to clade 20E. This cluster is characterized by 12 additional single nucleotide polymorphisms but no deletions. The available structural information on the S protein in the pre- and postfusion conformations predicts that both mutations confer rigidity, which could potentially decrease viral fitness. Accordingly, we observed reduced infectivity of this spike genotype relative to the ancestral 20E sequence in vitro, and the levels of viral RNA in nasopharyngeal swabs were not significantly higher. Furthermore, the mutations did not impact thermal stability or antibody neutrali- zation by sera from vaccinated individuals but moderately reduce neutralization by convalescent-phase sera from the early stages of the pandemic. Despite multi- ple successful appearances of the two spike mutations during the first year of SARS-CoV-2 evolution, the genotype with both mutations was displaced upon the expansion of the 20I (Alpha) variant. The midterm fate of the genotype investi- gated was consistent with the lack of advantage observed in the clinical and ex- perimental data

The International Virus Bioinformatics Meeting 2023

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24&ndash;26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting