Phylogenetic Analysis Of Virus Research Articles

Molecular Characterization and Phylogenetic Analysis of Marek's Disease Virus in Iran.

Marek's disease (MD) is a highly contagious, lymphoproliferative poultry disease caused by the oncogenic herpesvirus, serotype 1 Marek's disease virus (MDV-1), or Gallid herpesvirus 2 (GaHV-2). MDV strains have shown a continued evolution of virulence leading to immune failure, and MD cases continue to occur or surge. Meq, the major MDV-1 oncoprotein, induces T-cell neoplastic transformation through several mechanisms including inhibition of apoptosis, cell cycle regulation, and serum-anchorage independent growth. There is no current information on the MDV serotypes and pathotypes circulating in vaccinated commercial farms in Iran, where the birds are vaccinated at the hatchery with GaHV-2 and Meleagrid herpesvirus 1 (MeHV-1) vaccines. This study reports the molecular characterization of a GaHV-2 strain detected in 19 flocks of Iranian layer farms exhibiting MDV-1-like clinical signs and visceral lymphomas. Based on sequencing and phylogenetic analysis of the Meq gene, the Iranian GaHV-2 isolates could be divided into two separate clades regarding molecular features. The clade containing strains was closely related to Italian, Indian, and Hungarian virulent isolates, and the clade was related to American very virulent plus (vv+) isolates. For the first time, the MDV-1 virus was characterized by an outbreak in poultry flocks in Iran. Although MDV-1 strains obtained in Iran's present outbreak are presumably related to virulent (v) and vv+ pathotypes based on nucleotide, amino acid, and phylogenetic analysis of the viruses, they are not confirmed so far. Thus, it is highly recommended to perform further analyses to demonstrate the pathotype characteristics in vivo.

Molecular detection and phylogenetic analysis of viruses causing mosaic symptoms in new sugarcane varieties in China

Seventy-seven mosaic leaf samples from new sugarcane varieties from national regional trials in Kaiyuan, Mile and Yuanjiang, Yunnan Province, China, were collected in 2015 and analyzed using reverse-transcription polymerase chain reaction (RT-PCR) to determine the pathogen causing mosaic symptoms in sugarcane. Three viruses, Sugarcane streak mosaic virus (SCSMV), Sorghum mosaic virus (SrMV) and Sugarcane mosaic virus (SCMV), were detected in 100, 27.3 and 1.3% of the samples respectively. Co-infection with SCSMV, SrMV and SCMV was also found for the first time in the new variety Qiantang 5. Nucleotide sequences of the coat protein (CP) gene of 48 SCSMV and 17 SrMV isolates were subsequently sequenced and analyzed with the CP gene sequences of SCSMV and SrMV reported in GenBank to perform phylogenetic analyses. Geographic differences were observed in the phylogenetic tree of SCSMV and all SCSMV isolates from China clustered into a single China group. Moreover, SCSMV isolates from different new varieties were distributed across all subgroups or clustered into an independent branch in the China group. SrMV isolates obtained in this study and those published in GenBank clustered into two groups and were distributed into different subgroups within these groups. Furthermore, the distribution of SrMV isolates from different new varieties overlapped in these different groups and subgroups, with no obvious geographic differences. These results provide a scientific basis for sugarcane mosaic or streak mosaic disease resistance breeding and effective control of this disease.

Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral".

Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle “big data”, provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.

Revisiting the Issue of the Molecular-genetic Structure of the Causative Agent of the Bovine Leukemia Virus in the Russian Federation

Objectives: The study is aimed at investigating the genotypic diversity of the causative agent of Bovine Leukemia, circulating in animal populations from different regions of Russia. Methods: Genotyping and sequencing for samples of 444 bp gene DNA element of cattle HVL isolates of Russian regions were conducted and phylogenetic analysis of the isolated strains was performed. Findings: Blood samples, serum and leukoconcentrate of animal blood and DNA samples – env gene region, 444bp long, of cattle leukemia virus were a subject of investigation. Samples from Belgian subgroup (type B) and Australian subgroups (type A) of leukemia virus were singled out in the studied samples. The results of this study provide an opportunity to study features of leukemic epizootic process in the region. For the first time in the middle Urals in Russia the molecular-genetic structure of the cattle leukemia virus was singled out. Phylogenetic analysis of virus derived from DNA sequencing has allowed classifying the studied strains and comparing them with global isolates. Determination of the virus genotype allows for deeper research to identify the pathogenetic variants of leukemic process development in a particular region – in the middle Urals. Study of genotypic diversity of the cattle leukemia virus opens new opportunities and additional approaches to the development of methods for health improvement in leukemia disadvantaged populations. Applications/Improvements: The data obtained will serve as a base for the creation of highly sensitive, specific primers for effective PCR diagnostics.

Human bocavirus in Chile: clinical characteristics and epidemiological profile in children with acute respiratory tract infections

Human bocavirus (HBoV) is a newly discovered parvovirus found in children with acute respiratory tract infections (ARTI). To describe the epidemiological and clinical profile of children < 5 years old consulting for ARTI, comparing cases of HBoV monoinfection and coinfection with other known respiratory viruses. Furthermore, we aimed to estimate the prevalence of viral shedding in asymptomatic children and perform phylogenetic analysis. We investigated the presence of HBoV in nasopharyngeal secretions from children consulting for AlRTI and among asymptomatic controls, between 2007 and 2008, by polymerase chain reaction. HBoV was detected in 79 (21.8%) of 362 nasopharyngeal swabs obtained from children with ARTI. In 60/79 (76%), coinfection with other respiratory viruses was confirmed. Most common symptoms were cough, fever and rhinorrhea. Children infected only with HBoV showed significantly lower frequencies of respiratory distress, oxygen requirements and hospital admission than those with coinfection. HBoV was detected in 6/16 (37.5%) samples from asymptomatic children. The phylogenetic analysis of viruses from Chilean patients revealed that circulating HBoV was closely related to original strains. HBoV was found either in symptomatic and asymptomatic children. The severity of the disease was greater when HBoV was associated to other respiratory viruses.

Bocavirus humano en Chile: características clínicas y epidemiológicas en niños con infecciones respiratorias

Human bocavirus (HBoV) is a newly discovered parvovirus found in children with acute respiratory tract infections (ARTI).To describe the epidemiological and clinical profile of children < 5 years old consulting for ARTI, comparing cases of HBoV monoinfection and coinfection with other known respiratory viruses. Furthermore, we aimed to estimate the prevalence of viral shedding in asymptomatic children and perform phylogenetic analysis.We investigated the presence of HBoV in nasopharyngeal secretions from children consulting for AlRTI and among asymptomatic controls, between 2007 and 2008, by polymerase chain reaction.HBoV was detected in 79 (21.8%) of 362 nasopharyngeal swabs obtained from children with ARTI. In 60/79 (76%), coinfection with other respiratory viruses was confirmed. Most common symptoms were cough, fever and rhinorrhea. Children infected only with HBoV showed significantly lower frequencies of respiratory distress, oxygen requirements and hospital admission than those with coinfection. HBoV was detected in 6/16 (37.5%) samples from asymptomatic children. The phylogenetic analysis of viruses from Chilean patients revealed that circulating HBoV was closely related to original strains.HBoV was found either in symptomatic and asymptomatic children. The severity of the disease was greater when HBoV was associated to other respiratory viruses.

The Capacity of UL49.5 Proteins To Inhibit TAP Is Widely Distributed among Members of the Genus Varicellovirus

The lifelong infection by varicelloviruses is characterized by a fine balance between the host immune response and immune evasion strategies used by these viruses. Virus-derived peptides are presented to cytotoxic T lymphocytes by major histocompatibility complex (MHC) class I molecules. The transporter associated with antigen processing (TAP) transports the peptides from the cytosol into the endoplasmic reticulum, where the loading of MHC-I molecules occurs. The varicelloviruses bovine herpesvirus 1 (BoHV-1), pseudorabies virus, and equid herpesviruses 1 and 4 have been found to encode a UL49.5 protein that inhibits TAP-mediated peptide transport. To investigate to what extent UL49.5-mediated TAP inhibition is conserved within the family of Alphaherpesvirinae, the homologs of another five varicelloviruses, one mardivirus, and one iltovirus were studied. The UL49.5 proteins of BoHV-5, bubaline herpesvirus 1, cervid herpesvirus 1, and felid herpesvirus 1 were identified as potent TAP inhibitors. The varicella-zoster virus and simian varicellovirus UL49.5 proteins fail to block TAP; this is not due to the absence of viral cofactors that might assist in this process, since cells infected with these viruses did not show reduced TAP function either. The UL49.5 homologs of the mardivirus Marek's disease virus 1 and the iltovirus infectious laryngotracheitis virus did not block TAP, suggesting that the capacity to inhibit TAP via UL49.5 has been acquired by varicelloviruses only. A phylogenetic analysis of viruses that inhibit TAP through their UL49.5 proteins reveals an interesting hereditary pattern, pointing toward the presence of this capacity in defined clades within the genus Varicellovirus.

Transmission of hepatitis C virus quasispecies between human adults

To elucidate how hepatitis C virus (HCV) with multiple variants (quasispecies) is transmitted and adapts to the host during infection, we compared nucleotide and deduced amino acid sequences from hypervariable region1 (HVR1) of the E2 gene of HCV between a donor and a recipient who developed hepatitis after a needlestick accident. Thirty clones from each subject were sequenced after PCR amplification, cloning, and purification of plasmid DNA from single colonies of transformed bacteria. Genetic analysis revealed that the recipient's viral sequences were much less diverse than the donor's. We found a single predominant HCV HVR1 clone of the recipient in 22/30 isolates with the same amino acid sequence, and mimic clones in 8/30 isolates with only one amino acid substitution. These were all absent in the donor, who had 21 highly diverse sequences. Phylogenetic analysis of virus E1/E2 gene sequences showed that the recipient's unique sequences were related to the population of variants from the donor, in whom one isolate had 96% similarity to the recipient's predominant amino acid sequence. These results suggest that a minor subset of the donor's HCV variants is selectively transmitted to the recipient, and that the selection determines the predominant variant in the new host.

Simultaneous introduction of HIV type 1 subtype A and B viruses into injecting drug users in southern Ukraine at the beginning of the epidemic in the former Soviet Union.

The vast majority of HIV-1 strains from the epidemic in the former Soviet Union (FSU) belong to subtype A (IDU-A) and CRF03_AB (IDU-A/B), for which IDU-A is one of parental strains; no epidemic by another parental virus, belonging to subtype B (IDU-B), has yet been identified. To characterize viruses present during the early stage of the epidemic in southern Ukraine, where the first outbreaks in the FSU were registered, we obtained partial env and pol sequences from IDUs from Odessa and Nikolaev and compared them with viruses from other outbreaks. All viruses from Odessa belonged to the IDU-A type, which is in accord with previous studies. At the same time, we found that the outbreak in Nikolaev was caused by IDU-B viruses, indicating that this outbreak is the result of an independent virus introduction. Phylogenetic analysis of viruses from the FSU supported the epidemiological data suggesting that the HIV-1 epidemic in the FSU started in southern Ukraine.

Variation of hepatitis C virus following serial transmission: multiple mechanisms of diversification of the hypervariable region and evidence for convergent genome evolution.

We have studied the evolution of hepatitis C virus (HCV) from a common source following serial transmission from contaminated batches of anti-D immunoglobulin. Six secondary recipients were each infected with virus from identifiable primary recipients of HCV-contaminated anti-D immunoglobulin. Phylogenetic analysis of virus E1/E2 gene sequences [including the hypervariable region (HVR)] and part of NS5B confirmed their common origin, but failed to reproduce the known epidemiological relationships between pairs of viruses, probably because of the frequent occurrence of convergent substitutions at both synonymous and nonsynonymous sites. There was no evidence that the rate at which the HCV genome evolves is affected by transmission events. Three different mechanisms appear to have been involved in generating variation of the hypervariable region; nucleotide substitution, insertion/deletion of nucleotide triplets at the E1/E2 boundary and insertion of a duplicated segment replacing almost the entire HVR. These observations have important implications for the phylogenetic analysis of HCV sequences from epidemiologically linked isolates.