Virology reports最新文献

Among viral diseases transmitted by mosquitoes, dengue is characterized by its rapid dispersion around the world. Dengue severity is associated to a cytokine “storm” leading to vascular hemorrhagic manifestations, plasma leakage and shock, but also producing viral clearance. Macrophage/monocyte activation occurs during infection. Monocyte lineage cells are among those that allow virus replication. We investigated circulating human monocyte subsets - classical CD14⁺ CD16⁻ and non-classical CD14⁺ CD16⁺ - during DENV-4 infection in patients. Intracellular inducible nitric oxide synthase (iNOS) and indoleamine 2,3–dioxygenase (IDO) were detected in both monocyte subsets. Circulating CD14⁺ CD16⁺ monocyte frequency is mildly increased during DENV-4 infection. INOS is more intensely detected in CD14⁺ CD16⁻ than in CD16⁺ monocytes and IDO in CD14⁺ CD16⁺. DENV-4 patients show increase in NO, TNF-α, IFN-y, IP-10/CXL10, IL-10 and MCP-1/CCL2 plasma levels when compared to healthy individuals. The classical monocyte subset, CD14⁺ CD16⁻ was shown to be inversely correlated with IL-10 and IP-10/CXCL10 levels, while the non-classical CD14⁺ CD16⁺ is positively correlated with IL-10 cytokine. TNF-α, IL-10 cytokines and IP-10/CXL10 chemokine are positively correlated with the CD14⁺ iNOS⁺ monocyte population. Both CD14⁺ cells - CD16⁻ iNOS⁺ and CD16⁺ iNOS⁺ subsets - presented positive correlation with IL-10, IP-10/CXL10 and MCP-1/CCL2, besides TNF-α associated with CD16⁻ iNOS⁺ cells. CD14⁺ CD16⁻ IDO⁺ and CD16⁺ IDO⁺ populations correlated positively with IL-10. Furthermore, CD16⁻ IDO⁺ monocyte subset also presented a positive correlation with TNF-α and IP-10/CXCL10. According to these data, we considered that iNOS and IDO are activated in monocyte CD16⁻ and CD16⁺ subsets, likely exerting both antiviral effects and modulating exacerbated immunological responses during dengue fever.

MicroRNAs (miRNAs) have been reported to play an important role in influenza virus-host interactions. To gain more insight into the contribution of miRNAs to the host immune response, the miRNA expression profiles in the sera of H7N9-infected patients and healthy controls were analyzed using miRNA microarray. Among the ninety-four miRNAs that were significantly differentially expressed in H7N9 serum samples when compared with that of healthy controls, fifty-three miRNAs were up-regulated and forty-one down-regulated. Five serum miRNA candidates (hsa-miR-197-5p, hsa-miR-320a, hsa-miR-320d, hsa-miR-320e, and hsa-miR-765) were further verified by RT-qPCR. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the potential use of these miRNAs for the H7N9 infection diagnosis from the serum samples. In silico analyses indicate that most the target genes of these miRNAs are implicated in cell invasion, inflammatory response and apoptosis. Our results indicate that these miRNA biomarkers from serum samples can be used for influenza diagnosis.

The epidemiological significance of asymptomatic persistent foot-and-mouth disease virus (FMDV) infection in carrier animals, specifically its ability to seed new clinical outbreaks, is undetermined, and consistent viral determinants of FMDV persistence have not been identified. We analyzed 114 FMDV O/ME-SA/PanAsia VP1 sequences from naturally infected animals in Vietnam, of which 31 were obtained from persistently infected carrier animals. A site-specific substitution was identified at VP1 residue 172 where arginine was present in all 31 of the carrier-associated viruses, whereas outbreak viruses typically contained glutamine. Additionally, we characterized multiple viruses from a single persistently infected animal that were collected over the course of eight months and at multiple distinct anatomic sites (larynx, dorsal soft palate and dorsal nasopharynx). This work sheds new light on naturally occurring viral mutations within the host and provides a basis for understanding the viral evolution and persistence mechanisms of FMDV.

Infectious bronchitis virus (IBV), a major pathogen of commercial poultry flocks, circulates in the form of different genotypes. Three IB viruses were isolated from broiler chickens showing respiratory and renal lesions. The isolates were characterized by reverse transcriptase polymerase chain reaction and sequence analysis of the Full-length of the S1. Three isolates were belonged to Variant 2 like (IS/1494 like) IBV genotype. Phylogenetic analysis showed that Variant 2 like isolates formed two clusters and the Iranian and Iraqi isolates were included in the cluster II. Cluster I composed of Israeli, Egyptian and Turkish Variant 2 like IBV Isolates. Three hyper variable regions (HVR) of S1 were determined. The Most variation was seen in HVR2. The findings emphasize the importance of continuous monitoring of IBV, in addition to adjust diagnostic methods, molecular epidemiological studies, development and use of vaccines which are adapted to the changing disease scenario.

A number of PVs have been described in bats but to the best of our knowledge not from feces. Using a previously described NetoVIR protocol, Eidolon helvum pooled fecal samples (Eh) were treated and sequenced by Illumina next generation sequencing technology. Two complete genomes of novel PVs (EhPV2 and EhPV3) and 3 partial sequences (BATPV61, BATPV890a and BATPV890b) were obtained and analysis showed that the EhPV2 and EhPV3 major capsid proteins cluster with and share 60–64% nucleotide identity with that of Rousettus aegyptiacus PV1, thus representing new species of PVs within the genus Psipapillomavirus. The other PVs clustered in different branches of our phylogenetic tree and may potentially represent novel species and/or genera. This points to the vast diversity of PVs in bats and in Eidolon helvum bats in particular, therefore adding support to the current concept that PV evolution is more complex than merely strict PV-host co-evolution.

A T4-related phage infecting Ralstonia solanacearum was isolated in Thailand (ϕRP15). ϕRP15 virions showed unique morphology with star-like protrusions attached to the base plate via a stalk. The 168 kb genome sequence of ϕRP15 was determined and found to encode 17 tRNAs (plus two tRNA pseudogenes). Ten of these phage-encoded tRNAs corresponded to codons that are relatively abundant in the phage but rare in the host, while others matched to codons frequent in both phage and host. Phylogenetic and proteomic analyses demonstrate that ϕRP15 forms a clade with Delftia phage ϕW-14, which in turn is placed as a sister group of viunalikeviruses. The hosts of ϕRP15 and ϕW-14 (R. solanacearum and Delftia acidovorans, respectively) belong to Betaproteobacteria, while most of the hosts of viunalikeviruses are of the Enterobacteriaceae belonging to Gammaproteobacteria. These phages may have evolved closely associated with their hosts that have very different life-styles in the natural habitats.

Trubanaman (TRUV) and Gan Gan (GGV) viruses are members of the tentatively assigned Mapputta group of the genus Orthobunyavirus within the family Bunyaviridae. Despite reported associations with an acute polyarthritis-like illness in Australia, TRUV and GGV have remained genetically uncharacterised. Here we report the complete genome sequences of TRUV and GGV which were originally isolated from mosquitoes in 1966 and 1970, respectively. Sequence and phylogenetic analyses indicate close relationships to other characterised viruses within the Mapputta group. These viruses exhibit the same characteristic features observed in other viruses in the group including the absence of the NSs (non-structural) ORF and an apparent absence of glycosylation sites on the Gn protein of GGV. We comment on the distribution of these viruses based on the available seroprevalence data and vector feeding preferences. The significance of this group of viruses to public health, in terms of unidentified polyarthritic disease, warrants further investigation.

Comparative genomic analysis aims to underscore genetic assortment diversification in distinct viral isolates, to identify deletions and to carry out evolutionary studies. We sequenced the first complete genome of an ASFV p72 genotype I strain isolated from domestic pigs in Sardinia (Italy) using Next-Generation Sequence (NGS) technology. The genome is 182,906 bp long, contains 164 ORFs and has a 99.20% nucleotide identity to the L60 strain. Comparison analysis against the 16 ASFV genomes available in the database showed that 136 ORFs are present in nine ASFV isolates annotated to date. The most divergent ORFs codify for uncharacterized proteins such as X69R and DP96R, which have 51.3% and 70.4% nucleotide identity to the other isolates. A comparison between the Sardinian isolate and the avirulent isolates OURT 88/3, NHV, BA71V was also carried out. Major variations were found within the multigene families (MGFs) located in the left and right genome regions.

First study on the complete genome characterization of Dengue-3 virus is reported from dengue endemic state Rajasthan, India. The genome of 10,672 base pairs was studied with reference to global and the regional genomes of Dengue-3 virus. 388 variations were observed in the nucleotide sequences with reference to the NCBI genome, including 34 variations in the amino acids. Of these 34 AA variations, 4 variations showed AA substitution in Envelope proteins and 1 in Anchored capsid region. The remaining 29 variations were observed in amino acids constituting non structural (NS) proteins. The reported mutations, especially those leading to amino acid variations in non-structural proteins of virus may influence the clinical profile of patients and accuracy of ongoing diagnostic tests. Reported amino acid variations in virus envelope may influence the immune response of patients. Phylogenetic studies showed similarity of reported genome with genomes from India, Pakistan and China.

Background

Cotton is a major cash crop of Pakistan and its production is mainly hindered by cotton leaf curl disease (CLCuD). This disease is caused by monopartite begomovirus associated with two satellites named as betasatellite and alphasatellite. Betasatellites are true satellites entirely dependent on helper begomoviruses and are symptom determinants which are essentially required for the typical symptoms of the disease. Alphasatellites are self-replicating circular ssDNA molecules which are associated with CLCuD complex. The role of alphasatellite is not fully understood.

Result

Cotton samples showing typical CLCuD symptoms were collected from areas across central Punjab, Pakistan during year 2011–12. All samples contained alphasatellites. Mixed-infection of alphasatellites associated with CLCuD complex was documented. Few samples showed the presence of more than one species of alphasatellite. A total of 45 alphasatellites were cloned and sequenced. The size of these alphasatellite ranges from 1362 to 1378 bp. All alphasatellites showed three conserved features i.e. 1) A stem-loop structure with a nonanucleotide (TAGTATTAC) sequence (2) An ORF encoding a Rep protein of about 36.6 kDa, having up to 315 amino acids (3) An A-rich region of ~ 200 nt. Based on BLAST results we have found six distinct species of alphasatellites namely; Gossypium darwinii symptomless alphasatellite (GDarSLA), Guar leaf curl alphasatellite (GrLCuA), Okra leaf curl alphasatellite (OLCuA), Tomato leaf curl Pakistan alphasatellite (ToLCPKA), Cotton leaf curl Multan alphasatellite (CLCuMA), and Cotton leaf curl Burewala alphasatellite (CLCuBuA). This was also confirmed by phylogenetic analysis. By considering the species cut-off limit for alphasatellites (83%) the isolates fall into 5 species. But the percentage identity between some CLCuBuA and CLCuMA was 83.3, so they are proposed to be considered as two different species.

Conclusion

Our data shows that at least six species of alphasatellites are found associated with cotton leaf curl disease in Pakistan. Field samples are often associated with multiple species and one sample was found associated with three distinct alphasatellites in a single plant under field conditions. Infection of multiple alphasatellite and their probable role in CLCuD are discussed.