Virology reports最新文献

Concomitant circulation of dengue and chikungunya viruses has been sporadically reported and needs to be individually diagnosed. Several sensitive molecular diagnostics are currently deployed for the diagnosis of both DENV and CHIKV, it is very difficult to delineate the two viral infections based on symptomology, as both share similar clinical presentation. Due to the overlapping nature of clinical signs in DENV and CHIKV infections, there is an urgent need for early and accurate diagnosis to avoid outbreaks aimed at initiating disease specific interventions. The study encompasses the diagnosis of clinically suspected 1024 DENV/CHIKV patient samples which were collected from AndhraPradesh (AP) and Kerala, India by using in-house developed RT-PCR (reverse transcription-polymerase chain reaction). The results show 43.8% DENV RNA infection and32% CHIKV RNA infection of the total samples obtained from AP. In contrast, samples from Kerala show dengue infection of 16.1%, CHIKV infection of 2.3%. In our study, we found that 23%, 0.1% of the samples were concomitant circulation for CHIKV/DENV in AP and Kerala respectively, suggesting the co-infection of these two viruses.

Human parainfluenza virus 4 (HPIV-4) subtypes 4a and 4b are seldom sought during molecular diagnostic screening of respiratory samples from patients with influenza like illnesses (ILIs). Nonetheless, HPIV-4a and HPIV-4b are to be found in such cases, occasionally in the absence of another pathogen. Little is known about the spectrum of genetic variation among HPIV-4 genotypes; thus the impact of genetic change on transmission, pathogenicity, and shedding cannot yet be quantified. We deduced the near-complete genome of a divergent genotype of HPIV-4a (QPID08-0015) identified in a respiratory tract sample from an adult with prolonged ILI in Victoria, Australia, in 2008. Two other variants had been previously reported from Denmark during 2002–2003 (HPIV-4a|DK(459)) and Japan in 2010 (HPIV-4a| 321-Yamagata-2010).

A novel concentration, enrichment, purification and amplification (CEPA) deep sequencing process yielded > 90% coverage of the 17,140 bp HPIV-4a-QPID08-0015 genome, including all coding and intergenic regions using material from a single stored clinical sample. Genomic variation was highest between coding regions (Alquezar-Planas et al., 2013).

Deep sequencing allowed identification and genomic characterisation of a possible pathogen from an ILI as well as being an important tool to aid future understanding of the linkages between viral genetic variation, transmission and disease prognosis.

Multiple novel simian adenoviruses have been isolated over the past years and their potential to cross the species barrier and infect the human population is an ever present threat. Here we describe the isolation and full genome sequencing of a novel simian adenovirus (SAdV) isolated from the urine of two independent, never co-housed, late stage simian immunodeficiency virus (SIV)-infected rhesus macaques. The viral genome sequences revealed a novel type with a unique genome length, GC content, E3 region and DNA polymerase amino acid sequence that is sufficiently distinct from all currently known human- or simian adenovirus species to warrant classifying these isolates as a novel species of simian adenovirus. This new species, termed Simian mastadenovirus D (SAdV-D), displays the standard genome organization for the genus Mastadenovirus containing only one copy of the fiber gene which sets it apart from the old world monkey adenovirus species HAdV-G, SAdV-B and SAdV-C.

Newcastle disease (ND) is a highly contagious disease of many avian species and is particularly responsible for devastating disease outbreaks in commercial poultry flocks in Pakistan that incur huge economic losses to the national poultry industry annually. Despite implementation of an extensive vaccination program for poultry birds, the disease appears in an endemic form in commercial broiler and layer poultry farms. This study was conducted to identify the prevalent velogenic NDV strain responsible for disease outbreaks in commercial poultry farms in Punjab, Pakistan. The NDV strains isolated from pathological specimens through inoculation in embryonated chicken eggs were characterized biologically through the intracerebral pathogenicity index (ICPI), and genetically on the basis of the fusion (F) protein cleavage site. Among these, six NDV isolates showed an F protein cleavage site motif (¹¹²RRQKRF¹¹⁷) and an ICPI value ranging between 1.5 and 1.88, both are characteristics for velogenic strains of NDV. In addition, phylogenetic analysis based on a partial sequence of the F protein gene clustered these isolates within class II, genotype VII and specifically within genotype VII-e. This is the first report that demonstrated the presence of such NDV strains in commercial poultry farms in northern Punjab of Pakistan.

Rhabdoviridae represent a diverse group of viruses with the potential to cause disease in humans, animals and plants. Currently there are nine genera in the family; however a large number of rhabdoviruses remain unassigned. Here we characterise three novel rhabdoviruses genomes. Almpiwar virus (ALMV), isolated from skinks in northern Queensland, is the first completely sequenced rhabdovirus from squamates, with serological studies indicating multiple animal host species. Harrison Dam virus (HARDV) and Walkabout Creek virus (WACV) were isolated from mosquitoes in the Northern Territory and biting midges in southern Queensland respectively and their vertebrate hosts remain unknown. Serological cross-neutralisation tests with other Australian rhabdoviruses indicate that ALMV, WACV and HARDV are distinct viruses with little antigenic cross-reactivity. Next-generation sequencing revealed that all viruses encode the core proteins common to rhabdoviruses (N, P, M, G and L), plus additional ORFs between the M and G genes. HARDV also contains a small ORF between the G and L genes. Phylogenetic analysis of N and L proteins suggests that HARDV and WACV share a common lineage with the tupaviruses and Sandjimba group, whereas ALMV is a distinct and divergent virus showing no clear relationship to any rhabdovirus except the recently characterised Niahka virus (NIAV).

After a 75-year absence from Florida, substantial local transmission of dengue virus (DENV) occurred in Key West, Monroe County, Florida in 2009 and continued in 2010. The outbreak culminated in 85 reported cases. In 2011 and 2012, only isolated cases of local DENV transmission were reported in Florida; none were reported in Key West. In 2013, a new outbreak occurred, but this time in Martin County about 275 miles north of Key West with 22 reported cases. As the Key West and Martin County outbreaks involved DENV serotype 1 (DENV-1), we wanted to investigate whether the same strain or a different strain of DENV was responsible for the outbreaks. In this study, we report the sequence and phylogenetic analysis of the E gene region from a patient diagnosed with dengue in Martin County. Our results indicate that the 2013 Martin County DENV-1 strain is distinct from the 2009–2010 Key West DENV-1 and that it is most closely related to viruses from a recent expansion of South American DENV-1 strains into the Caribbean. We conclude that the 2013 Martin County outbreak was the result of a new introduction of DENV-1 in Florida.