Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies.

The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.

Draft Genome Sequence of a Novel Adenovirus Recovered from the Metagenome of Agile Wallabies.

Here, we report the draft genome sequence of a novel agile wallaby adenovirus that was detected in the fecal metagenome of agile wallabies. The genome is 31,512 bp long, with a G+C content of 34.4%. Currently, the pathogenic and zoonotic potential of this novel virus is unknown.

Detection of enteric viral and bacterial pathogens associated with paediatric diarrhoea in Goroka, Papua New Guinea.

OBJECTIVES: The aim of this study was to investigate the viral and bacterial causes of acute watery diarrhoea in hospitalized children in Papua New Guinea. METHODS: A retrospective analysis was conducted on stool samples collected from 199 children (age <5 years) admitted to the paediatric ward of Goroka General Hospital from August 2009 through November 2010. A large range of viral and bacterial enteric pathogens were targeted using real-time PCR/RT-PCR assays. RESULTS: Young children were much more likely to be admitted with acute gastroenteritis, with 62.8% of patients aged <1 year and 88.4% aged <2 years. An enteric pathogen was detected in 69.8% (n=138) of patients. The most commonly detected pathogens were Shigella spp (26.6%), rotavirus (25.6%), adenovirus types 40/41 (11.6%), enterotoxigenic Escherichia coli (11.1%), enteropathogenic E. coli (8.5%), norovirus G2 (6.0%), and Campylobacter spp (4.0%). Norovirus G1, sapovirus, and Salmonella spp were also detected, but below our statistical limit of detection. Vibrio cholerae and astrovirus were not detected in any patients. Mixed infections were detected in 22.1% of patients, with Shigella and rotavirus most commonly detected in co-infections with other pathogens. CONCLUSIONS: This study demonstrates that Shigella and rotavirus are the major pathogens associated with acute paediatric gastroenteritis in this setting.

Viruses associated with influenza-like-illnesses in Papua New Guinea, 2010.

Influenza-like-illness can be caused by a wide range of respiratory viruses. The etiology of influenza-like-illness in developing countries such as Papua New Guinea is poorly understood. The etiological agents associated with influenza-like-illness were investigated retrospectively for 300 nasopharyngeal swabs received by the Papua New Guinea National Influenza Centre in 2010. Real-time PCR/RT-PCR methods were used for the detection of 13 respiratory viruses. Patients with influenza-like-illness were identified according to the World Health Organization case definition: sudden onset of fever (>38°C), with cough and/or sore throat, in the absence of other diagnoses. At least one viral respiratory pathogen was detected in 66.3% of the samples tested. Rhinoviruses (17.0%), influenza A (16.7%), and influenza B (12.7%) were the pathogens detected most frequently. Children <5 years of age presented with a significantly higher rate of at least one viral pathogen and a significantly higher rate of co-infections with multiple viruses, when compared to all other patients >5 years of age. Influenza B, adenovirus, and respiratory syncytial virus were all detected at significantly higher rates in children <5 years of age. This study confirmed that multiple respiratory viruses are circulating and contributing to the presentation of influenza-like-illness in Papua New Guinea.

Outbreak of chikungunya virus infection, Vanimo, Papua New Guinea.

In June 2012, health authorities in Papua New Guinea detected an increase in febrile illnesses in Vanimo. Chikungunya virus of the Eastern/Central/Southern African genotype harboring the E1:A226V mutation was identified. This ongoing outbreak has spread to ≥8 other provinces and has had a harmful effect on public health.

Evaluation of a rapid immunochromatographic assay for the detection of rotavirus, norovirus and adenovirus from children hospitalized with acute watery diarrhea.

We evaluated the IP-Triple I immunochromatographic rapid test for the detection of rotavirus, norovirus and adenovirus using stool samples from children with diarrhoea. The detection of norovirus and adenovirus was poor compared to polymerase chain reaction assays. However, high sensitivity (92%) and specificity (99%) were obtained for the detection of rotavirus.