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1.
Emerg Infect Dis ; 27(12): 3185-3188, 2021 12.
Article in English | MEDLINE | ID: mdl-34708683

ABSTRACT

In June 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases surged in Liberia. SARS-CoV-2 sequences from patients hospitalized during March-July 2021 revealed the Delta variant was in Liberia in early March and was dominant in June, irrespective of geography. Mutations and deletions suggest multiple SARS-CoV-2 Delta variant introductions.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Liberia/epidemiology , Sequence Analysis
2.
BMC Bioinformatics ; 16: 416, 2015 Dec 29.
Article in English | MEDLINE | ID: mdl-26714571

ABSTRACT

BACKGROUND: The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. RESULTS: The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. CONCLUSIONS: By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.


Subject(s)
User-Computer Interface , Algorithms , Animals , Arenavirus/genetics , Arenavirus/isolation & purification , Computational Biology , Coronavirus/genetics , Coronavirus/isolation & purification , Databases, Factual , Flavivirus/genetics , Flavivirus/isolation & purification , High-Throughput Nucleotide Sequencing , Humans , Internet , RNA, Viral/chemistry , RNA, Viral/metabolism , Sequence Analysis, RNA
3.
Nat Commun ; 6: 8147, 2015 Sep 22.
Article in English | MEDLINE | ID: mdl-26391192

ABSTRACT

It is currently unclear whether changes in viral communities will ever be predictable. Here we investigate whether viral communities in wildlife are inherently structured (inferring predictability) by looking at whether communities are assembled through deterministic (often predictable) or stochastic (not predictable) processes. We sample macaque faeces across nine sites in Bangladesh and use consensus PCR and sequencing to discover 184 viruses from 14 viral families. We then use network modelling and statistical null-hypothesis testing to show the presence of non-random deterministic patterns at different scales, between sites and within individuals. We show that the effects of determinism are not absolute however, as stochastic patterns are also observed. In showing that determinism is an important process in viral community assembly we conclude that it should be possible to forecast changes to some portion of a viral community, however there will always be some portion for which prediction will be unlikely.


Subject(s)
Feces/virology , Genetic Variation , Macaca mulatta , Monkey Diseases/virology , Virus Diseases/veterinary , Viruses/genetics , Animals , Animals, Wild , Bangladesh/epidemiology , Molecular Sequence Data , Monkey Diseases/epidemiology , Virus Diseases/epidemiology , Virus Diseases/virology
4.
Virol J ; 11: 144, 2014 Aug 08.
Article in English | MEDLINE | ID: mdl-25106433

ABSTRACT

BACKGROUND: Respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified. FINDINGS: Pneumonia, tracheitis and esophagitis were reported in a collection of ball pythons (Python regius). Eight of 12 snakes had evidence of bacterial pneumonia. High-throughput sequencing of total extracted nucleic acids from lung, esophagus and spleen revealed a novel nidovirus. PCR indicated the presence of viral RNA in lung, trachea, esophagus, liver, and spleen. In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. CONCLUSIONS: This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses.


Subject(s)
Animal Diseases/epidemiology , Boidae/virology , Nidovirales Infections/veterinary , Nidovirales/genetics , Respiratory Tract Diseases/veterinary , Animal Diseases/pathology , Animal Diseases/virology , Animals , Disease Outbreaks , Female , Male , Molecular Sequence Data , Nidovirales/classification , Phylogeny , RNA, Viral/genetics , Sequence Analysis, DNA
5.
Virus Res ; 160(1-2): 206-13, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21740935

ABSTRACT

K13965, an uncharacterized virus, was isolated in 1993 from Anopheles annulipes mosquitoes collected in the Kimberley region of northern Western Australia. Here, we report its genomic sequence, identify it as a rhabdovirus, and characterize its phylogenetic relationships. The genome comprises a P' (C) and SH protein similar to the recently characterized Tupaia and Durham viruses, and shows overlap between G and L genes. Comparison of K13965 genome sequence to other rhabdoviruses identified K13965 as a strain of the unclassified Australian Oak Vale rhabdovirus, whose complete genome sequence we also determined. Phylogenetic analysis of N and L sequences indicated genetic relationship to a recently proposed Sandjima virus clade, although the Oak Vale virus sequences form a branch separate from the African members of that group.


Subject(s)
Anopheles/virology , Genome, Viral , Rhabdoviridae/genetics , Rhabdoviridae/isolation & purification , Sequence Analysis, DNA , Animals , Cluster Analysis , Female , Molecular Sequence Data , Phylogeny , RNA, Viral/genetics , Viral Proteins/genetics , Western Australia
6.
mBio ; 1(4)2010 Oct 12.
Article in English | MEDLINE | ID: mdl-21063474

ABSTRACT

Bats are reservoirs for emerging zoonotic viruses that can have a profound impact on human and animal health, including lyssaviruses, filoviruses, paramyxoviruses, and severe acute respiratory syndrome coronaviruses (SARS-CoVs). In the course of a project focused on pathogen discovery in contexts where human-bat contact might facilitate more efficient interspecies transmission of viruses, we surveyed gastrointestinal tissue obtained from bats collected in caves in Nigeria that are frequented by humans. Coronavirus consensus PCR and unbiased high-throughput pyrosequencing revealed the presence of coronavirus sequences related to those of SARS-CoV in a Commerson's leaf-nosed bat (Hipposideros commersoni). Additional genomic sequencing indicated that this virus, unlike subgroup 2b CoVs, which includes SARS-CoV, is unique, comprising three overlapping open reading frames between the M and N genes and two conserved stem-loop II motifs. Phylogenetic analyses in conjunction with these features suggest that this virus represents a new subgroup within group 2 CoVs.


Subject(s)
Chiroptera/virology , Disease Reservoirs/virology , Severe Acute Respiratory Syndrome/virology , Severe acute respiratory syndrome-related coronavirus/isolation & purification , Animals , Humans , Molecular Sequence Data , Nigeria , Phylogeny , Severe acute respiratory syndrome-related coronavirus/classification , Severe acute respiratory syndrome-related coronavirus/genetics , Severe Acute Respiratory Syndrome/transmission
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