Novel, Divergent Simian Hemorrhagic Fever Viruses in a Wild Ugandan Red Colobus Monkey Discovered Using Direct Pyrosequencing

Lauck, Michael; Holzmann, David; Tumukunde, Alex; Weny, Geoffrey; Lank, Simon M.; Chapman, Colin A.; O’Connor, David H.; Friedrich, Thomas C.; Goldberg, Tony L.

doi:10.1371/journal.pone.0019056

Cited by 67 publications

(95 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Black-and-white colobus (BWC) monkeys were sampled from Kibale National Park, Uganda, a 795-km 2 forested park in Western Uganda (0°13=-0°41ЉN, 30°19=-30°32ЉE) known for its exceptional primate diversity and biomass (16). As part of a long-term study of primate ecology and health (17), nine animals were immobilized and sampled as previously described (18). All animal protocols received prior approval from the Uganda National Council for Science and Technology, the Uganda Wildlife Authority, and the University of Wisconsin Animal Care and Use Committee, and all samples were shipped in accordance with international laws under Ugandan CITES permit no.…”

Section: Methodsmentioning

confidence: 99%

A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate

Lauck

Sibley

Lara

et al. 2013

J Virol

Self Cite

View full text Add to dashboard Cite

h GB virus B (GBV-B; family Flaviviridae, genus Hepacivirus) has been studied in New World primates as a model for human hepatitis C virus infection, but the distribution of GBV-B and its relatives in nature has remained obscure. Here, we report the discovery of a novel and highly divergent GBV-B-like virus in an Old World monkey, the black-and-white colobus (Colobus guereza), in Uganda. The new virus, guereza hepacivirus (GHV), clusters phylogenetically with GBV-B and recently described hepaciviruses infecting African bats and North American rodents, and it shows evidence of ancient recombination with these other hepaciviruses. Direct sequencing of reverse-transcribed RNA from blood plasma from three of nine colobus monkeys yielded near-complete GHV genomes, comprising two distinct viral variants. The viruses contain an exceptionally long nonstructural 5A (NS5A) gene, approximately half of which codes for a protein with no discernible homology to known proteins. Computational structure-based analyses indicate that the amino terminus of the GHV NS5A protein may serve a zinc-binding function, similar to the NS5A of other viruses within the family Flaviviridae. However, the 521-amino-acid carboxy terminus is intrinsically disordered, reflecting an unusual degree of structural plasticity and polyfunctionality. These findings shed new light on the natural history and evolution of the hepaciviruses and on the extent of structural variation within the Flaviviridae.

show abstract

Section: Methodsmentioning

confidence: 99%

A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate

Lauck

Sibley

Lara

et al. 2013

J Virol

Self Cite

View full text Add to dashboard Cite

show abstract

“…Blood samples from Kibale olive baboons (Papio anubis) were collected from 2010 to 2014 as described previously (13), and collection of the samples was approved by the Uganda Wildlife Authority (permit UWA/TDO/33/02), the Uganda National Council for Science and Technology (permit HS 364), and the University of Wisconsin Animal Care and Use Committee (protocol V01409-0-02-09). Samples from Mikumi yellow baboons (Papio cynocephalus) were collected by Jeffrey Rogers and colleagues in 1985 and 1986 using standard methods for field studies of baboons, as described previously (17).…”

Section: Methodsmentioning

confidence: 99%

“…Importantly, simian arterivirus infection has never been demonstrated in a free-living patas monkey, and monkeys from the two species known to harbor simian arteriviruses in nature, the red colobus (Procolobus rufomitratus tephrosceles) and the red-tailed guenon (Cercopithecus ascanius schmidti), were not associated with past outbreaks of SHF in macaques (2,13,14). Grivets (Chlorocebus aethiops) and baboons (genus Papio) have long been suspected of harboring simian arteriviruses in captivity, but empirical evidence demonstrating infection of these hosts, either in the wild or in captivity, has, to our knowledge, never been presented (6,15).…”

mentioning

confidence: 99%

Two Novel Simian Arteriviruses in Captive and Wild Baboons (Papio spp.)

Bailey

Lauck

Sibley

et al. 2014

J Virol

Self Cite

View full text Add to dashboard Cite

Since the 1960s, simian hemorrhagic fever virus (SHFV; Nidovirales, Arteriviridae) has caused highly fatal outbreaks of viral hemorrhagic fever in captive Asian macaque colonies. However, the source(s) of these outbreaks and the natural reservoir(s) of this virus remain obscure. Here we report the identification of two novel, highly divergent simian arteriviruses related to SHFV, Mikumi yellow baboon virus 1 (MYBV-1) and Southwest baboon virus 1 (SWBV-1), in wild and captive baboons, respectively, and demonstrate the recent transmission of SWBV-1 among captive baboons. These findings extend our knowledge of the genetic and geographic diversity of the simian arteriviruses, identify baboons as a natural host of these viruses, and provide further evidence that baboons may have played a role in previous outbreaks of simian hemorrhagic fever in macaques, as has long been suspected. This knowledge should aid in the prevention of disease outbreaks in captive macaques and supports the growing body of evidence that suggests that simian arterivirus infections are common in Old World monkeys of many different species throughout Africa. IMPORTANCEHistorically, the emergence of primate viruses both in humans and in other primate species has caused devastating outbreaks of disease. One strategy for preventing the emergence of novel primate pathogens is to identify microbes with the potential for cross-species transmission in their natural state within reservoir species from which they might emerge. Here, we detail the discovery and characterization of two related simian members of the Arteriviridae family that have a history of disease emergence and host switching. Our results expand the phylogenetic and geographic range of the simian arteriviruses and define baboons as a natural host for these viruses. Our findings also identify a potential threat to captive macaque colonies by showing that simian arteriviruses are actively circulating in captive baboons.

show abstract

“…The resulting libraries exhibit even coverage across the human genome when constructed from low amounts of genomic DNA (Adey et al 2010). Transposon-based library construction has also been successfully applied to pyrosequencing of the RNA genomes of strains of simian hemorrhagic fever virus (Lauck et al 2011). The success of transposon-based genomic library construction for genomic analyses suggests that it should be possible to use transposases to construct high-quality RNA-seq libraries.…”

mentioning

confidence: 99%

Transposase mediated construction of RNA-seq libraries

Gertz¹,

Varley²,

Davis³

et al. 2011

Genome Res.

102

View full text Add to dashboard Cite

RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with only two enzymatic reactions. We generated high-quality RNA-seq libraries from as little as 10 pg of mRNA (~1 ng of total RNA) with this approach. We also present a strand-specific RNA-seq library construction protocol that combines transposon-based library construction with uracil DNA glycosylase and endonuclease VIII to specifically degrade the second strand constructed during cDNA synthesis. The directional RNA-seq libraries maintain the same quality as the nondirectional libraries, while showing a high degree of strand specificity, such that 99.5% of reads map to the expected genomic strand. Each transposon-based library construction method performed well when compared with standard RNA-seq library construction methods with regard to complexity of the libraries, correlation between biological replicates, and the percentage of reads that align to the genome as well as exons. Our results show that high-quality RNA-seq libraries can be constructed efficiently and in an automatable fashion using transposition technology.

show abstract

Novel, Divergent Simian Hemorrhagic Fever Viruses in a Wild Ugandan Red Colobus Monkey Discovered Using Direct Pyrosequencing

Cited by 67 publications

References 26 publications

A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate

A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate

Two Novel Simian Arteriviruses in Captive and Wild Baboons (Papio spp.)

Transposase mediated construction of RNA-seq libraries

Contact Info

Product

Resources

About