Identification of a Novel Picorna-Like Virus, Burpengary Virus, That Is Negatively Associated with Chlamydial Disease in the Koala

Koalas (Phascolarctos cinereus) are native Australian marsupials whose populations are in decline from a range of threats. Infectious diseases caused by the bacterium Chlamydia pecorum and other pathogens are of particular concern. We analysed 26 poly-A selected RNA-sequencing libraries from a data set designed to study the immune response of koalas to ocular chlamydial infection. Using virus discovery techniques, we identified the coding-complete genome sequence of a novel picorna-like virus, denoted Burpengary virus, that was most common in south-east Queensland. Notably, abundance measurements of the virus across all 26 libraries revealed an inverse relationship in prevalence with ocular disease in Koalas, suggesting that co-infection between Burpengary virus and Chlamydia pecorum is inhibited.

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Identification of A Novel Picorna-Like Virus, Burpengary Virus, that is Negatively Associated with Chlamydial Disease in the Koala

Viruses ◽

10.3390/v11030211 ◽

2019 ◽

Vol 11 (3) ◽

pp. 211 ◽

Cited By ~ 3

Author(s):

Erin Harvey ◽

Danielle Madden ◽

Adam Polkinghorne ◽

Edward Holmes

Keyword(s):

Immune Response ◽

Infectious Diseases ◽

Complete Genome Sequence ◽

Complete Genome ◽

Chlamydial Infection ◽

Inverse Relationship ◽

Virus Discovery ◽

Data Set ◽

Phascolarctos Cinereus ◽

Chlamydia Pecorum

Koalas (Phascolarctos cinereus) are native Australian marsupials whose populations are in decline from a range of threats. Infectious diseases caused by the bacterium Chlamydia pecorum and other pathogens are of particular concern. We analysed 26 poly-A selected RNA-sequencing libraries from a data set designed to study the immune response of koalas to ocular chlamydial infection. Using virus discovery techniques, we identified the coding-complete genome sequence of a novel picorna-like virus, denoted Burpengary virus, that was most common in south-east Queensland. Notably, abundance measurements of the virus across all 26 libraries revealed an inverse relationship between abundance and ocular disease in koalas, suggesting that the co-infection of Burpengary virus and Chlamydia pecorum is inhibited.

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The Koala Immune Response to Chlamydial Infection and Vaccine Development—Advancing Our Immunological Understanding

Animals ◽

10.3390/ani11020380 ◽

2021 ◽

Vol 11 (2) ◽

pp. 380

Author(s):

Bonnie L Quigley ◽

Peter Timms

Keyword(s):

Immune Response ◽

Chlamydial Infection ◽

Vaccine Development ◽

Interleukin 17 ◽

Phascolarctos Cinereus ◽

Post Vaccination ◽

Research Systems ◽

Cytokine Levels ◽

Nucleic Acid Assay ◽

Immunological Research

Chlamydia is a significant pathogen for many species, including the much-loved Australian marsupial, the koala (Phascolarctos cinereus). To combat this situation, focused research has gone into the development and refinement of a chlamydial vaccine for koalas. The foundation of this process has involved characterising the immune response of koalas to both natural chlamydial infection as well as vaccination. From parallels in human and mouse research, it is well-established that an effective anti-chlamydial response will involve a balance of cell-mediated Th1 responses involving interferon-gamma (IFN-γ), humoral Th2 responses involving systemic IgG and mucosal IgA, and inflammatory Th17 responses involving interleukin 17 (IL-17) and neutrophils. Characterisation of koalas with chlamydial disease has shown increased expression within all three of these major immunological pathways and monitoring of koalas’ post-vaccination has detected further enhancements to these key pathways. These findings offer optimism that a chlamydial vaccine for wider distribution to koalas is not far off. Recent advances in marsupial genetic knowledge and general nucleic acid assay technology have moved koala immunological research a step closer to other mammalian research systems. However, koala-specific reagents to directly assay cytokine levels and cell-surface markers are still needed to progress our understanding of koala immunology.

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Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014

Genome Announcements ◽

10.1128/genomea.01646-15 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 2

Author(s):

Steven Van Borm ◽

Toon Rosseel ◽

Isabelle Behaeghel ◽

Marc Saulmont ◽

Laurent Delooz ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Data Set ◽

Protein Coding ◽

Protein Coding Genes ◽

Metagenomics Data ◽

Bovine Polyomavirus

The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set. The 4,697-bp circular dsDNA genome contains 6 protein-coding genes. Bovine polyomavirus is unlikely to be causally related to the abortion cases.

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Complete Genome Sequence of a Polyomavirus Recovered from a Pomona Leaf-Nosed Bat (Hipposideros pomona) Metagenome Data Set

Genome Announcements ◽

10.1128/genomea.01053-16 ◽

2017 ◽

Vol 5 (3) ◽

Cited By ~ 6

Author(s):

Paul G. Cantalupo ◽

Christopher B. Buck ◽

James M. Pipas

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Phylogenetic Relationships ◽

Complete Genome ◽

Data Set ◽

Content Type ◽

Genetic Organization

ABSTRACT We report here the complete genome sequence of a polyomavirus found in a nasal/rectal metagenome of Hipposideros pomona (Pomona leaf-nosed bat). Interestingly, the genetic organization and phylogenetic relationships of the new virus suggest greater similarity to recently discovered fish-associated polyomaviruses rather than to polyomavirus species previously observed in bats.

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Coding-Complete Genome Sequence of a Pollen-Associated Virus Belonging to the Secoviridae Family Recovered from a Japanese Apricot (Prunus mume) Metagenome Data Set

Microbiology Resource Announcements ◽

10.1128/mra.00881-19 ◽

2019 ◽

Vol 8 (40) ◽

Cited By ~ 1

Author(s):

Andrea M. Fetters ◽

Paul G. Cantalupo ◽

Tia-Lynn Ashman ◽

James M. Pipas

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Prunus Mume ◽

Japanese Apricot ◽

Data Set ◽

Content Type

We report the coding-complete genome sequence of Japanese apricot pollen-associated secovirus 1 (JAPSV1), a virus belonging to the Secoviridae family, recovered from Japanese apricot (Prunus mume) pollen that is closely related to Peach leaf pitting-associated virus (PLPAV). This discovery adds to the number of known pollen-associated viruses.

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Exceptional Convergent Evolution in a Virus

Genetics ◽

10.1093/genetics/147.4.1497 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1497-1507 ◽

Cited By ~ 20

Author(s):

J J Bull ◽

M R Badgett ◽

H A Wichman ◽

J P Huelsenbeck ◽

D M Hillis ◽

...

Keyword(s):

High Temperature ◽

Complete Genome Sequence ◽

Complete Genome ◽

Convergent Evolution ◽

Evolutionary History ◽

Initial Period ◽

Phylogenetic Reconstruction ◽

The Other ◽

Data Set ◽

Phage Propagation

Abstract Replicate lineages of the bacteriophage ϕX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

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The koala immunological toolkit: sequence identification and comparison of key markers of the koala (Phascolarctos cinereus) immune response

Australian Journal of Zoology ◽

10.1071/zo13105 ◽

2014 ◽

Vol 62 (3) ◽

pp. 195 ◽

Cited By ~ 12

Author(s):

Katrina Morris ◽

Peter J. Prentis ◽

Denis O'Meally ◽

Ana Pavasovic ◽

Alyce Taylor Brown ◽

...

Keyword(s):

Immune Response ◽

Infectious Diseases ◽

Adaptive Immune Response ◽

Population Declines ◽

Th2 Response ◽

Phascolarctos Cinereus ◽

Origin And Evolution ◽

Adaptive Immune ◽

Sequence Identification ◽

Species Specific

The koala (Phascolarctos cinereus) is an Australian marsupial that continues to experience significant population declines. Infectious diseases caused by pathogens such as Chlamydia are proposed to have a major role. Very few species-specific immunological reagents are available, severely hindering our ability to respond to the threat of infectious diseases in the koala. In this study, we utilise data from the sequencing of the koala transcriptome to identify key immunological markers of the koala adaptive immune response and cytokines known to be important in the host response to chlamydial infection in other species. This report describes the identification and preliminary sequence analysis of (1) T lymphocyte glycoprotein markers (CD4, CD8); (2) IL-4, a marker for the Th2 response; (3) cytokines such as IL-6, IL-12 and IL-1β, that have been shown to have a role in chlamydial clearance and pathology in other hosts; and (4) the sequences for the koala immunoglobulins, IgA, IgG, IgE and IgM. These sequences will enable the development of a range of immunological reagents for understanding the koala’s innate and adaptive immune responses, while also providing a resource that will enable continued investigations into the origin and evolution of the marsupial immune system.

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