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Divergent patterns of recent retroviral integrations in the human and chimpanzee genomes: probable transmissions between other primates and chimpanzees
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. (Blomberg)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. (Sperber)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. (Blomberg)
2006 (English)In: Journal of Virology, ISSN 0022-538X, E-ISSN 1098-5514, Vol. 80, no 3, 1367-1375 p.Article in journal (Refereed) Published
Abstract [en]

The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence. The sequencing of the human (Homo sapiens) and chimpanzee (Pan troglodytes) genomes has facilitated the evolutionary study of ERVs and related sequences. We screened both the human genome (version hg16) and the chimpanzee genome (version PanTro1) for ERVs and conducted a phylogenetic analysis of recent integrations. We found a number of recent integrations within both genomes. They segregated into four groups. Two larger gammaretrovirus-like groups (PtG1 and PtG2) occurred in chimpanzees but not in humans. The PtG sequences were most similar to two baboon ERVs and a macaque sequence but neither to other chimpanzee ERVs nor to any human gammaretrovirus-like ERVs. The pattern was consistent with cross-species transfer via predation. This appears to be an example of horizontal transfer of retroviruses with occasional fixation in the germ line.

Place, publisher, year, edition, pages
2006. Vol. 80, no 3, 1367-1375 p.
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-82748DOI: 10.1128/JVI.80.3.1367-1375.2006.PubMedID: 16415014OAI: oai:DiVA.org:uu-82748DiVA: diva2:110654
Available from: 2006-09-30 Created: 2006-09-30 Last updated: 2011-01-12Bibliographically approved
In thesis
1. Genomic Variation and Evolution of HERV-H and other Endogenous Retroviruses (ERVs)
Open this publication in new window or tab >>Genomic Variation and Evolution of HERV-H and other Endogenous Retroviruses (ERVs)
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

An exogenous retrovirus (XRV) that integrates into a germ cell may be inherited as a Mendelian gene; it becomes an endogenous retrovirus (ERV). The human genome consists of up to 8% HERVs.

The gammaretroviral (ERV class I) HERV-H, with 926 members, is the largest ERV group. Despite millions of years since integration, it has polymorphic envelope open reading frames in at least three loci. Selections for functional envelopes are indicated on chromosomes 1 and 2. However, envelopes were present only in a fraction of the total HERV-H. Mutated polymerases, indicating old ERVs, contradicted relatively intact long terminal repeats. To explain this, we formulated a “Midwife” element theory where proteins are complemented in trans.

A phylogenetic analysis did not support separate HERV-H and -F groups. The new taxonomy included HERV-H like (RGH2-like and RTVLH2-like subgroups) and Adjacent HERV-H like. A bioinformatic reconstruction of a putative ancestral HERV-H exposed novel traits. Two nucleocapsid zinc fingers and a pronounced nucleotide bias for C in the HERV-H like were unique among the gammaretroviruses.

Two recently integrated gammaretroviral groups (PtNeo-I[PTERV1] and -II) were found in chimpanzees but not in humans. The PtNeo groups were most similar to baboon ERVs and a macaque sequence, but neither to other chimpanzee nor to any human gammaretroviruses. The pattern was consistent with cross-species transfer via predation.

To advance the retroviral taxonomy, we projected structural markers over sequence phylogenetic trees. A number of markers were useful to distinguish between genera and to delineate groups.

Basic retroviral knowledge is vital to understand emerging infections. Phylogenetic analyses of taxonomically improved sequences, facilitates the search for common retroviral denominators to target. This thesis provided new insights in retroviral evolution and taxonomy using the ERVs, with special focus on the large gammaretroviral HERV-H group, as an additional source of information next to that of XRVs.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2005. 77 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 62
Keyword
Microbiology, Endogenous Retrovirus (ERV), HERV-H, Phylogeny, Evolution, Sequence Variation, Polymorphism, Recent Integrations, Horizontal Transfer, Master Elements, Taxonomy, Mikrobiologi
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-5906 (URN)91-554-6319-3 (ISBN)
Public defence
2005-10-01, Föreläsningssalen, Klinisk virologi, Akademiska Sjukhuset, ing. D1, Dag Hammarkjölds väg 17, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2005-09-09 Created: 2005-09-09 Last updated: 2011-09-06Bibliographically approved

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Jern, PatricSperber, GöranBlomberg, Jonas

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