Identification and Characterization of Novel Human Endogenous Retrovirus Families by Phylogenetic Screening of the Human Genome Mapping Project Database

doi:10.1128/JVI.74.8.3715-3730.2000

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Journal of Virology, April 2000, p. 3715-3730, Vol. 74, No. 8
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Identification and Characterization of Novel Human Endogenous Retrovirus Families by Phylogenetic Screening of the Human Genome Mapping Project Database

Michael Tristem^*

Department of Biology, Imperial College, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom

Received 19 October 1999/Accepted 25 January 2000

Human endogenous retroviruses (HERVs) were first identified almost 20 years ago, and since then numerous families have beendescribed. It has, however, been difficult to obtain a good estimateof both the total number of independently derived families andtheir relationship to each other as well as to other members ofthe family Retroviridae. In this study, I used sequence data derivedfrom over 150 novel HERVs, obtained from the Human Genome MappingProject database, and a variety of recently identified nonhumanretroviruses to classify the HERVs into 22 independently acquiredfamilies. Of these, 17 families were loosely assigned to the classI HERVs, 3 to the class II HERVs and 2 to the class III HERVs.Many of these families have been identified previously, but sixare described here for the first time and another four, for whichonly partial sequence information was previously available, werefurther characterized. Members of each of the 10 families aredefective, and calculation of their integration dates suggestedthat most of them are likely to have been present within the humanlineage since it diverged from the Old World monkeys more than25 million yearsago.

^* Mailing address: Department of Biology, Imperial College, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom. Phone: (1344)294 373. Fax: (1344) 294 339. E-mail: m.tristem{at}ic.ac.uk.

Journal of Virology, April 2000, p. 3715-3730, Vol. 74, No. 8
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

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