CoChat
Sign Up
Cited by 315

The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.

Classification and characterization of human endogenous retroviruses; mosaic forms are common

Vargiu, Laura, Rodriguez-Tomé, Patricia, Sperber, Göran O., Cadeddu, Marta, Grandi, Nicole, Blikstad, Vidar, Tramontano, Enzo, Blomberg, Jonas·2016·Retrovirology
DOI 10.1186/s12977-015-0232-yPMC PMC4724089
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s12977-015-0232-y

Cites

10 of 10 references verified0 citation errors · 0 not checkable

Statistics

Figures

Fig. 1 Some retroviral genetic structures encountered during this work. a Prototypical provirus, with genes and subgenes. Abbreviations are explained in the text, and/or in [35]. dUTPase occurred in either the protease or polymerase genes. b Partial, truncated, provirus. c Provirus with secondary integration, often an LTR in sense or antisense direction. d Recombinant provirus with contributions from different ERVs, in this case a Harlequin element. e Processed pseudogene, i.e. a reverse transcribed genomic retroviral mRNA. Processed pseudogenes were not distinguished from proviruses in the present work
Fig. 1 Some retroviral genetic structures encountered during this work. a Prototypical provirus, with genes and subgenes. Abbreviations are explained in the text, and/or in [35]. dUTPase occurred in either the protease or polymerase genes. b Partial, truncated, provirus. c Provirus with secondary integration, often an LTR in sense or antisense direction. d Recombinant provirus with contributions from different ERVs, in this case a Harlequin element. e Processed pseudogene, i.e. a reverse transcribed genomic retroviral mRNA. Processed pseudogenes were not distinguished from proviruses in the present workCC BY · PubMed Central
Fig. 2 Simages. Panel a The principle. A proviral sequence is divided into twentieths, each of which is BLASTed against a reference sequence collection. 1 A homogeneous, canonical, provirus. 2 A heterogeneous, noncanonical, provirus. Panel b A canonical chain. The chain id (“rvnr” in Additional file 1: Table S1), HERV classification, the chromosomal position and LTR divergence (if both LTRs were recognized by ReTe) are shown in the uppermost row. The subsequent three rows depict the RepeatMasker nucleic acids with the highest degree of identity, the next three rows which of the 39 consensus sequences determined in this paper (Additional file 3: List S3) has the highest degree of identity, all per twentieth of the chain. The lowest row depicts the ReTe putein interpretation per twentieth. 5 means 5′LTR, G Gag, R Pro, P Pol, E Env and 3 3′LTR. Panel c Three noncanonical chains containing secondary integrations which left a single LTR inside another retroviral chain. Annotation as in b. Colour is used here and in ensuing panels to distinguish components of mosaic chains. C1: HML4 LTR inside an HML2. LTR5 and HERVK refer to HML2. LTR13 is an HML4 LTR. C2: HERV9 LTR inside a HERVH. LTR12 and HylERV9-LTR are HERV9 LTR equivalents. A small pol piece most similar to HERVE is also present. C3: HML2 inside a HERVH. HylNERVH1 and HylNERVH2 are HERVH equivalents (see Additional file 2: List S2). LTR5 is an HML2 LTR. “0” depicts that no similarity was found with the respective query sequences. Panel d Noncanonical chains with signs of recombination. Annotation as in b. D1: HERV9 chain with a short piece similar to HERVIP at the end of pol and beginning of env. D2: a mosaic HERVE with HERVIP, HERVW and HML10 inside. ReTe recognized mainly one gene, env. As described in the text, this is a common pattern for chains labeled as “Harlequin”. D3: a complex HML3 chain where the RepeatMasker based Simage indicates contributions from six different HMLs. D4: An HML3 chain with short pieces of HML1, HML9/10 and HML8. D5: a complex chain which contains undetermined HML sequences in the end of pol, and whole of env. The differences between the consensus and RepeatMasker results in D3-5 indicate that the HML groups and HERVK families contain microheterogeneities, mainly in env, which sometimes can cause classification confusion. The HML10 consensus contains an HML9 like stretch in pol and an HML8 like stretch in env, which may explain some of the discrepancies between the RepeatMasker and Consensus Simages. HERVK14 = HML1, HERVK = HML2, LTR5 = HML2 LTR, HERVK9 = HML3, MER9 = HML3 LTR, HERVK14C = HML9, HERVK11D = HML7, HERVK11 = HML8
Fig. 2 Simages. Panel a The principle. A proviral sequence is divided into twentieths, each of which is BLASTed against a reference sequence collection. 1 A homogeneous, canonical, provirus. 2 A heterogeneous, noncanonical, provirus. Panel b A canonical chain. The chain id (“rvnr” in Additional file 1: Table S1), HERV classification, the chromosomal position and LTR divergence (if both LTRs were recognized by ReTe) are shown in the uppermost row. The subsequent three rows depict the RepeatMasker nucleic acids with the highest degree of identity, the next three rows which of the 39 consensus sequences determined in this paper (Additional file 3: List S3) has the highest degree of identity, all per twentieth of the chain. The lowest row depicts the ReTe putein interpretation per twentieth. 5 means 5′LTR, G Gag, R Pro, P Pol, E Env and 3 3′LTR. Panel c Three noncanonical chains containing secondary integrations which left a single LTR inside another retroviral chain. Annotation as in b. Colour is used here and in ensuing panels to distinguish components of mosaic chains. C1: HML4 LTR inside an HML2. LTR5 and HERVK refer to HML2. LTR13 is an HML4 LTR. C2: HERV9 LTR inside a HERVH. LTR12 and HylERV9-LTR are HERV9 LTR equivalents. A small pol piece most similar to HERVE is also present. C3: HML2 inside a HERVH. HylNERVH1 and HylNERVH2 are HERVH equivalents (see Additional file 2: List S2). LTR5 is an HML2 LTR. “0” depicts that no similarity was found with the respective query sequences. Panel d Noncanonical chains with signs of recombination. Annotation as in b. D1: HERV9 chain with a short piece similar to HERVIP at the end of pol and beginning of env. D2: a mosaic HERVE with HERVIP, HERVW and HML10 inside. ReTe recognized mainly one gene, env. As described in the text, this is a common pattern for chains labeled as “Harlequin”. D3: a complex HML3 chain where the RepeatMasker based Simage indicates contributions from six different HMLs. D4: An HML3 chain with short pieces of HML1, HML9/10 and HML8. D5: a complex chain which contains undetermined HML sequences in the end of pol, and whole of env. The differences between the consensus and RepeatMasker results in D3-5 indicate that the HML groups and HERVK families contain microheterogeneities, mainly in env, which sometimes can cause classification confusion. The HML10 consensus contains an HML9 like stretch in pol and an HML8 like stretch in env, which may explain some of the discrepancies between the RepeatMasker and Consensus Simages. HERVK14 = HML1, HERVK = HML2, LTR5 = HML2 LTR, HERVK9 = HML3, MER9 = HML3 LTR, HERVK14C = HML9, HERVK11D = HML7, HERVK11 = HML8CC BY · PubMed Central
Fig. 3 Mapping of taxonomic markers on an unrooted consensus maximum likelihood cladogram of the HERV groups and supergroups. At the left, HERV supergroups are shown with the first 13 amino acids of a representative ISD within parenthesis. HSERVIII have no known envelope proteins of their own, symbolized with a question mark. The occurrence of nucleotide bias (High T or A, or low g), predominant number of zinc fingers in Gag, predominant gag;pro and pro;pol frame shift strategy, occurrence of dUTPase and GPATCH domains together with the protease and occurrence of dUTPase and Chromo and/or GPY/F domains in the C terminus of the integrase, are shown. Colour codes for branch names: consensus sequences (con) are magenta, best representatives (bre) are in brown. The Chromo and/or GPY/F reddish fill was weaker for some groups because of inconsistent (HEPSI) or weak fit (HML6)
Fig. 3 Mapping of taxonomic markers on an unrooted consensus maximum likelihood cladogram of the HERV groups and supergroups. At the left, HERV supergroups are shown with the first 13 amino acids of a representative ISD within parenthesis. HSERVIII have no known envelope proteins of their own, symbolized with a question mark. The occurrence of nucleotide bias (High T or A, or low g), predominant number of zinc fingers in Gag, predominant gag;pro and pro;pol frame shift strategy, occurrence of dUTPase and GPATCH domains together with the protease and occurrence of dUTPase and Chromo and/or GPY/F domains in the C terminus of the integrase, are shown. Colour codes for branch names: consensus sequences (con) are magenta, best representatives (bre) are in brown. The Chromo and/or GPY/F reddish fill was weaker for some groups because of inconsistent (HEPSI) or weak fit (HML6)CC BY · PubMed Central
Fig. 4 Unrooted phylogram of Pol consensus sequences (“con”, magenta) of canonical and best representatives (“bre”; brown) of some noncanonical proviruses together with reference Pols from GenBank (with Genbank id, black), and previous work by the authors (“2-con” were previous consensus sequences). Pol sequences were aligned with Muscle. A maximum likelihood tree was calculated. The asterisks mark the three supergroups which contain RepBase clades belonging to RepBase group MER4I
Fig. 4 Unrooted phylogram of Pol consensus sequences (“con”, magenta) of canonical and best representatives (“bre”; brown) of some noncanonical proviruses together with reference Pols from GenBank (with Genbank id, black), and previous work by the authors (“2-con” were previous consensus sequences). Pol sequences were aligned with Muscle. A maximum likelihood tree was calculated. The asterisks mark the three supergroups which contain RepBase clades belonging to RepBase group MER4ICC BY · PubMed Central
Fig. 5 Unrooted phylograms of Gag, Pro, Pol and Env from the consensus sequences in Additional file 4: List S4, with fewer reference sequences than in Fig. 4. A maximum likelihood tree was calculated from Muscle alignments. The asterisks mark instances of possible Env recombination
Fig. 5 Unrooted phylograms of Gag, Pro, Pol and Env from the consensus sequences in Additional file 4: List S4, with fewer reference sequences than in Fig. 4. A maximum likelihood tree was calculated from Muscle alignments. The asterisks mark instances of possible Env recombinationCC BY · PubMed Central
Fig. 6 Retroviral envelopes encountered in hg19. Env subgroup consensuses (see Additional file 4: List S4) and reference envelope proteins were aligned by Muscle. A Maximum Likelihood tree was then produced. Branch names of the subgroup consensuses contain, in this order, taxorder nr, “con”, subgroup name, subgroup average percent identity to consensus for the envputein (if the subgroup had only one member, a 0 is shown), a 13 amino acids subdomain from the ISD (if identified), subgroup average percent identity to consensus for 23 ISD amino acids (Additional file 1: Table S1) and bootstrap value of the relation (percent of 100 bootstraps)
Fig. 6 Retroviral envelopes encountered in hg19. Env subgroup consensuses (see Additional file 4: List S4) and reference envelope proteins were aligned by Muscle. A Maximum Likelihood tree was then produced. Branch names of the subgroup consensuses contain, in this order, taxorder nr, “con”, subgroup name, subgroup average percent identity to consensus for the envputein (if the subgroup had only one member, a 0 is shown), a 13 amino acids subdomain from the ISD (if identified), subgroup average percent identity to consensus for 23 ISD amino acids (Additional file 1: Table S1) and bootstrap value of the relation (percent of 100 bootstraps)CC BY · PubMed Central
Fig. 7 Retroviral envelopes with high similarity between Env subgroups. Envelope subgroups (A, B, C, etc) with high intersupergroup similarity are shown interconnected, superimposed on the cladogram of Fig. 3. Significant relations (branches with bootstrap >50) were obtained from neighbour joining (not shown) and maximum likelihood trees (same as in Fig. 6). To avoid cluttering, only intersupergroup relations were shown, except for the HML supergroup, where intergroup relations are presented. Relations shown indicate, but do not prove, an envelope transfer event
Fig. 7 Retroviral envelopes with high similarity between Env subgroups. Envelope subgroups (A, B, C, etc) with high intersupergroup similarity are shown interconnected, superimposed on the cladogram of Fig. 3. Significant relations (branches with bootstrap >50) were obtained from neighbour joining (not shown) and maximum likelihood trees (same as in Fig. 6). To avoid cluttering, only intersupergroup relations were shown, except for the HML supergroup, where intergroup relations are presented. Relations shown indicate, but do not prove, an envelope transfer eventCC BY · PubMed Central
Fig. 8 LTR divergence of frequent HERV groups. LTR divergence as calculated by ReTe is presented as a histogram divided into percent bins, from 0–1 to 39–40 %. A very approximate estimate of age since integration was calculated by multiplying percent divergence with 2.5. It is primarily intended to show the distribution of divergence of prominent HERV groups relative to that of other HERV groups
Fig. 8 LTR divergence of frequent HERV groups. LTR divergence as calculated by ReTe is presented as a histogram divided into percent bins, from 0–1 to 39–40 %. A very approximate estimate of age since integration was calculated by multiplying percent divergence with 2.5. It is primarily intended to show the distribution of divergence of prominent HERV groups relative to that of other HERV groupsCC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 10 references

Research works printed but not linked: 86

  1. Benveniste RE, Todaro GJ. Homology between type-C viruses of various species as determined by molecular hybridization. Proc Natl Acad Sci USA. 1973;70(12):3316–20. · DOI
  2. Benveniste RE, Todaro GJ. Evolution of type C viral genes: evidence for an Asian origin of man. Nature. 1976;261(5556):101–8. · DOI
  3. Boeke JD, Stoye JP. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In: Coffin JM, Hughes SH, Varmus HE, editors. retroviruses. New York: Cold Spring Harbor; 1997.
  4. Goff SP. Retroviridae: the retroviruses and their replication. In: Knipe D, Howley P, editors. Fields virology 5ed. Philadelpa: Lippincott Williams and Wilkins; 2007.
  5. Tarlinton R, Meers J, Young P. Biology and evolution of the endogenous koala retrovirus. Cell Mol Life Sci CMLS. 2008;65:3413–21. doi: 10.1007/s00018-008-8499-y . · DOI
  6. Bannert N, Kurth R. The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet. 2006;7:149–73. doi: 10.1146/annurev.genom.7.080505.115700 . · DOI
  7. Katzourakis A, Rambaut A, Pybus OG. The evolutionary dynamics of endogenous retroviruses. Trends Microbiol. 2005;13:463–8. doi: 10.1016/j.tim.2005.08.004 . · DOI
  8. Benachenhou F, Blikstad V, Blomberg J. The phylogeny of orthoretroviral long terminal repeats (LTRs). Gene. 2009;448:134–8. doi: 10.1016/j.gene.2009.07.002 . · DOI
  9. Copeland NG, Hutchison KW, Jenkins NA. Excision of the DBA ecotropic provirus in dilute coat-color revertants of mice occurs by homologous recombination involving the viral LTRs. Cell. 1983;33:379–87. · DOI
  10. Marchi E, Kanapin A, Magiorkinis G, Belshaw R. Unfixed endogenous retroviral insertions in the human population. J Virol. 2014;88(17):9529–37. doi: 10.1128/JVI.00919-14 . · DOI
  11. Agoni L, Golden A, Guha C, Lenz J. Neandertal and Denisovan retroviruses. Current Biol CB. 2012;22(11):R437–8. doi: 10.1016/j.cub.2012.04.049 . · DOI
  12. Faff O, Murray AB, Schmidt J, Leib-Mosch C, Erfle V, Hehlmann R. Retrovirus-like particles from the human T47D cell line are related to mouse mammary tumour virus and are of human endogenous origin. J Gen Virol. 1992;73(Pt 5):1087–97. · DOI
  13. Jern P, Coffin JM. Effects of retroviruses on host genome function. Annu Rev Genet. 2008;42:709–32. doi: 10.1146/annurev.genet.42.110807.091501 . · DOI · Paper page
  14. Medstrand P, Landry JR, Mager DL. Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J Biol Chem. 2001;276(3):1896–903. doi: 10.1074/jbc.M006557200 . · DOI
  15. Balada E, Ordi-Ros J, Vilardell-Tarrés M. Molecular mechanisms mediated by human endogenous retroviruses (HERVs) in autoimmunity. New Jersey: Wiley Online Library; 2009.
  16. Brodziak A, Ziolko E, Muc-Wierzgon E, Nowakowska-Zajdel E, Kokot T, Klakla K. The role of human endogenous retroviruses in the pathogenesis of autoimmune diseases. Med Sci Moni. 2012;18:RA80–8.
  17. Cegolon L, Salata C, Weiderpass E, Vineis P, Palù G, Mastrangelo G. Human endogenous retroviruses and cancer prevention: evidence and prospects. BMC Cancer. 2013;13:4. doi: 10.1186/1471-2407-13-4 . · DOI
  18. Kamp C, Hirschmann P, Voss H, Huellen K, Vogt PH. Two long homologous retroviral sequence blocks in proximal Yq11 cause AZFa microdeletions as a result of intrachromosomal recombination events. Hum Mol Genet. 2000;9:2563–72. · DOI · Paper page
  19. Andersson ML, Lindeskog M, Medstrand P, Westley B, May F, Blomberg J. Diversity of human endogenous retrovirus class II-like sequences. J Gen Virol. 1999;80(Pt 1):255–60. · DOI
  20. Blomberg J, Benachenhou F, Blikstad V, Sperber GO, Mayer J. Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations. Gene. 2009;448:115–23. doi: 10.1016/j.gene.2009.06.007 . · DOI
  21. Mayer J, Blomberg J, Seal RL. A revised nomenclature for transcribed human endogenous retroviral loci. Mobile DNA. 2011;2:7. doi: 10.1186/1759-8753-2-7 . · DOI
  22. Jurka J. Repbase Update a database and an electronic journal of repetitive elements. Mol Biol. 2000;16:1–3.
  23. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7. doi: 10.1159/000084979 . · DOI
  24. Smit AF. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Current Opin Genet Develop. 1999;6:657–63. · DOI · Paper page
  25. Sperber GO, Airola T, Jern P, Blomberg J. Automated recognition of retroviral sequences in genomic data–RetroTector. Nucleic Acids Res. 2007;35:4964–76. doi: 10.1093/nar/gkm515 . · DOI
  26. Blikstad V, Benachenhou F, Sperber GO, Blomberg J. Evolution of human endogenous retroviral sequences: a conceptual account. Cell Mole Life Sci CMLS. 2008;65(21):3348–65. doi: 10.1007/s00018-008-8495-2 . · DOI
  27. Sperber GO, Lövgren A, Eriksson NE, Benachenhou F, Blomberg J. RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences. BMC Bioinform. 2009;10(Suppl 6):S4. doi: 10.1186/1471-2105-10-S6-S4 . · DOI
  28. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. doi: 10.1038/35057062 . · DOI · Paper page
  29. Blanchong CA, Chung EK, Rupert KL, Yang Y, Yang Z, Zhou B, et al. Genetic, structural and functional diversities of human complement components C4A and C4B and their mouse homologues, Slp and C4. Int Immunopharmacol. 2001;1(3):365–92. · DOI
  30. Elfaitouri A, Shao X, Mattsson Ulfstedt J, Muradrasoli S, Bölin Wiener A, Golbob S, et al. Murine gammaretrovirus group G3 was not found in Swedish patients with myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia. PLoS One. 2011;6:e24602. doi: 10.1371/journal.pone.0024602 . · DOI
  31. Bolisetty M, Blomberg J, Benachenhou F, Sperber G, Beemon K. Unexpected diversity and expression of avian endogenous retroviruses. mBio. 2012;3(5):e00344–512. doi: 10.1128/mBio.00344-12 . · DOI
  32. Smit AF. The origin of interspersed repeats in the human genome. Current Opin Genet Develop. 1996;6(6):743–8. · DOI
  33. Smit AF. Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Res. 1993;21(8):1863–72. · DOI
  34. Cohen M, Larsson E. Human endogenous retroviruses. BioEssays. 1988;9(6):191–6. doi: 10.1002/bies.950090603 . · DOI
  35. Bishop KN, Holmes RK, Sheehy AM, Malim MH. APOBEC-mediated editing of viral RNA. Science. 2004;305(5684):645. doi: 10.1126/science.1100658 . · DOI
  36. Sheehy AM, Gaddis NC, Choi JD, Malim MH. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature. 2002;418(6898):646–50. doi: 10.1038/nature00939 . · DOI
  37. Sanchez-Martinez S, Aloia AL, Harvin D, Mirro J, Gorelick RJ, Jern P, et al. Studies on the restriction of murine leukemia viruses by mouse APOBEC3. PLoS One. 2012;7(5):e38190. doi: 10.1371/journal.pone.0038190 . · DOI
  38. Esnault C, Priet S, Ribet D, Heidmann O, Heidmann T. Restriction by APOBEC3 proteins of endogenous retroviruses with an extracellular life cycle: ex vivo effects and in vivo “traces” on the murine IAPE and human HERV-K elements. Retrovirology. 2008;5:75. doi: 10.1186/1742-4690-5-75 . · DOI
  39. Jern P, Sperber GO, Blomberg J. Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology. 2005;2:50. doi: 10.1186/1742-4690-2-50 . · DOI
  40. Nelson M, Nelson DS, Cianciolo GJ, Snyderman R. Effects of CKS-17, a synthetic retroviral envelope peptide, on cell-mediated immunity in vivo: immunosuppression, immunogenicity, and relation to immunosuppressive tumor products. Cancer Immunol Immunother CII. 1989;30(2):113–8. · DOI
  41. Chong AY, Kojima KK, Jurka J, Ray DA, Smit AF, Isberg SR, et al. Evolution and gene capture in ancient endogenous retroviruses—insights from the crocodilian genomes. Retrovirology. 2014;11(1):71. doi: 10.1186/s12977-014-0071-2 . · DOI
  42. Cordonnier A, Casella JF, Heidmann T. Isolation of novel human endogenous retrovirus-like elements with foamy virus-related pol sequence. J Virol. 1995;69(9):5890–7. · DOI
  43. Benit L, De Parseval N, Casella JF, Callebaut I, Cordonnier A, Heidmann T. Cloning of a new murine endogenous retrovirus, MuERV-L, with strong similarity to the human HERV-L element and with a gag coding sequence closely related to the Fv1 restriction gene. J Virol. 1997;71(7):5652–7. · DOI
  44. Oja M, Sperber GO, Blomberg J, Kaski S. Self-organizing map-based discovery and visualization of human endogenous retroviral sequence groups. Int J Neural Syst. 2005;15(3):163–79. doi: 10.1142/S0129065705000177 . · DOI
  45. Mager DL, Medstrand P. Retroviral repeat sequences. In: eLS. Chichester: Wiley. 2003. http://www.els.net . doi: 10.1038/npg.els.0005062 . · DOI
  46. Jern P, Sperber GO, Blomberg J. Definition and variation of human endogenous retrovirus H. Virology. 2004;327(1):93–110. doi: 10.1016/j.virol.2004.06.023 . · DOI
  47. Blaise S, de Parseval N, Benit L, Heidmann T. Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc Natl Acad Sci USA. 2003;100(22):13013–8. doi: 10.1073/pnas.2132646100 . · DOI
  48. Borysenko L, Stepanets V, Rynditch AV. Molecular characterization of full-length MLV-related endogenous retrovirus ChiRV1 from the chicken, Gallus gallus. Virology. 2008;376(1):199–204. doi: 10.1016/j.virol.2008.03.006 . · DOI
  49. Villesen P, Aagaard L, Wiuf C, Pedersen FS. Identification of endogenous retroviral reading frames in the human genome. Retrovirology. 2004;1:32. doi: 10.1186/1742-4690-1-32 . · DOI
  50. Aagaard L, Villesen P, Kjeldbjerg AL, Pedersen FS. The approximately 30-million-year-old ERVPb1 envelope gene is evolutionarily conserved among hominoids and Old World monkeys. Genomics. 2005;86(6):685–91. doi: 10.1016/j.ygeno.2005.08.011 . · DOI
  51. Brown K, Emes RD, Tarlinton RE. Multiple groups of endogenous epsilon-like retroviruses conserved across primates. J Virol. 2014;88(21):12464–71. doi: 10.1128/JVI.00966-14 . · DOI
  52. Lavie L, Medstrand P, Schempp W, Meese E, Mayer J. Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome. J Virol. 2004;78(16):8788–98. doi: 10.1128/JVI.78.16.8788-8798.2004 . · DOI
  53. Marchi E, Kanapin A, Byott M, Magiorkinis G, Belshaw R. Neanderthal and Denisovan retroviruses in modern humans. Current Biol CB. 2013;23(22):R994–5. doi: 10.1016/j.cub.2013.10.028 . · DOI
  54. Lee A, Huntley D, Aiewsakun P, Kanda RK, Lynn C, Tristem M. Novel Denisovan and Neanderthal retroviruses. J Virol. 2014;88(21):12907–9. doi: 10.1128/JVI.01825-14 . · DOI
  55. Magiorkinis G, Gifford RJ, Katzourakis A, De Ranter J, Belshaw R. Env-less endogenous retroviruses are genomic superspreaders. Proc Natl Acad Sci USA. 2012;109(19):7385–90. doi: 10.1073/pnas.1200913109 . · DOI
  56. Martins H, Villesen P. Improved integration time estimation of endogenous retroviruses with phylogenetic data. PLoS One. 2011;6(3):e14745. doi: 10.1371/journal.pone.0014745 . · DOI
  57. Nachman MW, Crowell SL. Estimate of the mutation rate per nucleotide in humans. Genetics. 2000;156(1):297–304. · DOI
  58. Stoye JP. Endogenous retroviruses: still active after all these years? Current Biol CB. 2001;11(22):R914–6. · DOI
  59. Friedli M, Turelli P, Kapopoulou A, Rauwel B, Castro-Diaz N, Rowe HM, et al. Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency. Genome Res. 2014;24(8):1251–9. doi: 10.1101/gr.172809.114 . · DOI
  60. Takahashi Y, Harashima N, Kajigaya S, Yokoyama H, Cherkasova E, McCoy JP, et al. Regression of human kidney cancer following allogeneic stem cell transplantation is associated with recognition of an HERV-E antigen by T cells. J Clin Investig. 2008;118(3):1099–109. doi: 10.1172/JCI34409 . · DOI
  61. Schiavetti F, Thonnard J, Colau D, Boon T, Coulie PG. A human endogenous retroviral sequence encoding an antigen recognized on melanoma by cytolytic T lymphocytes. Cancer Res. 2002;62(19):5510–6.
  62. Paces J, Pavlicek A, Zika R, Kapitonov VV, Jurka J, Paces V. HERVd: the Human Endogenous RetroViruses Database: update. Nucleic Acids Res. 2004;32:D50. doi: 10.1093/nar/gkh075 . · DOI
  63. Campillos M, Doerks T, Shah PK, Bork P. Computational characterization of multiple Gag-like human proteins. Trends Genet TIG. 2006;22:585–9. doi: 10.1016/j.tig.2006.08.001 . · DOI
  64. Belshaw R, Watson J, Katzourakis A, Howe A, Woolven-Allen J, Burt A, et al. Rate of recombinational deletion among human endogenous retroviruses. J Virol. 2007;81:9437–42. doi: 10.1128/JVI.02216-06 . · DOI
  65. Katzourakis A. Paleovirology: inferring viral evolution from host genome sequence data. Philos Trans R Soc Lond B Biol Sci. 2013;368(1626):20120493. doi: 10.1098/rstb.2012.0493 . · DOI
  66. Katzourakis A, Pereira V, Tristem M. Effects of recombination rate on human endogenous retrovirus fixation and persistence. J Virol. 2007;81:10712–7. doi: 10.1128/JVI.00410-07 . · DOI
  67. Henzy JE, Gifford RJ, Johnson WE, Coffin JM. A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J Virol. 2014;88(5):2398–405. doi: 10.1128/JVI.02863-13 . · DOI
  68. Kozak CA. Origins of the endogenous and infectious laboratory mouse gammaretroviruses. Viruses. 2015;7(1):1–26. doi: 10.3390/v7010001 . · DOI
  69. Jarrett O. Pathogenicity of feline leukemia virus is commonly associated with variant viruses. Leukemia. 1992;6(Suppl 3):153S–4S.
  70. Neil JC, Fulton R, Rigby M, Stewart M. Feline leukaemia virus: generation of pathogenic and oncogenic variants. Curr Top Microbiol Immunol. 1991;171:67–93.
  71. Onions D. Epidemiology of feline leukaemia virus infections. Bailliere’s Clin Haematol. 1987;1(1):45–58. · DOI
  72. Roy-Burman P. Endogenous env elements: partners in generation of pathogenic feline leukemia viruses. Virus Genes. 1995;11(2–3):147–61. · DOI
  73. Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2009;37:D159–62. doi: 10.1093/nar/gkn772 (Database issue). · DOI
  74. La Mantia G, Maglione D, Pengue G, Di Cristofano A, Simeone A, Lanfrancone L, et al. Identification and characterization of novel human endogenous retroviral sequences prefentially expressed in undifferentiated embryonal carcinoma cells. Nucleic Acids Res. 1991;19(7):1513–20. · DOI
  75. Barnett AL, Davey RA, Cunningham JM. Modular organization of the Friend murine leukemia virus envelope protein underlies the mechanism of infection. Proc Natl Acad Sci USA. 2001;98(7):4113–8. doi: 10.1073/pnas.071432398 . · DOI
  76. Smith JG, Mothes W, Blacklow SC, Cunningham JM. The mature avian leukosis virus subgroup A envelope glycoprotein is metastable, and refolding induced by the synergistic effects of receptor binding and low pH is coupled to infection. J Virol. 2004;78(3):1403–10. · DOI
  77. Henzy JE, Coffin JM. Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class. J Virol. 2013;87(4):1937–46. doi: 10.1128/JVI.01442-12 . · DOI
  78. Henzy JE, Johnson WE. Pushing the endogenous envelope. Philos Trans R Soc Lond B Biol Sci. 2013;368(1626):20120506. doi: 10.1098/rstb.2012.0506 . · DOI
  79. Aravind L, Koonin EV. G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins. Trends Biochem Sci. 1999;24(9):342–4. · DOI
  80. Koonin EV, Zhou S, Lucchesi JC. The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids Res. 1995;23(21):4229–33. · DOI
  81. Malik HS, Eickbush TH. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J Virol. 1999;73(6):5186–90. · DOI
  82. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9. doi: 10.1093/molbev/msr121 . · DOI
  83. Bénit L, Calteau A, Heidmann T. Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes. Virology. 2003;312(1):159–68. · DOI
  84. Subramanian RP, Wildschutte JH, Russo C, Coffin JM. Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology. 2011;8:90. doi: 10.1186/1742-4690-8-90 . · DOI · Paper page
  85. Hervé CA, Forrest G, Lower R, Griffiths DJ, Venables PJ. Conservation and loss of the ERV3 open reading frame in primates. Genomics. 2004;83(5):940–3. doi: 10.1016/j.ygeno.2003.10.003 . · DOI
  86. Fei C, Atterby C, Edqvist PH, Ponten F, Zhang WW, Larsson E et al. Detection of the human endogenous retrovirus ERV3-encoded Env-protein in human tissues using antibody-based proteomics. J R Soc Med. 2014;107(1):22–9. doi: 10.1177/0141076813509981 . · DOI

Cited by

Sorted by citations

See all 315

Metadata

Authors
Vargiu, L., Rodriguez-Tomé, P., Sperber, G. O., Cadeddu, M., Grandi, N., Blikstad, V., Tramontano, E., & Blomberg, J.
Venue
Retrovirology
Publisher
Springer Science and Business Media LLC
Published
2016-01-22
Volume
13
Issue
1
ISSN
1742-4690
DOI
10.1186/s12977-015-0232-y
PMC
PMC4724089
Cited by
315
References
10
Language
en
Funders
Vetenskapsrådet (2003-5693)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Classification and characterization of human endogenous retroviruses; mosaic forms are common. https://app.cochat.ai/papers/10.1186/s12977-015-0232-y
The paper
Vargiu, L., Rodriguez-Tomé, P., Sperber, G. O., Cadeddu, M., Grandi, N., Blikstad, V., Tramontano, E., & Blomberg, J. (2016). Classification and characterization of human endogenous retroviruses; mosaic forms are common. Retrovirology. https://doi.org/10.1186/s12977-015-0232-y