{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T20:21:17Z","timestamp":1790022077808,"version":"4.0.1"},"reference-count":40,"publisher":"American Society for Microbiology","issue":"11","license":[{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T00:00:00Z","timestamp":1762214400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,11,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Endogenous retroviruses (ERVs), remnants of ancient viral infections integrated into host genomes, serve as invaluable molecular fossils for studying viral evolution. In this study, we performed a genomic analysis of the Chinese pangolin (\n                      <jats:italic toggle=\"yes\">Manis pentadactyla<\/jats:italic>\n                      ), identifying novel full-length endogenous retroviruses, designated as\n                      <jats:italic toggle=\"yes\">Manis pentadactyla<\/jats:italic>\n                      ERVs (MPERVs). MPERVs span three retroviral genera:\n                      <jats:italic toggle=\"yes\">Alpha<\/jats:italic>\n                      -,\n                      <jats:italic toggle=\"yes\">Beta<\/jats:italic>\n                      -, and\n                      <jats:italic toggle=\"yes\">Gamma-retroviruses<\/jats:italic>\n                      . Using genomic screening and phylogenetic analysis, we classified MPERVs and reconstructed their evolutionary history, uncovering evidence of complex recombination events and cross-species transmission. Estimated insertion times for MPERVs range from very recent to 18.38 million years ago. MPERVs exhibit diverse structural features, notably including conserved retroviral domains and functional motifs and highlighting their preservation across extensive evolutionary periods. These findings shed light on the evolutionary dynamics of ERVs in Chinese pangolin and suggest the potential for expanded host ranges among certain retrovirus genera.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Endogenous retroviruses are unique viruses distinguished by the fact that they are retained as part of the host genome after an exogenous retrovirus infects the host. The Chinese pangolin, as a host with a long independent evolutionary history, likely holds valuable insights in its genome regarding retrovirus endogenization and transmission. In this study, we identified the footprints of exogenous retroviruses from three different genera in the pangolin genome:\n                        <jats:italic toggle=\"yes\">Alpharetrovirus<\/jats:italic>\n                        ,\n                        <jats:italic toggle=\"yes\">Betaretrovirus<\/jats:italic>\n                        , and\n                        <jats:italic toggle=\"yes\">Gammaretrovirus<\/jats:italic>\n                        . Additionally, by calculating the integration times of the pangolin\u2019s endogenous retroviruses and analyzing the domains of the three main functional proteins (GAG, POL, and ENV), we found that the insertions are relatively young. This suggests that these endogenous retroviruses infected the Chinese pangolin long before their endogenization. This study represents the exploration of endogenous retroviruses in the Chinese pangolin genome, expanding our understanding of endogenous retroviruses in mammals. Furthermore, our findings provide new evidence for the phenomenon of the cross-species transmission of retroviruses prior to endogenization.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03203-24","type":"journal-article","created":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T13:03:02Z","timestamp":1759237382000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Diversity and evolutionary history of endogenous retroviruses in the genome of\n                    <i>Manis pentadactyla<\/i>"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-5489-6385","authenticated-orcid":true,"given":"Tiancheng","family":"Zhang","sequence":"first","affiliation":[{"name":"Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University","place":["Zhenjiang, China"]},{"id":[{"id":"https:\/\/ror.org\/03jc41j30","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Laboratory Medicine, School of Medicine, Jiangsu University","place":["Zhenjiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9253-1225","authenticated-orcid":false,"given":"Juan","family":"Xu","sequence":"additional","affiliation":[{"name":"Clinical Laboratory Center, The Affiliated Taizhou People\u2019s Hospital of Nanjing Medical University","place":["Taizhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9624-6109","authenticated-orcid":true,"given":"Hongfeng","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University","place":["Zhenjiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2661-2067","authenticated-orcid":false,"given":"Chenglin","family":"Zhou","sequence":"additional","affiliation":[{"name":"Clinical Laboratory Center, The Affiliated Taizhou People\u2019s Hospital of Nanjing Medical University","place":["Taizhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9352-6153","authenticated-orcid":false,"given":"Wen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Critical Care Medicine, The Affiliated People's Hospital, Jiangsu University","place":["Zhenjiang, China"]},{"id":[{"id":"https:\/\/ror.org\/03jc41j30","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Laboratory Medicine, School of Medicine, Jiangsu University","place":["Zhenjiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010458"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1915400117"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01354-09"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.3390\/v7112927"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1139\/gen-2021-0047"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1177\/03009858211002198"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.988730"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2021.145596"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005279"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.27564"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12977-018-0442-1"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(19)86619-X"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.69.5.3090-3097.1995"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.3390\/v15020274"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02698-15"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-82-7-1597"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0913122107"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-82-10-2515"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.02072-21"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00044-17"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.coviro.2017.07.020"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-020-00230-y"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.18.10254"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-virology-100114-054945"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1414980112"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2019.103995"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2012.0506"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.76.15.7607-7615.2002"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-78536-8_5"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3176"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm286"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-18"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz991"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy096"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/sys029"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt389"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp348"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msu300"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.022629899"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03203-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03203-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T14:10:20Z","timestamp":1762265420000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.03203-24"}},"subtitle":[],"editor":[{"given":"Leiliang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,11,4]]},"references-count":40,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2025,11,4]]}},"alternative-id":["10.1128\/spectrum.03203-24"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.03203-24","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,4]]},"assertion":[{"value":"2024-12-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-08-24","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-09-30","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03203-24"}}