PMC:8275577 / 6856-8293
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/8275577","sourcedb":"PMC","sourceid":"8275577","source_url":"https://www.ncbi.nlm.nih.gov/pmc/8275577","text":"Until now, SCoV2rCs have been found in four bat species of the genus Rhinolophus: R. acuminatus, R. affinis, R. malayanus, and R. shameli. The haplotype networks constructed using CO1 sequences of these four species are shown in Fig. 3. A star-like genetic pattern, characterized by one dominant haplotype and several satellite haplotypes was found for the two bat species endemic to Southeast Asia, i.e. R. acuminatus and R. shameli.\nFigure 3 Haplotype networks based on CO1 sequences of the four Rhinolophus species found positive for viruses closely related to SARS-CoV-2 (SCoV2rCs). The networks were constructed with the median joining method available in PopART 1.513 and modified under Adobe Illustrator CS6 (version 16.0). The codes used for the countries are the following: B (Myanmar), C (Cambodia), Ch (China), I (Indonesia), L (Laos), M (Malaysia), T (Thailand), and V (Vietnam). Colours indicate the geographic origin of haplotypes according to Fig. 2 (see online supplementary Table S1). The circles indicate haplotypes separated by at least one mutation. The black lines on the branches show the number of mutations ≥ 2. Black circles represent missing haplotypes. Circle size is proportional to the number of haplotypes. Haplogroups separated by more than seven mutations (pairwise nucleotide distances \u003e 1%) are highlighted by dotted lines. The red arrows show the positions of the nine bats found positive for SCoV2rCs.","divisions":[{"label":"label","span":{"begin":435,"end":443}}],"tracks":[{"project":"Zoonoses","denotations":[{"id":"T130","span":{"begin":786,"end":793},"obj":"Area"},{"id":"T1095","span":{"begin":310,"end":317},"obj":"Number"},{"id":"T1130","span":{"begin":97,"end":107},"obj":"Species"},{"id":"T1142","span":{"begin":109,"end":121},"obj":"Species"},{"id":"T1154","span":{"begin":82,"end":95},"obj":"Species"},{"id":"T1155","span":{"begin":405,"end":418},"obj":"Species"},{"id":"T1190","span":{"begin":127,"end":137},"obj":"Species"},{"id":"T1191","span":{"begin":423,"end":433},"obj":"Species"},{"id":"T1246","span":{"begin":143,"end":152},"obj":"Biological"},{"id":"T1247","span":{"begin":296,"end":305},"obj":"Biological"},{"id":"T1264","span":{"begin":825,"end":834},"obj":"Area"},{"id":"T1269","span":{"begin":850,"end":858},"obj":"Area"},{"id":"T1278","span":{"begin":879,"end":880},"obj":"Area"},{"id":"T1279","span":{"begin":861,"end":862},"obj":"Area"},{"id":"T1280","span":{"begin":783,"end":784},"obj":"Area"},{"id":"T1281","span":{"begin":796,"end":797},"obj":"Area"},{"id":"T1282","span":{"begin":810,"end":812},"obj":"Area"},{"id":"T1283","span":{"begin":822,"end":823},"obj":"Area"},{"id":"T1284","span":{"begin":837,"end":838},"obj":"Area"},{"id":"T1285","span":{"begin":847,"end":848},"obj":"Area"},{"id":"T1286","span":{"begin":1060,"end":1068},"obj":"Variation"},{"id":"T1287","span":{"begin":1121,"end":1130},"obj":"Variation"},{"id":"T1288","span":{"begin":1278,"end":1287},"obj":"Variation"},{"id":"T1355","span":{"begin":1318,"end":1322},"obj":"Number"},{"id":"T1388","span":{"begin":208,"end":215},"obj":"Species"},{"id":"T141","span":{"begin":882,"end":889},"obj":"Area"},{"id":"T1412","span":{"begin":283,"end":286},"obj":"Number"},{"id":"T1413","span":{"begin":287,"end":295},"obj":"Type"},{"id":"T1414","span":{"begin":318,"end":327},"obj":"Type"},{"id":"T1415","span":{"begin":180,"end":183},"obj":"Gene"},{"id":"T179","span":{"begin":44,"end":47},"obj":"Species"},{"id":"T180","span":{"begin":361,"end":364},"obj":"Species"},{"id":"T295","span":{"begin":799,"end":807},"obj":"Area"},{"id":"T332","span":{"begin":1322,"end":1323},"obj":"Unit"},{"id":"T386","span":{"begin":840,"end":844},"obj":"Area"},{"id":"T414","span":{"begin":537,"end":574},"obj":"Species"},{"id":"T433","span":{"begin":814,"end":819},"obj":"Area"},{"id":"T452","span":{"begin":864,"end":872},"obj":"Area"},{"id":"T473","span":{"begin":384,"end":398},"obj":"Area"},{"id":"T502","span":{"begin":39,"end":43},"obj":"Number"},{"id":"T503","span":{"begin":203,"end":207},"obj":"Number"},{"id":"T504","span":{"begin":493,"end":497},"obj":"Number"},{"id":"T542","span":{"begin":1404,"end":1408},"obj":"Species"},{"id":"T598","span":{"begin":180,"end":183},"obj":"Gene"},{"id":"T599","span":{"begin":472,"end":475},"obj":"Gene"},{"id":"T625","span":{"begin":184,"end":193},"obj":"Unit"},{"id":"T626","span":{"begin":476,"end":485},"obj":"Unit"},{"id":"T641","span":{"begin":444,"end":453},"obj":"Biological"},{"id":"T674","span":{"begin":913,"end":923},"obj":"Environment"},{"id":"T693","span":{"begin":328,"end":338},"obj":"Biological"},{"id":"T694","span":{"begin":934,"end":944},"obj":"Biological"},{"id":"T695","span":{"begin":1023,"end":1033},"obj":"Biological"},{"id":"T696","span":{"begin":1168,"end":1178},"obj":"Biological"},{"id":"T697","span":{"begin":1225,"end":1235},"obj":"Biological"},{"id":"T840","span":{"begin":357,"end":360},"obj":"Number"},{"id":"T88","span":{"begin":69,"end":80},"obj":"Species"},{"id":"T89","span":{"begin":498,"end":509},"obj":"Species"},{"id":"T960","span":{"begin":11,"end":19},"obj":"Species"},{"id":"T961","span":{"begin":576,"end":584},"obj":"Species"},{"id":"T962","span":{"begin":1428,"end":1436},"obj":"Species"},{"id":"T1417","span":{"begin":626,"end":647},"obj":"Method"},{"id":"T1418","span":{"begin":1047,"end":1059},"obj":"Number"},{"id":"T1419","span":{"begin":1131,"end":1134},"obj":"Number"},{"id":"T1420","span":{"begin":1160,"end":1167},"obj":"Without"},{"id":"T1421","span":{"begin":1262,"end":1277},"obj":"Number"},{"id":"T1422","span":{"begin":1289,"end":1318},"obj":"Index"},{"id":"T1423","span":{"begin":1399,"end":1403},"obj":"Number"}],"relations":[{"id":"R581","pred":"associate_with","subj":"T1418","obj":"T1286"},{"id":"R582","pred":"associate_with","subj":"T1419","obj":"T1287"},{"id":"R583","pred":"associate_with","subj":"T1420","obj":"T696"},{"id":"R584","pred":"associate_with","subj":"T1421","obj":"T1288"},{"id":"R585","pred":"associate_with","subj":"T1423","obj":"T542"},{"id":"R586","pred":"associate_with","subj":"T1355","obj":"T1422"},{"id":"R587","pred":"in","subj":"T542","obj":"T962"},{"id":"R390","pred":"abbreviation","subj":"T1280","obj":"T130"},{"id":"R391","pred":"abbreviation","subj":"T1282","obj":"T433"},{"id":"R392","pred":"abbreviation","subj":"T1281","obj":"T295"},{"id":"R393","pred":"abbreviation","subj":"T1283","obj":"T1264"},{"id":"R394","pred":"abbreviation","subj":"T1278","obj":"T141"},{"id":"R395","pred":"abbreviation","subj":"T1279","obj":"T452"},{"id":"R396","pred":"abbreviation","subj":"T1285","obj":"T1269"},{"id":"R397","pred":"abbreviation","subj":"T1284","obj":"T386"},{"id":"R426","pred":"associate_with","subj":"T1355","obj":"T332"},{"id":"R508","pred":"associate_with","subj":"T502","obj":"T179"},{"id":"R509","pred":"coreference","subj":"T179","obj":"T88"},{"id":"R510","pred":"in","subj":"T179","obj":"T960"},{"id":"R511","pred":"in","subj":"T1154","obj":"T960"},{"id":"R512","pred":"in","subj":"T1130","obj":"T960"},{"id":"R513","pred":"in","subj":"T1142","obj":"T960"},{"id":"R514","pred":"in","subj":"T1190","obj":"T960"},{"id":"R515","pred":"associate_with","subj":"T840","obj":"T180"},{"id":"R516","pred":"associate_with","subj":"T503","obj":"T1388"},{"id":"R517","pred":"coreference","subj":"T1388","obj":"T179"},{"id":"R518","pred":"associate_with","subj":"T504","obj":"T89"},{"id":"R562","pred":"of_a","subj":"T598","obj":"T1246"},{"id":"R563","pred":"of_a","subj":"T1388","obj":"T598"},{"id":"R564","pred":"of_a","subj":"T598","obj":"T625"},{"id":"R565","pred":"associate_with","subj":"T1412","obj":"T1247"},{"id":"R566","pred":"associate_with","subj":"T1095","obj":"T693"},{"id":"R567","pred":"of_a","subj":"T1413","obj":"T1247"},{"id":"R568","pred":"of_a","subj":"T1414","obj":"T693"},{"id":"R569","pred":"in","subj":"T473","obj":"T1155"},{"id":"R570","pred":"in","subj":"T473","obj":"T1191"},{"id":"R571","pred":"in","subj":"T473","obj":"T180"},{"id":"R572","pred":"of_a","subj":"T1415","obj":"T1247"},{"id":"R573","pred":"of_a","subj":"T1415","obj":"T693"},{"id":"R574","pred":"of_a","subj":"T1191","obj":"T1415"},{"id":"R575","pred":"of_a","subj":"T1155","obj":"T1415"},{"id":"R576","pred":"of_a","subj":"T180","obj":"T1415"},{"id":"R577","pred":"abbreviation","subj":"T961","obj":"T414"},{"id":"R578","pred":"in","subj":"T89","obj":"T414"},{"id":"R579","pred":"of_a","subj":"T89","obj":"T599"},{"id":"R580","pred":"of_a","subj":"T599","obj":"T641"}],"attributes":[{"id":"A132","pred":"tao:has_database_id","subj":"T141","obj":"MESH:D014744"},{"id":"A383","pred":"tao:has_database_id","subj":"T452","obj":"MESH:D013785"},{"id":"A434","pred":"tao:has_database_id","subj":"T542","obj":"Tax:9397"},{"id":"A550","pred":"tao:has_database_id","subj":"T694","obj":"MESH:D006239"},{"id":"A851","pred":"tao:has_database_id","subj":"T1281","obj":"MESH:D002160"},{"id":"A858","pred":"tao:has_database_id","subj":"T1288","obj":"MESH:D009154"},{"id":"A533","pred":"tao:has_database_id","subj":"T674","obj":"MESH:D005843"},{"id":"A551","pred":"tao:has_database_id","subj":"T695","obj":"MESH:D006239"},{"id":"A316","pred":"tao:has_database_id","subj":"T386","obj":"MESH:D007812"},{"id":"A476","pred":"tao:has_database_id","subj":"T599","obj":"https://www.ncbi.nlm.nih.gov/nuccore/?term=MW712891:MW713034[pacc]"},{"id":"A894","pred":"tao:has_database_id","subj":"T1388","obj":"Tax:49442"},{"id":"A364","pred":"tao:has_database_id","subj":"T433","obj":"MESH:D002681"},{"id":"A345","pred":"Memo","subj":"T414","obj":"Tax:2697049"},{"id":"A81","pred":"tao:has_database_id","subj":"T89","obj":"Tax:49442"},{"id":"A286","pred":"tao:has_database_id","subj":"T295","obj":"MESH:D002160"},{"id":"A829","pred":"tao:has_database_id","subj":"T1247","obj":"MESH:D006239"},{"id":"A857","pred":"tao:has_database_id","subj":"T1287","obj":"MESH:D009154"},{"id":"A900","pred":"tao:has_database_id","subj":"T1415","obj":"https://www.ncbi.nlm.nih.gov/nuccore/?term=MW712891:MW713034[pacc]"},{"id":"A171","pred":"tao:has_database_id","subj":"T180","obj":"Tax:49442"},{"id":"A501","pred":"tao:has_database_id","subj":"T641","obj":"MESH:D006239"},{"id":"A475","pred":"tao:has_database_id","subj":"T598","obj":"https://www.ncbi.nlm.nih.gov/nuccore/?term=MW712891:MW713034[pacc]"},{"id":"A842","pred":"tao:has_database_id","subj":"T1264","obj":"MESH:D007214"},{"id":"A404","pred":"tao:has_database_id","subj":"T473","obj":"MESH:D001210"},{"id":"A80","pred":"tao:has_database_id","subj":"T88","obj":"Tax:49442"},{"id":"A625","pred":"Memo","subj":"T962","obj":"Tax:2697049"},{"id":"A828","pred":"tao:has_database_id","subj":"T1246","obj":"MESH:D006239"},{"id":"A170","pred":"tao:has_database_id","subj":"T179","obj":"Tax:49442"},{"id":"A848","pred":"tao:has_database_id","subj":"T1278","obj":"MESH:D014744"},{"id":"A624","pred":"Memo","subj":"T961","obj":"Tax:2697049"},{"id":"A549","pred":"tao:has_database_id","subj":"T693","obj":"MESH:D006239"},{"id":"A757","pred":"tao:has_database_id","subj":"T1130","obj":"Tax:59477"},{"id":"A855","pred":"tao:has_database_id","subj":"T1285","obj":"MESH:D008296"},{"id":"A853","pred":"tao:has_database_id","subj":"T1283","obj":"MESH:D007214"},{"id":"A121","pred":"tao:has_database_id","subj":"T130","obj":"MESH:D002052"},{"id":"A781","pred":"tao:has_database_id","subj":"T1155","obj":"Tax:320431"},{"id":"A799","pred":"tao:has_database_id","subj":"T1190","obj":"Tax:608708"},{"id":"A623","pred":"Memo","subj":"T960","obj":"Tax:2697049"},{"id":"A780","pred":"tao:has_database_id","subj":"T1154","obj":"Tax:320431"},{"id":"A850","pred":"tao:has_database_id","subj":"T1280","obj":"MESH:D002052"},{"id":"A800","pred":"tao:has_database_id","subj":"T1191","obj":"Tax:608708"},{"id":"A768","pred":"tao:has_database_id","subj":"T1142","obj":"Tax:608659"},{"id":"A552","pred":"tao:has_database_id","subj":"T696","obj":"MESH:D006239"},{"id":"A847","pred":"tao:has_database_id","subj":"T1269","obj":"MESH:D008296"},{"id":"A553","pred":"tao:has_database_id","subj":"T697","obj":"MESH:D006239"},{"id":"A849","pred":"tao:has_database_id","subj":"T1279","obj":"MESH:D013785"},{"id":"A852","pred":"tao:has_database_id","subj":"T1282","obj":"MESH:D002681"},{"id":"A856","pred":"tao:has_database_id","subj":"T1286","obj":"MESH:D009154"},{"id":"A854","pred":"tao:has_database_id","subj":"T1284","obj":"MESH:D007812"},{"subj":"T130","pred":"source","obj":"Zoonoses"},{"subj":"T1095","pred":"source","obj":"Zoonoses"},{"subj":"T1130","pred":"source","obj":"Zoonoses"},{"subj":"T1142","pred":"source","obj":"Zoonoses"},{"subj":"T1154","pred":"source","obj":"Zoonoses"},{"subj":"T1155","pred":"source","obj":"Zoonoses"},{"subj":"T1190","pred":"source","obj":"Zoonoses"},{"subj":"T1191","pred":"source","obj":"Zoonoses"},{"subj":"T1246","pred":"source","obj":"Zoonoses"},{"subj":"T1247","pred":"source","obj":"Zoonoses"},{"subj":"T1264","pred":"source","obj":"Zoonoses"},{"subj":"T1269","pred":"source","obj":"Zoonoses"},{"subj":"T1278","pred":"source","obj":"Zoonoses"},{"subj":"T1279","pred":"source","obj":"Zoonoses"},{"subj":"T1280","pred":"source","obj":"Zoonoses"},{"subj":"T1281","pred":"source","obj":"Zoonoses"},{"subj":"T1282","pred":"source","obj":"Zoonoses"},{"subj":"T1283","pred":"source","obj":"Zoonoses"},{"subj":"T1284","pred":"source","obj":"Zoonoses"},{"subj":"T1285","pred":"source","obj":"Zoonoses"},{"subj":"T1286","pred":"source","obj":"Zoonoses"},{"subj":"T1287","pred":"source","obj":"Zoonoses"},{"subj":"T1288","pred":"source","obj":"Zoonoses"},{"subj":"T1355","pred":"source","obj":"Zoonoses"},{"subj":"T1388","pred":"source","obj":"Zoonoses"},{"subj":"T141","pred":"source","obj":"Zoonoses"},{"subj":"T1412","pred":"source","obj":"Zoonoses"},{"subj":"T1413","pred":"source","obj":"Zoonoses"},{"subj":"T1414","pred":"source","obj":"Zoonoses"},{"subj":"T1415","pred":"source","obj":"Zoonoses"},{"subj":"T179","pred":"source","obj":"Zoonoses"},{"subj":"T180","pred":"source","obj":"Zoonoses"},{"subj":"T295","pred":"source","obj":"Zoonoses"},{"subj":"T332","pred":"source","obj":"Zoonoses"},{"subj":"T386","pred":"source","obj":"Zoonoses"},{"subj":"T414","pred":"source","obj":"Zoonoses"},{"subj":"T433","pred":"source","obj":"Zoonoses"},{"subj":"T452","pred":"source","obj":"Zoonoses"},{"subj":"T473","pred":"source","obj":"Zoonoses"},{"subj":"T502","pred":"source","obj":"Zoonoses"},{"subj":"T503","pred":"source","obj":"Zoonoses"},{"subj":"T504","pred":"source","obj":"Zoonoses"},{"subj":"T542","pred":"source","obj":"Zoonoses"},{"subj":"T598","pred":"source","obj":"Zoonoses"},{"subj":"T599","pred":"source","obj":"Zoonoses"},{"subj":"T625","pred":"source","obj":"Zoonoses"},{"subj":"T626","pred":"source","obj":"Zoonoses"},{"subj":"T641","pred":"source","obj":"Zoonoses"},{"subj":"T674","pred":"source","obj":"Zoonoses"},{"subj":"T693","pred":"source","obj":"Zoonoses"},{"subj":"T694","pred":"source","obj":"Zoonoses"},{"subj":"T695","pred":"source","obj":"Zoonoses"},{"subj":"T696","pred":"source","obj":"Zoonoses"},{"subj":"T697","pred":"source","obj":"Zoonoses"},{"subj":"T840","pred":"source","obj":"Zoonoses"},{"subj":"T88","pred":"source","obj":"Zoonoses"},{"subj":"T89","pred":"source","obj":"Zoonoses"},{"subj":"T960","pred":"source","obj":"Zoonoses"},{"subj":"T961","pred":"source","obj":"Zoonoses"},{"subj":"T962","pred":"source","obj":"Zoonoses"},{"subj":"T1417","pred":"source","obj":"Zoonoses"},{"subj":"T1418","pred":"source","obj":"Zoonoses"},{"subj":"T1419","pred":"source","obj":"Zoonoses"},{"subj":"T1420","pred":"source","obj":"Zoonoses"},{"subj":"T1421","pred":"source","obj":"Zoonoses"},{"subj":"T1422","pred":"source","obj":"Zoonoses"},{"subj":"T1423","pred":"source","obj":"Zoonoses"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"Zoonoses","color":"#93ecb4","default":true}]}]}}