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Details and fragments #2

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9546db1
updates outbreaks and genomes
jtmccr1 Jan 15, 2025
fa38ba5
adds information about fragments
jtmccr1 Jan 31, 2025
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69 changes: 36 additions & 33 deletions ebov/EBOV_Outbreak_Genomes.csv
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label,country,accession,name,date,range,outbreak,exclude?,notes
KR063671|Yambuku-Mayinga|DRC|1976-10-01,DRC,KR063671,Yambuku-Mayinga,1976-10-01,,Yambuku/1976,,
KC242801|deRoover|DRC|1976-09,DRC,KC242801,deRoover,1976-09,,Yambuku/1976,y, 'de Roover' name of patient
KM655246|Yambuku-Ecran|DRC|1976-09,DRC,KM655246,Yambuku-Ecran,1976-09,,Yambuku/1976,y, 'Ecran' name of patient; date from Kuhn et al but not definative
KC242791|Bonduni|DRC|1977-06,DRC,KC242791,Bonduni,1977-06,,Bonduni/1977,,
KC242792|Gabon|Gabon|1994-12-27,GAB,KC242792,Gabon,1994-12-27,,Minkebe/1994,,Date from Amblard et al (1997) Lancet
KU182905|Kikwit-9510621|DRC|1995-05-04,DRC,KU182905,Kikwit-9510621,1995-05-04,,Kikwit/1995,,
KC242799|13709_Kikwit|DRC|1995-06-17,DRC,KC242799,13709_Kikwit,1995-06-17?,,Kikwit/1995,y,Date is last from this outbreak? Not sure why.
KC242793|1Eko|Gabon|1996-02,GAB,KC242793,1Eko,1996-02,,Mayibout/1996,,Inferred as Mayibout due to genetic proximity to EBOV|EU051639_HQ849547|Mayibout|Gabon|1996 - genome fragments.
KC242795|1Mbie|Gabon|1996-02,GAB,KC242795,1Mbie,1996-02,,Mayibout/1996,y,Dates are Feb-8 or Feb-22 from Georges-Courbot et al (1997) Emerg Infect Dis
KC242797|1Oba|Gabon|1996-02,GAB,KC242797,1Oba,1996-02,,Mayibout/1996,y,
KC242794|2Nza|Gabon|1996-10-27,GAB,KC242794,2Nza,1996-10,,Booue/1996,y,Inferred as Booue due to genetic proximity to EBOV|AY058898|Bouee_96|Gabon|1996 - genome fragments.
KC242798|1Ikot|Gabon|1996-10-27,GAB,KC242798,1Ikot,1996-10-27,,Booue/1996,,Date of sampling from Georges-Courbot et al (1997) Emerg Infect Dis
KY471124|inoculum_strain_Gabon||Gabon|2001-11-30,GAB,KY471124,inoculum_strain_Gabon,2001-11-30,,Mekambo/2001,y,Date of sampling from WHO WER June 2003
KC242800|Ilembe|Gabon|2002-02-23,GAB,KC242800,Ilembe,2002-02-23,,Mekambo/2001,,"Pers comm from Eric Leroy: ""Ilembe is the last name of a patient who died of Ebola infection. She lived in the town of Makokou. She was 77 years old. She was sampled on 23 February 2002, the same day of her death."""
KF113528|Kelle_1|COG|2003-10,COG,KF113528,Kelle_1,2003-10,,Mbomo/2003,y,Outbreak: Oct-Dec 2003
KF113529|Kelle_2|COG|2003-10,COG,KF113529,Kelle_2,2003-10,,Mbomo/2003,,Outbreak: Oct-Dec 2003
KC242784|9_Luebo|DRC|2007,DRC,KC242784,9_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242785|0_Luebo|DRC|2007,DRC,KC242785,0_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242786|1_Luebo|DRC|2007,DRC,KC242786,1_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242787|23_Luebo|DRC|2007,DRC,KC242787,23_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242789|4_Luebo|DRC|2007,DRC,KC242789,4_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242790|5_Luebo|DRC|2007,DRC,KC242790,5_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242788|43_Luebo|DRC|2007,DRC,KC242788,43_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
HQ613403|M-M|DRC|2007-08-31,DRC,HQ613403,M-M,2007-08-31,,Luebo/2007,,
HQ613402|034-KS|DRC|2008-12-31,DRC,HQ613402,034-KS,2008-12-31,,Luebo/2008,,
KJ660347|Makona-Gueckedou-C07|Guinea|2014-03-20,GIN,KJ660347,Makona-Gueckedou-C07,2014-03-20,,West_Africa/2013,,
KP271018|Lomela-Lokolia16|DRC|2014-08-20,DRC,KP271018,Lomela-Lokolia16,2014-08-20,,Boende-Lokolia/2014,,
KP271020|Lomela-Lokolia19|DRC|2014-08-20,DRC,KP271020,Lomela-Lokolia19,2014-08-20,,Boende-Lokolia/2014,y,
KM519951|Boende-Lokolia|DRC|2014,DRC,KM519951,Boende-Lokolia,2014-08,,Boende-Lokolia/2014,y,
MH613311|Muembe.1|DRC|2017-05,DRC,MH613311,Muembe.1,2017-05-07,,Likati/2017,,Sampling date taken from MH481611 (same sample?)
MH733477|BIK009-Bikoro|DRC|2018-05-10,DRC,MH733477,BIK009,2018-05-10,,Bikoro-Mbandaka/2018,,
MK007330|18FHV090-Beni|DRC|2018-07-28,DRC,MK007330,18FHV090,2018-07-28,,Kivu/2018,,
label,country,accession,name,date,range,outbreak,exclude?,notes
KR063671|Yambuku-Mayinga|DRC|1976-10-01,DRC,KR063671,Yambuku-Mayinga,1976-10-01,,Yambuku/1976,,
KC242801|deRoover|DRC|1976-09,DRC,KC242801,deRoover,1976-09,,Yambuku/1976,y, 'de Roover' name of patient
KM655246|Yambuku-Ecran|DRC|1976-09,DRC,KM655246,Yambuku-Ecran,1976-09,,Yambuku/1976,y, 'Ecran' name of patient; date from Kuhn et al but not definative
KC242791|Bonduni|DRC|1977-06,DRC,KC242791,Bonduni,1977-06,,Bonduni/1977,,
KC242792|Gabon|Gabon|1994-12-27,GAB,KC242792,Gabon,1994-12-27,,Minkebe/1994,,Date from Amblard et al (1997) Lancet
KU182905|Kikwit-9510621|DRC|1995-05-04,DRC,KU182905,Kikwit-9510621,1995-05-04,,Kikwit/1995,,
KC242799|13709_Kikwit|DRC|1995-06-17,DRC,KC242799,13709_Kikwit,1995-06-17?,,Kikwit/1995,y,Date is last from this outbreak? Not sure why.
KC242793|1Eko|Gabon|1996-02,GAB,KC242793,1Eko,1996-02,,Mayibout/1996,,Inferred as Mayibout due to genetic proximity to EBOV|EU051639_HQ849547|Mayibout|Gabon|1996 - genome fragments.
KC242795|1Mbie|Gabon|1996-02,GAB,KC242795,1Mbie,1996-02,,Mayibout/1996,y,Dates are Feb-8 or Feb-22 from Georges-Courbot et al (1997) Emerg Infect Dis
KC242797|1Oba|Gabon|1996-02,GAB,KC242797,1Oba,1996-02,,Mayibout/1996,y,
KC242794|2Nza|Gabon|1996-10-27,GAB,KC242794,2Nza,1996-10,,Booue/1996,y,Inferred as Booue due to genetic proximity to EBOV|AY058898|Bouee_96|Gabon|1996 - genome fragments.
KC242798|1Ikot|Gabon|1996-10-27,GAB,KC242798,1Ikot,1996-10-27,,Booue/1996,,Date of sampling from Georges-Courbot et al (1997) Emerg Infect Dis
KY471124|inoculum_strain_Gabon||Gabon|2001-11-30,GAB,KY471124,inoculum_strain_Gabon,2001-11-30,,Mekambo/2001,y,Date of sampling from WHO WER June 2003
KC242800|Ilembe|Gabon|2002-02-23,GAB,KC242800,Ilembe,2002-02-23,,Mekambo/2001,,"Pers comm from Eric Leroy: ""Ilembe is the last name of a patient who died of Ebola infection. She lived in the town of Makokou. She was 77 years old. She was sampled on 23 February 2002, the same day of her death."""
KF113528|Kelle_1|COG|2003-10,COG,KF113528,Kelle_1,2003-10,,Mbomo/2003,y,Outbreak: Oct-Dec 2003
KF113529|Kelle_2|COG|2003-10,COG,KF113529,Kelle_2,2003-10,,Mbomo/2003,,Outbreak: Oct-Dec 2003
KC242784|9_Luebo|DRC|2007,DRC,KC242784,9_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242785|0_Luebo|DRC|2007,DRC,KC242785,0_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242786|1_Luebo|DRC|2007,DRC,KC242786,1_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242787|23_Luebo|DRC|2007,DRC,KC242787,23_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242789|4_Luebo|DRC|2007,DRC,KC242789,4_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242790|5_Luebo|DRC|2007,DRC,KC242790,5_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
KC242788|43_Luebo|DRC|2007,DRC,KC242788,43_Luebo,2007-,May-Nov 2007,Luebo/2007,y,Outbreak: May-Nov 2007
HQ613403|M-M|DRC|2007-08-31,DRC,HQ613403,M-M,2007-08-31,,Luebo/2007,,
HQ613402|034-KS|DRC|2008-12-31,DRC,HQ613402,034-KS,2008-12-31,,Luebo/2008,,
KJ660347|Makona-Gueckedou-C07|Guinea|2014-03-20,GIN,KJ660347,Makona-Gueckedou-C07,2014-03-20,,West_Africa/2013,,
KP271018|Lomela-Lokolia16|DRC|2014-08-20,DRC,KP271018,Lomela-Lokolia16,2014-08-20,,Boende-Lokolia/2014,,
KP271020|Lomela-Lokolia19|DRC|2014-08-20,DRC,KP271020,Lomela-Lokolia19,2014-08-20,,Boende-Lokolia/2014,y,
KM519951|Boende-Lokolia|DRC|2014,DRC,KM519951,Boende-Lokolia,2014-08,,Boende-Lokolia/2014,y,
MH613311|Muembe.1|DRC|2017-05,DRC,MH613311,Muembe.1,2017-05-07,,Likati/2017,,Sampling date taken from MH481611 (same sample? Sequences identical except ambiguities and terminal positions ) - Case 7 sequenced in Nsio et. al (https://doi.org/10.1093/infdis/jiz107) onset April 30 - death 09
MH733477|BIK009-Bikoro|DRC|2018-05-10,DRC,MH733477,BIK009,2018-05-10,,Bikoro-Mbandaka/2018,,
MK007330|18FHV090-Beni|DRC|2018-07-28,DRC,MK007330,18FHV090,2018-07-28,,Kivu/2018,,
OR084849|Mandaka|DRC|2020-05-31,DRC,OR084849,Mandaka,2020-05-31,,Equateur/2020,,
OR084846|MBK67|DRC|2020-06-12,DRC,OR084846,MBK67,2020-06-12,,Equateur/2020,,Tumba like - initially thought to be re-emergence of 2018 although no known link and epidemiological links to animals
|22MBK-004|DRC|2022-04-25,DRC,,22MBK-004,2022-04-25,,Équateur/2022,,https://virological.org/t/april-2022-ebola-virus-disease-case-in-equateur-province-drc-represents-a-new-spillover-event/795 case 2
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