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tidy up annots more
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@emmahodcroft
emmahodcroft committed Sep 17, 2020
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44 changes: 21 additions & 23 deletions source-data/gisaid_annotations.tsv
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# Egypt/C-CU001a-S1/2020 EPI_ISL_529031 additional_location_info: Cairo University (Abol-Reesh) Pediatric Hospital (CUSPH) Mounira, Cairo
# Egypt/C-CU002b-S3/2020 EPI_ISL_529032 additional_host_info: Healthcare worker: Hospital employee
# Egypt/C-CU002b-S3/2020 EPI_ISL_529032 additional_location_info: Cairo University (Abol-Reesh) Pediatric Hospital (CUSPH) Mounira, Cairo
# env/USA/FL-UF-20/2020 EPI_ISL_477160 Air in the hospital room of COVID-19 patients
# Brazil/RJ-0395/2020 EPI_ISL_500864 # sample obtained 1 hour after birth
# HongKong/HKU-200823-001/2020 EPI_ISL_516798 Reported case of reinfection (1st infection EPI_ISL_516798 2nd infection EPI_ISL_516799)
# HongKong/HKU-200823-002/2020 EPI_ISL_516799 Reported case of reinfection (1st infection EPI_ISL_516798 2nd infection EPI_ISL_516799)
# ZZZ note UPHL-03 (EPI_ISL_415541) and -04 (EPI_ISL_415542) are same patient
# ZZZ note UPHL-05 and -06 are same patient
## location & data info come first, then 'paper' data comes second
Expand Down Expand Up @@ -2923,7 +2927,6 @@ Brazil/SPBR-12/2020 EPI_ISL_416034 division_exposure USA
Brazil/SPBR-14/2020 EPI_ISL_416036 region_exposure Europe
Brazil/SPBR-14/2020 EPI_ISL_416036 country_exposure Italy
Brazil/SPBR-14/2020 EPI_ISL_416036 division_exposure Italy
# Brazil/RJ-0395/2020 EPI_ISL_500864 # sample obtained 1 hour after birth
Brazil/RJ-2422/2020 EPI_ISL_467352 location Queimados
Brazil/RJ-1555/2020 EPI_ISL_467344 location Petropolis
Brazil/RJ-2669/2020 EPI_ISL_467353 location Niteroi
Expand Down Expand Up @@ -4568,6 +4571,9 @@ Ecuador/USFQ-707/2020 EPI_ISL_471269 location Quito
Ecuador/USFQ-193/2020 EPI_ISL_527809 division Bolivar EC # previously Bolivar
Ecuador/USFQ-194/2020 EPI_ISL_527810 division Bolivar EC # previously Bolivar
Ecuador/USFQ-195/2020 EPI_ISL_527811 division Bolivar EC # previously Bolivar
Egypt/HCoV2-Egy-002/2020 EPI_ISL_510532 region Africa # previously Asia
Egypt/Army-MCL001/2020 EPI_ISL_510526 division Faiyum # previously Fayoum
Egypt/HCoV2-Egy-002/2020 EPI_ISL_510532 division Faiyum # previously Fayoum
England/01/2020 EPI_ISL_407071 division_exposure Hubei # first cases were reported in media as being son & mother from China
England/01/2020 EPI_ISL_407071 country_exposure China # first cases were reported in media as being son & mother from China
England/01/2020 EPI_ISL_407071 country United Kingdom
Expand Down Expand Up @@ -17129,8 +17135,6 @@ HongKong/HKU-200723-103/2020 EPI_ISL_497870 country Hong Kong #previously China
HongKong/HKU-200723-104/2020 EPI_ISL_498269 country Hong Kong #previously China
HongKong/HKU-200723-105/2020 EPI_ISL_498270 country Hong Kong #previously China
HongKong/HKU-200723-106/2020 EPI_ISL_498271 country Hong Kong #previously China
#HongKong/HKU-200823-001/2020 EPI_ISL_516798 Reported case of reinfection (1st infection EPI_ISL_516798 2nd infection EPI_ISL_516799)
#HongKong/HKU-200823-002/2020 EPI_ISL_516799 Reported case of reinfection (1st infection EPI_ISL_516798 2nd infection EPI_ISL_516799)
HongKong/HKU-200823-002/2020 EPI_ISL_516799 division_exposure Europe #travel from Spain via the United Kingdom
HongKong/HKU-200823-002/2020 EPI_ISL_516799 country_exposure Europe #travel from Spain via the United Kingdom
HongKong/HKU-200823-002/2020 EPI_ISL_516799 region_exposure Europe #travel from Spain via the United Kingdom
Expand Down Expand Up @@ -18073,6 +18077,20 @@ Indonesia/JB-TFRIC19-R4975/2020 EPI_ISL_528749 division West Java # previously J
Indonesia/JB-TFRIC19-R53817/2020 EPI_ISL_528753 division West Java # previously Jawa Barat
Iran/KHGRC-3-2178/2020 EPI_ISL_445088 division Iran # whitespace
Iran/KHGRC-3-2178/2020 EPI_ISL_445088 country Iran # whitespace
Italy/VR-IZSVe-101-12/2020 EPI_ISL_522855 location Verona IT # previously Verona
Italy/VR-IZSVe-46-41/2020 EPI_ISL_522856 location Verona IT # previously Verona
Italy/VR-IZSVe-50893/2020 EPI_ISL_522857 location Verona IT # previously Verona
Italy/VR-IZSVe-51-5/2020 EPI_ISL_522858 location Verona IT # previously Verona
Italy/VR-IZSVe-51635/2020 EPI_ISL_522859 location Verona IT # previously Verona
Italy/VR-IZSVe-54-17/2020 EPI_ISL_522860 location Verona IT # previously Verona
Italy/VR-IZSVe-55-111/2020 EPI_ISL_522861 location Verona IT # previously Verona
Italy/VR-IZSVe-55-16/2020 EPI_ISL_522862 location Verona IT # previously Verona
Italy/VR-IZSVe-55-18/2020 EPI_ISL_522863 location Verona IT # previously Verona
Italy/VR-IZSVe-55-56/2020 EPI_ISL_522864 location Verona IT # previously Verona
Italy/VR-IZSVe-60-40/2020 EPI_ISL_522865 location Verona IT # previously Verona
Italy/VR-IZSVe-63-7/2020 EPI_ISL_522866 location Verona IT # previously Verona
Italy/VR-IZSVe-71-10/2020 EPI_ISL_522867 location Verona IT # previously Verona
Italy/VR-IZSVe-94-28/2020 EPI_ISL_522868 location Verona IT # previously Verona
Italy/BG-11639-28Feb/2020 EPI_ISL_460080 division Lombardy
Italy/BG-5825-22Feb/2020 EPI_ISL_460079 division Lombardy
Italy/BG-7158-24Feb/2020 EPI_ISL_460081 division Lombardy
Expand Down Expand Up @@ -32885,7 +32903,6 @@ USA/FL_6318/2020 EPI_ISL_420785 region North America
USA/FL-CDC-7619/2020 EPI_ISL_447841 region North America
USA/FL-UW-MAYO68/2020 EPI_ISL_490988 division Florida # previously Fl
USA/FL-UW-1387/2020 EPI_ISL_536758 location # Los Angeles County doesn't exist in Florida
# env/USA/FL-UF-20/2020 EPI_ISL_477160 Air in the hospital room of COVID-19 patients
USA/GA_1299/2020 EPI_ISL_420787 division Georgia
USA/GA_1299/2020 EPI_ISL_420787 region North America
USA/GA_1299/2020 EPI_ISL_420787 country USA
Expand Down Expand Up @@ -35780,8 +35797,6 @@ mink/Netherlands/NB-EMC-7-3/2020 EPI_ISL_523111 division North Brabant # previou
mink/Netherlands/NB-EMC-7-6/2020 EPI_ISL_523112 division North Brabant # previously Noord Brabant
mink/Netherlands/NB-EMC-9-1/2020 EPI_ISL_523119 division North Brabant # previously Noord Brabant
mink/Netherlands/NB-EMC-9-3/2020 EPI_ISL_523120 division North Brabant # previously Noord Brabant
#
# Beginning of paper data
Brazil/AMBR-02/2020 EPI_ISL_417034 division Amazonas # previously Amazonas State
France/220_95/2020 EPI_ISL_469282 division Ile de France
France/220_95/2020 EPI_ISL_469282 location Paris
Expand Down Expand Up @@ -41523,9 +41538,6 @@ Egypt/NRC-01/2020 EPI_ISL_430820 title "SARS-CoV-2 Genome Analysis of Japanese T
Egypt/NRC-01/2020 EPI_ISL_430820 paper_url https://dx.doi.org/10.3389/fmicb.2020.01316
Egypt/NRC-03/2020 EPI_ISL_430819 title "SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise"
Egypt/NRC-03/2020 EPI_ISL_430819 paper_url https://dx.doi.org/10.3389/fmicb.2020.01316
Egypt/HCoV2-Egy-002/2020 EPI_ISL_510532 region Africa # previously Asia
Egypt/Army-MCL001/2020 EPI_ISL_510526 division Faiyum # previously Fayoum
Egypt/HCoV2-Egy-002/2020 EPI_ISL_510532 division Faiyum # previously Fayoum
England/01/2020 EPI_ISL_407071 title "Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages"
England/01/2020 EPI_ISL_407071 paper_url https://virological.org/t/preliminary-analysis-of-sars-cov-2-importation-establishment-of-uk-transmission-lineages/507
England/02/2020 EPI_ISL_407073 title "Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages"
Expand Down Expand Up @@ -46384,20 +46396,6 @@ Italy/UniMI02/2020 EPI_ISL_417446 title "Genomic characterization and phylogenet
Italy/UniMI02/2020 EPI_ISL_417446 paper_url https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25794
Italy/UniMI03/2020 EPI_ISL_417447 title "Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy"
Italy/UniMI03/2020 EPI_ISL_417447 paper_url https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25794
Italy/VR-IZSVe-101-12/2020 EPI_ISL_522855 location Verona IT # previously Verona
Italy/VR-IZSVe-46-41/2020 EPI_ISL_522856 location Verona IT # previously Verona
Italy/VR-IZSVe-50893/2020 EPI_ISL_522857 location Verona IT # previously Verona
Italy/VR-IZSVe-51-5/2020 EPI_ISL_522858 location Verona IT # previously Verona
Italy/VR-IZSVe-51635/2020 EPI_ISL_522859 location Verona IT # previously Verona
Italy/VR-IZSVe-54-17/2020 EPI_ISL_522860 location Verona IT # previously Verona
Italy/VR-IZSVe-55-111/2020 EPI_ISL_522861 location Verona IT # previously Verona
Italy/VR-IZSVe-55-16/2020 EPI_ISL_522862 location Verona IT # previously Verona
Italy/VR-IZSVe-55-18/2020 EPI_ISL_522863 location Verona IT # previously Verona
Italy/VR-IZSVe-55-56/2020 EPI_ISL_522864 location Verona IT # previously Verona
Italy/VR-IZSVe-60-40/2020 EPI_ISL_522865 location Verona IT # previously Verona
Italy/VR-IZSVe-63-7/2020 EPI_ISL_522866 location Verona IT # previously Verona
Italy/VR-IZSVe-71-10/2020 EPI_ISL_522867 location Verona IT # previously Verona
Italy/VR-IZSVe-94-28/2020 EPI_ISL_522868 location Verona IT # previously Verona
Japan/DP0005/2020 EPI_ISL_416565 title "Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak"
Japan/DP0005/2020 EPI_ISL_416565 paper_url https://dx.doi.org/10.1101/2020.03.23.20041970
Japan/DP0027/2020 EPI_ISL_416566 title "Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak"
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