SupplementalTABLE S2 Previously published genome sequences used in the analysis, and unpublished genomes from recent outbreaks.

Sample / Geographic Origin / Date of Collectiona / Subtypeb / Sourcec / Accessiond
2010EL-1786 / St. Marc Hospital, Artibonite, Haiti / 10/19/2010 / O1 OGET / C / SRX031665
2010EL-1792 / St. Marc Hospital, Artibonite, Haiti / 10/20/2010 / O1 OGET / C / SRX032204
2010EL-1798 / St. Nicholas Hospital, Artibonite, Haiti / 10/21/2010 / O1 OGET / C / SRX032202
cp1032 / Mexico / 1991 / O1 OGET / C / SRX067359
cp1038 / Zimbabwe / 2009 / O1 OGET / C / SRX067358
cp1041 / Zambia / 2004 / O1 OGET / C / SRX067356
cp1042 / Thailand / 2010 / O1 OGET / C / SRX067370
cp1048 / Bangladesh / 2010 / O1 OGET / C / SRX067350
cp1050 / Bangladesh / 2010 / O1 El Tor / C / SRX067381
hc-06a1 / Saint-Marc, Artibonite , Haiti / 2010 / O1 OGET / C / SRX059318
hc-19a1 / Saint-Marc, Artibonite , Haiti / 2010 / O1 OGET / C / SRX059383
hc-21a1 / Saint-Marc, Artibonite , Haiti / 2010 / O1 OGET / C / SRX059386
hc-22a1 / Saint-Marc, Artibonite , Haiti / 2010 / O1 OGET / C / SRX059380
hc-23a1 / Bassin Bleu, Nord-Ouest, Haiti / 2010 / O1 OGET / C / SRX049122
hc-28a1 / Gonaïves, Ouest, Haiti / 2010 / O1 OGET / C / SRX059375
hc-32a1 / Port-au-Prince, Ouest , Haiti / 2010 / O1 OGET / C / SRX059387
hc-33a2 / Port-au-Prince, Ouest , Haiti / 2010 / O1 OGET / C / SRX059384
hc-38a1 / Croix-des-Bouquets, Ouest, Haiti / 2010 / O1 OGET / C / SRX049128
hc-40a1 / Arcahaie, Ouest, Haiti / 2010 / O1 OGET / C / SRX049121
hc-43a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX049126
hc-48a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX049144
hc-48b2 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059382
hc-49a2 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX049120
hc-61a1 / Croix-des-Bouquets, Ouest, Haiti / 2010 / O1 OGET / C / SRX049119
hc-62a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX098262
hc-64a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059354
hc-65a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059324
hc-67a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059358
hc-68a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059359
hc-70a1 / Montrouis, Ouest, Haiti / 2010 / O1 OGET / C / SRX049129
hc-71a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059356
hc-72a2 / Arcahaie, Ouest, Haiti / 2010 / O1 OGET / C / SRX059699
hc-7a1 / Dessalines, Artibonite, Haiti / 2010 / O1 OGET / C / SRX059355
hc-80a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059357
hc-81a1 / Port-au-Prince, Ouest, Haiti / 2010 / O1 OGET / C / SRX059326
hcuf01 / Saint-Marc, Artibonite, Haiti / 2010 / O1 OGET / C / SRX049116
hfu-02 / Saint-Marc, Artibonite, Haiti / 2010 / O1 OGET / C / SRX049143
vc-1 / Banke district, Nepalgunj municipality / 7/30/2010 / O1 OGET / C / SRX082797
vc-10 / Banke district, Nepalgunj municipality, ward 12 / 8/1/2010 / O1 OGET / C / SRX082841
vc-11 / Kailali district, Dhangadhi / 8/1/2010 / O1 OGET / C / SRX082842
vc-12 / Dang Deokhuri district, Narayanpur VDC, ward 7 / 8/1/2010 / O1 OGET / C / SRX082843
vc-13 / Banke district, Nepalgunj municipality, ward 8 / 8/1/2010 / O1 OGET / C / SRX082938
vc-14 / Banke district, Nepalgunj municipality, ward 5 / 8/1/2010 / O1 OGET / C / SRX082939
vc-15 / Dang Deokhuri district, Narayanpur VDC, ward 5 / 8/8/2010 / O1 OGET / C / SRX082940
vc-16 / Banke district, Nepalgunj municipality, ward 6 / 8/8/2010 / O1 OGET / C / SRX082941
vc-17 / Banke district, Nepalgunj municipality / 8/31/2010 / O1 OGET / C / SRX082942
vc-18 / Banke district, Nepalgunj municipality / 8/31/2010 / O1 OGET / C / SRX082943
vc-19 / Kathmandu district, Kathmandu city / 8/15/2010 / O1 OGET / C / SRX082944
vc-2 / Banke district, Nepalgunj municipality / 7/30/2010 / O1 OGET / C / SRX082833
vc-20 / Kathmandu district, Kathmandu city / 11/1/2010 / O1 OGET / C / SRX082945
vc-21 / Rupandehi district, Butawal municipality / 8/30/2010 / O1 OGET / C / SRX082946
vc-22 / Rupandehi district, Butawal municipality / 8/30/2010 / O1 OGET / C / SRX082947
vc-25 / Rupandehi district, Butawal municipality / 8/30/2010 / O1 OGET / C / SRX082948
vc-26 / Rupandehi district, Butawal municipality / 8/30/2010 / O1 OGET / C / SRX082949
vc-3 / Banke district, Nepalgunj municipality, ward 5 / 8/1/2010 / O1 OGET / C / SRX082834
vc-4 / Banke district, Nepalgunj municipality, ward 4 / 8/1/2010 / O1 OGET / C / SRX082835
vc-5 / Banke district, Nepalgunj municipality, ward 5 / 8/1/2010 / O1 OGET / C / SRX082836
vc-6 / Banke district, Nepalgunj municipality, ward 4 / 8/1/2010 / O1 OGET / C / SRX082837
vc-7 / Banke district, Nepalgunj municipality, ward 6 / 8/1/2010 / O1 OGET / C / SRX082838
vc-8 / Banke district, Nepalgunj municipality, ward 5 / 8/1/2010 / O1 OGET / C / SRX082839
vc-9 / Banke district, Nepalgunj municipality, ward 4 / 8/1/2010 / O1 OGET / C / SRX082840
2010EL-1961 / Centre, Haiti / 10/19/2010 / O1 OGET / C / SRX249464
2010EL-2010N / Ouest, Haiti / 11/3/2010 / O1 OGET / C / SRX249466
2010EL-2010H / Ouest, Haiti / 11/3/2010 / O1 OGET / C / SRX249465
2011EL-1089 / Sud, Haiti / 11/27/2010 / O1 OGET / C / SRX249468
2011EL-1133 / Nord-Ouest, Haiti / 1/26/2011 / O1 OGET / C / SRX249469
2011V-1021 / Dominican Republic / 1/30/2011 / O1 OGET / C / SRX249662
2009V-1085 / Sri Lanka/India / 2009 / O1 OGET / C / SRX249422
2009V-1096 / India / 2009 / O1 INET / C / SRX249431
2010EL-1749 / Cameroon / 2010 / O1 OGET / C / SRX249463
2009V-1131 / India / 2009 / O1 OGET / C / SRX249462
3554–08 / Nepal / 2008 / O1 OGET / C / SRX249691
2011EL-1137 / South Africa / 2009 / O1 OGET / C / SRX249661
2009V-1046 / Pakistan / 2009 / O1 OGET / C / SRX249421
2009V-1116 / Pakistan / 2009 / O1 OGET / C / SRX249461
2010V-1014 / Pakistan / 2010 / O1 OGET / C / SRX249467
3582-05 / Pakistan / 2005 / O1 INET / C / SRX249692
3500-05 / India / 2005 / O1 INET / C / SRX249663
3546-06 / India / 2006 / O1 INET / C / SRX249690
C6706 / Peru / 1991 / O1 INET / C / SRX249693
2011EL-1938 / Orissa, India / 2009 / O1 OGET / C / SRX298898
2011EL-1939 / Sundarban, West Bengal, India / 2009 / O1 OGET / C / SRX298922
2011EL-1141 / Samangan, Afghanistan / 2008 / O1 OGET / C / SRX298934
2011EL-1941 / Kolkata, West Bengal, India / 2010 / O1 OGET / C / SRX298945
2012V-1001 / United States (Travel to Benin) / 2011 / O1 OGET / C / SRX298948

aMM/DD/YYYY format

bOGET: Ogawa El Tor; INET: Inaba El Tor

cC: clinical

dNCBI accession number.