TABLE 1

Overview of sequenced samplesa

Isolate IDProbable country of infectionYr of isolationGP60 subtype (accession no.)Avg coverage (×)DNA concn (ng/μl)No. of reads% mapped
SWEH1bEthiopia2014IbA9G3 (DQ665688 )490.510.0721,889,00185.48
SWEH2Kenya or Rwanda2012IdA14 (FJ153247 )23.92below LOD1,232,76681.91
SWEH3Tanzania2013IaA20R3 (KU727289 )17.73below LOD755,43394.29
SWEH4Burkina Faso2013IbA13G3 (KM539004 )43.64below LOD2,313,14468.43
SWEH5Denmark2013IfA12G1 (HQ149036 )41.34below LOD2,053,70882.03
SWEH6India2013IaA23R3 (JQ798143 )42.19below LOD1,953,21891.36
SWEH7South Africa2014IeA11G3T3 (GU214354 )26.35below LOD1,976,45647.20
SWEH8Spain20141bA10G2 (AY262031 )38.47below LOD1,281,98995.87
SWEH9Spain20141bA10G2 (AY262031 )21.84below LOD2,451,13148.03
SWEH10Greece20141bA10G2 (AY262031 )62.610.122,663,17282.44
SWEH11Spain20131bA10G2 (AY262031 )30.23below LOD1,546,95388.53
SWEH12Guatemala20141bA10G2 (AY262031 )43.16below LOD1,980,67393.23
SWEH13Sweden20141bA10G2 (AY262031 )29.41below LOD2,030,55255.83
SWEH14Sweden2013IkA18G1 (KU727290 )239.27NAc13,979,59483.41
  • a The purity of the samples (inferred from the percentage of mapped reads) ranged from 47% to 95%.

  • b Genome data from Andersson et al. (18).

  • c NA, concentration not measured.