TABLE 1

ZIKV and CHIKV testing of 15 PCR-positive ZIKV cases in Bahia, Brazil, from April 2015 to January 2016a

SampleTest result before mNGSMetagenomic next-generation sequencingTest result after mNGS
ZIKV RT-PCRbDENV AbNo. of raw readsNo. of ZIKV reads% ZIKV readsZIKV mNGS (run 1/run 2)% ZIKV coverageNo. of CHIKV reads% CHIKV readsCHIKV mNGS (run 1/run 2)% CHIKV coverageCHIKV RT-PCRZIKV qRT-PCRcZIKV viral load (no. of copies/ml)DENV RT-PCR
Bahia01+3,507,3761030.003+/+34.100−/−0.0+1,042
Bahia02+3,668,6731290.003+/+39.500−/−0.0+4,086
Bahia03+24,06320.008+/+1.300−/−0.0+3,272
Bahia04+3,060,229140.0005+/+9.600−/−0.0+1,464
Bahia05+3,501,316190.0005+/+11.800−/−0.0+1,091
Bahia06+2,576,002110.0004+/+5.440.0002+/+1.1<31
Bahia07+6,903,397281,0994.1+100.0000.0+9.00E+08
Bahia08+1,094,355550.005+35.1252,64923.1+100.0++2,470
Bahia09+743,2667190.1+97.6840.01+49.1++23,121
Bahia10+2,482,665220.0009+/+5.700−/−0.0<31
Bahia11+2,384,4162340.01+/+40.9370.002+/+8.6+3,981
Bahia12+3,712,405440.001+/+21.3230.0006+/+9.8+1,327
Bahia13+2,556,55600−/−0.010+/−1.4<31
Bahia14+3,658,14300−/−0.000−/−0.0+517
Bahia15+2,848,486170.001+/+7.900−/−0.0<31
  • a Abbreviations: mNGS, metagenomic next-generation sequencing; Ab, antibody.

  • b RT-PCR assay using the primers and conditions used by Balm et al. (6).

  • c SYBR green qRT-PCR assay using PCR primers targeting the envelope gene (ZIKV-1086/ZIKV-1162) and conditions used by Lanciotti et al. (12).