TABLE 1.

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

Sample	Test result before mNGS		Metagenomic next-generation sequencing									Test result after mNGS
	ZIKV RT-PCRb	DENV Ab	No. of raw reads	No. of ZIKV reads	% ZIKV reads	ZIKV mNGS (run 1/run 2)	% ZIKV coverage	No. of CHIKV reads	% CHIKV reads	CHIKV mNGS (run 1/run 2)	% CHIKV coverage	CHIKV RT-PCR	ZIKV qRT-PCRc	ZIKV viral load (no. of copies/ml)	DENV RT-PCR
Bahia01	+	−	3,507,376	103	0.003	+/+	34.1	0	0	−/−	0.0	−	+	1,042	−
Bahia02	+	−	3,668,673	129	0.003	+/+	39.5	0	0	−/−	0.0	−	+	4,086	−
Bahia03	+	−	24,063	2	0.008	+/+	1.3	0	0	−/−	0.0	−	+	3,272	−
Bahia04	+	−	3,060,229	14	0.0005	+/+	9.6	0	0	−/−	0.0	−	+	1,464	−
Bahia05	+	−	3,501,316	19	0.0005	+/+	11.8	0	0	−/−	0.0	−	+	1,091	−
Bahia06	+	−	2,576,002	11	0.0004	+/+	5.4	4	0.0002	+/+	1.1	−	−	<31	−
Bahia07	+	−	6,903,397	281,099	4.1	+	100.0	0	0	−	0.0	−	+	9.00E+08	−
Bahia08	+	−	1,094,355	55	0.005	+	35.1	252,649	23.1	+	100.0	+	+	2,470	−
Bahia09	+	−	743,266	719	0.1	+	97.6	84	0.01	+	49.1	+	+	23,121	−
Bahia10	+	−	2,482,665	22	0.0009	+/+	5.7	0	0	−/−	0.0	−	−	<31	−
Bahia11	+	−	2,384,416	234	0.01	+/+	40.9	37	0.002	+/+	8.6	−	+	3,981	−
Bahia12	+	−	3,712,405	44	0.001	+/+	21.3	23	0.0006	+/+	9.8	−	+	1,327	−
Bahia13	+	−	2,556,556	0	0	−/−	0.0	1	0	+/−	1.4	−	−	<31	−
Bahia14	+	−	3,658,143	0	0	−/−	0.0	0	0	−/−	0.0	−	+	517	−
Bahia15	+	−	2,848,486	17	0.001	+/+	7.9	0	0	−/−	0.0	−	−	<31	−

^aAbbreviations: mNGS, metagenomic next-generation sequencing; Ab, antibody.

^bRT-PCR assay using the primers and conditions used by Balm et al. (6).

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