Table 5.

Sequencing metrics for clinical isolates from The Philippines

ID	Serotype	Genotype	Reads passing QC	Coding-Region Coverage (%)		Nucleotide Consensus Similarity (%)		Single-plex Amplification Result (5′ → 3′)
				1X	20X	1X	20X	1	2	3	4	5
130,158	1	IV	6852	99.80	79.22	99.57	99.86	+	+	+	+	–
130,104	2	Cosmo.	12,932	99.99	94.57	99.80	99.92	+	+	+	+	–
1,601,002	3	I	4605	99.93	89.40	99.17	99.70	+	+	+	+	+
130,343	4	II	7805	99.90	90.40	99.24a	99.70a	+	+	+	+	–

^aSeveral of the single-plex reactions were unsuccessful (−), and had to be repeated using primers from the multiplex primer set to generate the reference amplicons that were sequenced on the Illumina platform. The single-plex approach was unable to generate an amplicon covering the 3′ end of the DENV-4 genome, despite repeated attempts with a range of primers. Therefore, it should be noted that the accuracy of the multiplex-generated consensus sequence is not for the full coding region, but only accounts for 10,117 of the 10,163 coding bases