Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

Table 2 Accuracy of consensus sequence from serial dilutions (EID₅₀/ml) of NDV LaSota during MinION sequencing run 1

Sequencing run time (min)	Total Raw reads	10^6		10^5		10^4		10^3		10^2		10^1
Sequencing run time (min)	Total Raw reads	NDV reads^a	% Identity^b	NDV reads	% Identity	NDV reads	% Identity	NDV reads	% Identity	NDV reads	% Identity	NDV reads	% Identity
5	4000	283	100	199	100	182	100	10	99.18	2	NA	3	NA
7	8000	644	100	406	100	368	100	14	99.32	8	98.77	5	98.37
10	12,000	1029	100	661	100	571	100	23	99.32	16	99.32	8	99.18
12	16,000	1397	100	901	100	759	100	29	99.86	17	99.32	14	99.45
14	20,000	1772	100	1173	100	1014	100	36	99.73	20	99.45	17	99.59
16	24,000	2183	100	1451	100	1231	100	43	99.73	23	99.45	21	99.59
19	28,000	2643	100	1775	100	1498	100	56	99.86	29	99.73	25	99.45

^aThe numbers represent total number of NDV reads obtained from LAclust. A maximum of 200 reads (optional cut-off value) were used to generate full length consensus sequence. Minimum 5 reads were used as a cut-off to build consensus sequence
^bConsensus sequence identity to the reference sequence of NDV LaSota sequenced with MiSeq
(MH392212/chicken/USA/LaSota/1946)
Consensus sequences were BLAST searched against NDV custom database
Note: Only 28,000 out of total 60,000 reads were utilized for the analysis