Skip to main content

Table 1 Comparison of MinION sequencing to RT-qPCR for detection of NDV LaSota (runs 1 and 2)

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

Dilution (EID50/ml)

Total readsa

Total NDV readsb

Reads per consensusc

Percent identityd

Consensus length

RT-qPCRe (Ct)

R1f | R2g

R1 | R2

R1 | R2

R1 | R2

R1 | R2

R1 | R2

10^6

6667 | 11,366

6577 | 10,861

200 | 200

100 | 100

734 | 734

21.8, 21.1 | 22.7, 22.7

10^5

4519 | 6801

4439 | 6540

200 | 200

100 | 100

734 | 734

26.3, 25.8 | 26.2, 26.4

10^4

3856 | 8289

3829 | 7890

200 | 200

100 | 100

734 | 734

28.9, 27.8 | 29.1, 29.3

10^3

164 | 9484

157 | 9061

157 | 200

100 | 100

734 | 734

31.4, 31.1 | 32.7, 32.8

10^2

94 | 4939

85 | 4725

85 | 200

100 | 100

734 | 734

34.2, 34.8 | 34.8, 35.3

10^1

133 | 2652

131 | 2520

131 | 200

99.04 | 99.86

729 | 734

34.9, 34.8 | 36.9, 36.7

  1. aObtained from output of Porechop
  2. bObtained from output of LAclust
  3. cObtained from output of BWA-MEM. Input into BWA-MEM was limited to 200 reads based on LAclust options
  4. dConsensus sequence identity to the reference sequence of NDV LaSota sequenced with MiSeq
  5. (MH392212/chicken/USA/LaSota/1946)
  6. eEach dilution performed in duplicate and threshold cycle (Ct) values from each well are shown here
  7. fRun 1
  8. gRun 2
  9. Note: All 60,000 reads obtained during 32 min of sequencing run (R1) were utilized for the analysis. All 98,916 reads from R2 were utilized for the analysis
Back to article page

Virology Journal

ISSN: 1743-422X