Comparison and application of a novel genotyping method, semiautomated primer-specific and mispair extension analysis, and four other genotyping assays for detection of hepatitis C virus mixed-genotype infections
Yw. Hu et al., Comparison and application of a novel genotyping method, semiautomated primer-specific and mispair extension analysis, and four other genotyping assays for detection of hepatitis C virus mixed-genotype infections, J CLIN MICR, 38(8), 2000, pp. 2807-2813
To date the true prevalence of hepatitis C virus (HCV) mixed-genotype infec
tions has not been established mainly because currently available methods a
re not suitable for the detection of mixed genotypes in a viral population.
A novel semiautomated genotyping method, primer-specific and mispair exten
sion analysis (S-PSMEA), which is more reliable than other genotyping assay
s was developed for detection of HCV mixed-genotype infections. A genotype
present at levels as low as 0.8% in a defined mix of HCV genotypes was dete
cted, showing a 20-fold increase in sensitivity over that of direct DNA seq
uencing. A total of 434 HCV isolates were genotyped and analyzed for a comp
arative study of the accuracy between S-PSMEA and four current genotyping m
ethods. The results showed that viruses in approximately 40% of the samples
from this group determined to be infected with mixed genotypes by S-PSMEA
were undetected by direct DNA sequencing due to its low sensitivity. Type-s
pecific PCR, line probe assay, and restriction fragment length polymorphism
analysis performed poorly, being able to identify only 38.5, 16.1, and 15.
4% of mixed-genotype infections, respectively, that were detected by direct
DNA sequencing. The prevalence of mixed-genotype infections detected by S-
PSMEA was 7.9% (12 of 152 donors) among HCV-infected blood donors, 14.3% (1
5 of 105) among patients with chronic hepatitis C, and 17.1% (6 of 36) amon
g thalassemia patients who had received multiple transfusions. The data lea
d us to conclude that HCV mixed-genotype infections are more common than pr
eviously estimated and that S-PSMEA may be the method of choice when detect
ion of genotypes present at low levels in mixed-genotype infections is requ
ired due to its higher level of sensitivity.