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Journal of Clinical Microbiology, July 2005, p. 3576-3577, Vol. 43, No. 7
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.7.3576-3577.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

LETTER TO THE EDITOR

Primer Sequence Modification Enhances Hepatitis C Virus Genotype Coverage


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LETTER
 
We applaud the efforts of Cook et al. to develop a real-time reverse transcription-PCR (RT-PCR) assay for ultrasensitive quantification of hepatitis C virus (HCV) RNA (4). The assay uses three forward primers, one reverse primer, and two TaqMan probes targeting the HCV highly conserved 5' untranslated region (UTR) and has a linear dynamic range from 50 to 109 IU/ml plasma specimens, which is significantly superior to several currently available commercial kits (1). As the authors declared, the assay covers the main HCV genotypes encountered in the United States and detects genotypes 1a, 2a, and 3a with equal efficiency; however, the authors’ experience in covering other genotypes was limited.

We have spent time adapting the assay and validating it initially on a panel of 12 plasma specimens (Table 1), including HCV genotypes/subtypes 1a, 1b, 2a, 2b, 3a, 4a, 6, and 6b and a negative control (genotypes/subtypes were determined by a sequencing-based TRUGENE HCV 5'NC genotyping kit [Bayer Diagnostics, Terrytown, NY] according to the manufacturer's instructions [5]). The 11 positive specimens had HCV viral loads from 58,300 to 4,870,000 IU/ml (viral loads were quantitated by a COBAS MONITOR HCV test [Roche Diagnostic Corporation, Indianapolis, IN] as described previously [5]). With the exception of one specimen (genotype 6b) that was collected from a patient whose HCV infection was contracted in South Korea, all 11 positive specimens were amplified correctly. An alignment of nucleotide sequences in the 5' UTR of several HCV isolates circulating in Asia was performed (2, 3, 6-8). The results indicated that, in comparison to genotypes encountered in the United States, most of these Asian strains had a single- nucleotide truncation at the region where the forward primers were designed (4).


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  		TABLE 1. Threshold cycle values for HCV quantitation by TaqMan real-time RT-PCR

We then explored two solutions to extend the coverage of these Asian genotypes by modifying the forward primers used in the RT-PCR: (i) an additional forward primer (HCV-F4 [5'-GAC ACT CCR CCA TKA TCA CT-3', where R is A or G and K is G or T]) was designed and added to cover the one nucleotide truncation, and (ii) the three original forward primers were replaced with one newly designed forward primer (KY80M [5'-AAG CGT CTA GCC ATG GCG T-3']), which was modified from the original KY80 primer published previously (9).

Both implementations were able to cover the 6b genotype (specimen no. 3250) that was missed by the original primer/probe set (Table 1). Based on the values of the threshold cycle (CT), i.e., the cycle number at which the amount of amplified gene of interest reached a fixed threshold, the analytical sensitivity was slightly decreased by the addition of the first new primer into the RT-PCR, but the difference between the CT values was not statistically significant (P > 0.05). On the other hand, when the new single forward primer was implemented to replace the original three forward primers, there was a significant improvement in the test's analytical sensitivity, as indicated by decreased CT values (P = 0.016) (Table 1).

Although the KY80M primer was based on a highly conserved region of the HCV genome, we hesitated to implement the primer in a real-time RT-PCR since the primer can form a four-pair nucleotide hairpin, which was probably the reason for exclusion by the Primer Express software (Applied Biosystems, Foster City, Calif.). However, when the annealing temperature reaches 60°C, the temperature used in the TaqMan real-time procedure, no hairpin formation is indicated (data not shown).

Based on the findings, we have replaced the original three forward primers in Cook's paper with the single KY80M forward primer for our routine HCV quantitation practice. Efforts are being spent to determine the analytical and clinical sensitivity of the TaqMan assay with the new forward primer for HCV quantitation on larger numbers of clinical specimens with a variety of genotypes.


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  1. Barbeau, J. M., J. Goforth, A. M. Caliendo, and F. S. Nolte. 2004. Performance characteristics of a quantitative TaqMan hepatitis C virus RNA analyte-specific reagent. J. Clin. Microbiol. 42:3739-3746.[Abstract/Free Full Text]
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  2. Bukh, J., R. H. Purcell, and R. H. Miller. 1994. Sequence analysis of the core gene of 14 hepatitis C virus genotypes. Proc. Natl. Acad. Sci. USA 91:8239-8243.[Abstract/Free Full Text]
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  3. Chaudhuri, S., S. Das, A. Chowdhury, A. Santra, S. K. Bhattacharya, and T. N. Naik. 2005. Molecular epidemiology of HCV infection among acute and chronic liver disease patients in Kolkata, India. J. Clin. Virol. 32:38-46.[CrossRef][Medline]
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  4. Cook, L., K. W. Ng, A. Bagabag, L. Corey, and K. R. Jerome. 2004. Use of the MagNA pure LC automated nucleic acid extraction system followed by real-time reverse transcription-PCR for ultrasensitive quantitation of hepatitis C virus RNA. J. Clin. Microbiol. 42:4130-4136.[Abstract/Free Full Text]
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  5. Tang, Y. W., H. Li, A. Roberto, D. Warner, and B. Yen-Lieberman. 2004. Detection of hepatitis C virus by a user-developed reverse transcriptase-PCR and use of amplification products for subsequent genotyping. J. Clin. Virol. 31:148-152.[CrossRef][Medline]
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  6. Tokita, H., H. Okamoto, H. Iizuka, J. Kishimoto, F. Tsuda, Y. Miyakawa, M. Mayumi, P. Luengrojanakul, K. Vareesangthip, T. Chainuvati, P. Song, S. Nakata, T. Chosa, and S. Mishiro. 1998. The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7-9 and comparison with those in the other eight genetic groups. J. Gen. Virol. 79:1847-1857.[Abstract]
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  7. Tokita, H., H. Okamoto, P. Luengrojanakul, K. Vareesangthip, T. Chainuvati, H. Iizuka, F. Tsuda, Y. Miyakawa, and M. Mayumi. 1995. Hepatitis C virus variants from Thailand classifiable into five novel genotypes in the sixth (6b), seventh (7c, 7d) and ninth (9b, 9c) major genetic groups. J. Gen. Virol. 76:2329-2335.[Abstract/Free Full Text]
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  8. Tokita, H., H. Okamoto, F. Tsuda, P. Song, S. Nakata, T. Chosa, H. Iizuka, S. Mishiro, Y. Miyakawa, and M. Mayumi. 1994. Hepatitis C virus variants from Vietnam are classifiable into the seventh, eighth, and ninth major genetic groups. Proc. Natl. Acad. Sci. USA 91:11022-11026.[Abstract/Free Full Text]
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  9. Young, K. K., R. M. Resnick, and T. W. Myers. 1993. Detection of hepatitis C virus RNA by a combined reverse transcription-polymerase chain reaction assay. J. Clin. Microbiol. 31:882-886.[Abstract/Free Full Text]
Yi-Wei Tang*
Susan E. Sefers
Haijing Li
Departments of Medicine and Pathology
Vanderbilt University Medical Center
4605 TVC, 1161 21st Ave. S.
Nashville, TN 37232-5310

* Phone: (615) 322-2035,Fax: (615) 343-8420,E-mail: yiwei.tang{at}vanderbilt.edu

Journal of Clinical Microbiology, July 2005, p. 3576-3577, Vol. 43, No. 7
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.7.3576-3577.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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