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Journal of Clinical Microbiology, September 2004, p. 4261-4267, Vol. 42, No. 9
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.9.4261-4267.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Division of Virology and Immunology, National Center for AIDS/STD Prevention and Control, China Center for Disease Prevention and Control, Beijing, Peoples Republic of China
Received 16 December 2003/ Returned for modification 4 May 2004/ Accepted 5 June 2004
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In China, since the first case of HIV infection was identified in 1985, the number of HIV-infected people has increased alarmingly, especially in recent years. Although the recorded cumulative number of HIV infections and AIDS cases was only 40,560 at the end of 2002, it is estimated that the actual number of people with HIV/AIDS is more than 850,000 (NCAIDS, China CDC [http://www.chinaids.org.cn]). Considering the potential gravity of China's situation, all possible measures should be taken to prevent the further spread of HIV. Monitoring HIV genetic characteristics and subtyping prevalent isolates in China will provide essential data for HIV candidate vaccine design and HIV/AIDS prevention policy issues. The first national molecular epidemiology survey from 1996 to 2000 demonstrated that HIV-1 subtypes A, B, C, D, F, G, CRF01-AE, CRF07-BC, CRF08-BC, and HIV-2 have been found in China (5, 12, 13, 17, 19-22; Y. Shao, L. Su, X. Sun, H. Xing, P. Pan, H. Wolf, and J. Shen, XIIth Int. Conf. AIDS, abstr. 13132, 1998). HIV-1 subtype B, CRF07-BC, CRF08-BC, and CRF01-AE infections represented >90% of the circulating strains (13, 17, 19; Shao et al., XIIth Int. Conf. AIDS; unpublished data); other strain infections were scarce.
The primary assays for HIV subtyping are sequence-based phylogenetic analysis and the heteroduplex mobility assay (HMA). Sequence-based phylogenetic analysis is the "gold standard" for HIV subtyping, in which a part of the viral genome is sequenced and phylogenetic analysis is used in comparison with a set of reference sequences having known subtypes. This assay is reliable but labor-intensive and time-consuming. HMA, although much easier and more widely used, is also laborious (1, 3).
We have just completed the development of a simple, rapid, and low-cost subtype screening assay for subtypes B, C, and CRF01-AE that uses reverse transcription-PCR (RT-PCR) and a single nested multiplex PCR without the need for sequencing or HMA. After the initial assay development, improvements were made through the redesign of subtype-specific primers and optimization of PCR conditions. A panel of more than 200 clinical samples was used to evaluate the sensitivity and specificity of the assay.
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Assay design. The basic design of the new assay is to use RT-PCR and nested PCR to subtype HIV strains, in which outer primers were universal for HIV-1 M group strains, and the inner primers were subtype-specific primers that were only reactive to one designated subtype of HIV-1. Accurate primer design plays a key role in this assay, especially in the generation of subtype-specific primers. To identify one subtype from others successfully, the sequences of these subtype-specific primers should be highly specific in intersubtype and highly conserved in intrasubtype comparisons. This pattern was actually a subtype signature pattern (SSP). Signature pattern analysis was first applied in a study of HIV transmission in dental practice in 1990 (8, 11). In the present study, SSPs were defined as unique nucleic acid sites that are distinctly representative of a subtype or CRF relative to a background of the rest of the HIV-1 subtypes or CRFs. The design of subtype-specific primers with SSPs ensures both high sensitivity and high specificity of the assay. Several primer sets were carefully designed and tested for the present study. The best set of primers was selected for subtypes B, C, and CRF01-AE (Table 1 and Fig. 1). In addition, recombinant strains CRF07-BC and CRF08-BC, prevalent CRFs in China, have subtype C backbones with small portions of subtype B (10, 13, 19) (Fig. 1). The subtype C-specific primer set cn-gag-C1/cn-gag-c3 was reactive to pure subtype C and CRF07- and CRF08-BC. To further distinguish CRF07- and CRF08-BC from pure subtype C, the additional primer set cn-gag-C1 and cn-gag-BC was designed to detect only CRF07- and CRF08-BC. However, this set of primers cannot differentiate between CRF07- and CRF08-BC.
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TABLE 1. All primers used in this study
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FIG. 1. Schematic diagram of subtype-specific nested multiplex PCR. The upper part of the figure is the gag gene region diagram of subtypes B, C, CRF01-AE, CRF07-BC, and CRF08-BC (10). The lower part of the diagram shows the primer sets in nested multiplex PCR. Primer pair GagF2/Gage2 are universal primers for HIV-1 M group strains. Primer sets cn-gag-B1/cn-gag-b2, cn-gagC1/cn-gag-c3, cn-gag-E2/cn-gag-e3 are subtype-specific primers for subtypes B, C, and CRF01-AE, respectively. Primer set cn-gag-C1/cn-gag-BC is specific for CRF07- and CRF08-BC.
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(ii) Nested multiplex PCR. In the first round PCR, all 20 µl of RT product was added to a 80-µl reaction mixture that ultimately contained 35 mM KCl (pH 9.0), 0.1% Triton X-100, 1.5 mM MgCl2, 0.4 µM forward primer GagF2, and 5 U of Taq polymerase (Promega, Shanghai, Peoples Republic of China) without using the buffer for Taq polymerase provided by the company. Then, 5 µl of the first-round products was added to the second-round 50-µl mixtures containing 1x buffer, 1.5 mM MgCl2, 2.5 U of Taq polymerase, and 0.4 µM concentrations of the primer sets. In the second round, three primer sets detecting subtypes B (cn-gag-B1/cn-gag-b2), C (cn-gag-C1/cn-gag-c3), and CRF01-AE (cn-gag-E2/cn-gag-e3) were added to one tube. Because three sets of primers were added in one tube, it was called a nested multiplex PCR. Hot-start and touchdown techniques were used to decrease the frequency of nonspecific reactions (15). The reaction conditions are listed in Table 2. The PCR products were separated by electrophoresis on a 2% agarose gel (1x TAE, 100 V, 40 min) with ethidium bromide staining. Subtype determination was made based on PCR product size (subtype B, 900 bp; subtype C, 230 bp; subtype CRF01-AE, 740 bp). When the bands were not found in the expected subtype positions, the results were considered negative. Primer set cn-gag-C1/cn-gag-c2 can also be used as alternative subtype C-specific primers, but it was not as effective as cn-gag-C1/cn-gag-c3.
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TABLE 2. Primer sets for PCR and reaction conditions
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Evaluation of the new assay by using reference strains. To evaluate the newly developed subtyping tool, we used it to subtype reference isolates. The following HIV-1 and HIV-2 reference strains were subtyped: M group subtype A, 92UG029 and 92RW008; M group subtype B, RL42 (B') and 93BR029(B/F); M group subtype C, 92BR025, 93IN905, and 97CN001 (CRF07-BC); M group subtype D, 94UG114; CRF01-AE, CMU10, and 93TH023; M group subtype F, 93BR020; M group subtype G, JV1083; N group, YBF30; O group, MVP5180; and HIV-2 reference strain subtype A, UC2. In addition, M group subtype H and Euro-American B full-length cloning plasmids, p90CF056.1 and pNL4-3, were also analyzed. These reference strains and plasmids were generously provided by the AIDS Research and Reference Reagent Program of the Nationals Institute of Health. Virus RNA was extracted, and RT-PCR and nested multiplex PCR were performed as described above.
Evaluation and validation of the assay by sequence-based phylogenetic analysis. We used a panel of more than 200 HIV-positive and 30 HIV-negative clinical samples to evaluate the assay's sensitivity and specificity. To check whether the subtyping results by nested multiplex PCR were accurate, all HIV-positive samples were analyzed by sequencing and phylogenetic analysis. By PCR with one set of inner universal primers, 306/cn-gag, we obtained the products for sequencing. The first-round PCR products obtained by using GagF2/Gage2 were used as the template in this round of PCR, saving both time and DNA sample. The products were separated by agarose gel electrophoresis and purified by using a Qiagen gel extraction kit. DNA sequencing was performed by using fluorescent dye terminators (Prism BigDye terminator cycle sequencing ready reaction kit; Applied Biosystems) and an automated DNA sequencer (Applied Biosystems model 377). To exclude the possibility of nonspecific amplification, some of the nested multiplex PCR products amplified by subtype-specific primers were also purified and sequenced.
DNA sequences were aligned with reference sequences of HIV-1 M group subtypes A to D, F to H, J, and K and the N and O groups by using CLUSTAL X. Subtype reference sequences were downloaded from Los Alamos National Laboratory (http://www.hiv.lanl.gov). Genetic distances were calculated by using the Kimura two-parameter approach, and a phylogenetic tree was constructed by the neighbor-joining method, both included in the MEGA package (Molecular Evolutionary Genetics Analysis; version 2.1. [http://www.megasoftware.net]). The topology reliability of the phylogenetic tree was estimated by performing bootstrap analysis with 100 replicates. Bootstrap values of
70% were considered statistically significant.
We also randomly selected 31 samples to repeat the test five times to assess the reproducibility of the assay.
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FIG. 2. Nucleotide sequence alignments of HIV-1 subtypes and CRFs. The name of the subtype or CRF labeled with "CON_X" means consensus of subtype X or CRF X, e.g., "CON_B" stands for consensus of subtype B strains. Some subtypes or CRFs are only represented by one sequence, e.g., 05.VI1310, meaning CRF05-VI1310. The sequences are not continuous, numbered according to the HXB2. The positions for subtype-specific primers are underlined.
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TABLE 3. SSP analysis in gag region
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FIG. 3. Nested multiplex PCR of HIV reference isolates. Lanes: M, DNA Marker; A1, 92UG029; A2, 92RW008; B1, RL42; B2, 93BR029; B3, pNL4-3; C1, 92BR025; C2, 93IN905; C3, 97CN001; D, 94UG114; E1, CMU10; E2, 93TH023; F, 93BR020; G, JV1083; H, p90CF056.1; O, MVP5180; N, YBF30; II, HIV-2 UC2.
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FIG. 4. Agarose-gel electrophoresis of samples analyzed by nested multiplex PCR. Lanes: M, DNA Marker; S1, CQ2010 (CRF01-AE); S2, FJ9909 (CRF01-AE); S3, SC9712 (D); S4, JS11 (D); S5, SC0227 (C); S6, JS0121 (C); S7, HEN0217 (B'); S8, JS0127 (B'); S9, EC9005 (B); S10, SD20 (A); S11, JS17 (A).
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Assay validation by the phylogenetic analyses. We compared the subtype results of the nested multiplex PCR with those of phylogenetic analyses (Table 4). The subtype determination by nested multiplex PCR corresponded well to the phylogenetic analyses. The subtype B-specific primer set can amplify both Thailand B (93.7% [59 of 63]) and Euro-American B (90.9% [10 of 11]) samples. The designated subtype sensitivities of this new assay were adequate: subtype B, 93.2% (69 of 74); subtype C, 95.1% (117 of 123); and CRF01-AE, 94.0% (47 of 50). In addition, the primer set for CRF07- and CRF08-BC detected 95.0% (115 of 121) of the samples correctly. Furthermore and most importantly, the intersubtype specificity of the assay was 100%, which means false-positive results were rare. Since the 30 HIV-negative samples were also found to be negative by this assay, the specificity of this assay for the presence of HIV is also 100%.
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TABLE 4. Comparison of phylogenetic analyses and nested multiplex PCR
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TABLE 5. Reproducibility of the nested multiplex PCR
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However, occasional nonspecific bands do appear. Weak bands appeared near the position of the subtype B-specific band in several subtype C samples. False-priming in several subtype C samples is likely responsible. After measures to reduce nonspecific reactions were taken, such as "hot-start" and "touchdown" techniques, the nonspecific bands were generally no longer visible. In addition, not only RNA samples from the plasma but also DNA samples from the peripheral blood mononuclear cells can be used in this assay. The subtype-specific primers in the second-round PCR could also be performed separately instead of being combined in one tube.
In the present study, the subtype determination was based on the size of the PCR products. Thus, the factors that influence the size of fragments, such as gene deletions or insertions, typically occurring with HIV, could interfere with the result interpretation (16). In our experiments, only one sample had two strong bands. One band was found near the position of subtype C, and the other was located at the position of subtype B. These two bands were each purified and DNA sequenced. The sequence analysis indicates that this sample belongs to subtype B. An
600-bp deletion was identified between the subtype B-specific primer pairs leading to bands representing both the deleted and nondeleted template forms. This pattern was unique to this sample. Because the target fragments we amplified are very short, gene deletion or insertion occurring exactly in this region is unusual. Insertions or deletions of the template DNA should only lead to three possible scenarios. (i) When DNA deletion or insertion happens out of the target region, it imposes no effect on the result. (ii) When deletions or insertions span upper, lower, or both primers, the result would be negative. (iii) When deletions or insertions occur between the upper and lower primers, the target PCR products would extend or shorten. Only the third condition will influence the result interpretation. Thus, if a strong band is found near but not on the subtype-specific position, the possibility of gene deletion or insertion should be considered. DNA sequencing is necessary for further subtype determination.
Globally, the prevalence of HIV infection is increasing rapidly. The variation among HIV strains will increase as additional mosaic strains are discovered. Characterizing HIV is important, but the currently available assays for HIV subtyping are laborious. Many scientists are developing new simple and rapid assays for HIV subtyping, including a solid phase plate assay (4) and a DNA enzyme immunoassay method for HIV subtyping (14). The sensitivity and specificity of these assays are satisfactory. Yagyu developed a PCR subtyping method only differentiating subtype B and CRF01-AE, but the specificity of that assay was found to be lacking (23). Recently, a real-time isothermal amplification assay has been developed to distinguish HIV-1 subtypes A, B, C, CRF01-AE, and CRF02-AG (2). Another real-time PCR with multiregion amplification and fluorescent, subtype-specific probes, the multiregion hybridization assay, is in fact a robust tool for HIV-1 subtyping, not only for one gene region genotyping but also for recombination detection (6). However, low sensitivity, local strain match, and high cost are still the barriers for its application in developing countries.
Our nested multiplex PCR assay is simpler, faster, and more practical for use in developing countries such as China. The specificity and sensitivity are the most important parameters for evaluation of any assay. Subtype-specific primers, based on the SSP analysis, were carefully designed. The use of two subtype-specific primers for this assay should be an improvement over other assays that use only one subtype-specific probe. The idea of the present study can also be applied in the other subtype-specific primer design. Because the selected samples in this panel were biased toward subtypes Thailand B, C, and CRF01-AE, additional subtype samples such as, for example, subtypes A, Euro-American B, CRF02-AG, and CRF04-cpx, are needed to further evaluate this assay if it is to be used outside of China.
In summary, we have developed a simpler and more rapid subtype screening assay for HIV-1 subtypes B, C, CRF01-AECRF07-BC, and CRF08-BC in China. This assay has potential applications in HIV laboratories located not only in China but also in other countries around the world.
This study was supported by China 973 National Key Project G1999054107 and National Outstanding Youth Grant 39925030.
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