Simple DNA extraction method for dried blood spots and comparison of two PCR assays for diagnosis of vertical human immunodeficiency virus type 1 transmission in Rwanda

Early diagnosis of human immunodeficiency virus in infants using polymerase chain reaction on dried blood spots in Botswana's national program for prevention of mother-to-child transmission

BACKGROUND

Botswana has high antenatal human immunodeficiency virus (HIV) prevalence (33.4%). The public health system provides free services for prevention of mother to child transmission of HIV (PMTCT) and antiretroviral therapy, which can reduce vertical HIV transmission from 35% to <5%. Infant HIV diagnosis is challenging in resource-limited settings, and HIV prevalence among HIV-exposed infants in Botswana is unknown. Dried blood spot (DBS) polymerase chain reaction (PCR) provides a feasible method to assess PMTCT programs and identify HIV-infected children.

METHODS

We trained staff in 15 clinics and a hospital to obtain DBS on HIV-exposed infants age 6 weeks to 17 months receiving routine care. Samples were sent to the national HIV reference laboratory. Roche Amplicor 1.5 DNA PCR testing was performed.

RESULTS

Between June-December 2005, 1931 HIV-exposed infants age 6 weeks to 17 months were tested for HIV, of whom 136 (7.0%) were HIV infected. Among infants <or=8 weeks old, 27 of 544 (5.0%) were HIV infected. Among infants tested in clinics (primarily during routine health visits), 65 of 1376 (4.7%) were infected; among infants tested in the hospital, 71 of 555 (12.8%) were infected.

CONCLUSIONS

Collection and testing of DBS was successfully integrated into routine infant care in the public health system. HIV prevalence among infants in the Botswana PMTCT program is low. National expansion of infant DBS PCR in Botswana is planned.

Early infant human immunodeficiency virus type 1 detection suitable for resource-limited settings with multiple circulating subtypes by use of nested three-monoplex DNA PCR and dried blood spots

The early detection of human immunodeficiency virus type 1 (HIV-1) infection in infants is complicated by the persistence of maternal antibodies and by diverse HIV-1 subtypes. We developed a nested, three-monoplex HIV-1 DNA PCR (N3M-PCR) assay to detect diverse HIV-1 subtypes in infants born to infected mothers. We optimized the test for use with dried blood spot (DBS) samples for ease of storage and transport from rural China to central laboratories. Six pairs of primers were designed that targeted env, gag, and pol genes, and the test was run in three reactions with an analytical sensitivity of 10 copies DNA per reaction to cover nine HIV-1 subtypes, A, B, C, D, F, G, CRF01-AE, CRF08-BC, and CRF07-BC. The assay performance was evaluated on 347 DBS specimens from 151 exposed infants in four diverse provinces of China in which multiple subtypes were circulating. The results of this test were compared to those of HIV antibody enzyme immunoassay and Western blotting confirmation for the infants at > or =18 months of age or to convincing clinical and epidemiologic data for deceased infants. The sensitivity of the N3M-PCR assay was 30.0% (3/10) for infants at 48 h after birth, 91.7% (11/12) at 1 to 2 months of age, and 93.7% (15/16) at 3 to 6 months of age. The specificity was 100% (94/94) at all three time points. The PCR reproducibility in the three DNA regions was 100% for samples at 48 h after birth, 96.7% at 1 to 2 months, and 100% at 3 to 6 months of age. The HIV-1 DNA N3M-PCR assay on DBSs offers a simple and affordable approach for early infant HIV-1 diagnosis in regions with diverse HIV-1 circulating subtypes.

Feasibility of detecting human immunodeficiency virus type 1 drug resistance in DNA extracted from whole blood or dried blood spots

Due to high cost, availability of human immunodeficiency virus type 1 (HIV-1) drug resistance testing in resource-poor settings is still limited. We therefore evaluated the usefulness of viral DNA extracted from either whole blood or dried blood spots (DBS). Samples were collected from 50 patients receiving therapy and 10 therapy-naïve patients. Amplification and sequencing of RNA and DNA was performed using an in-house assay. Protease (PR) and reverse transcriptase (RT) sequences of plasma viral RNA were obtained for 96.6% and 89.7%, respectively, of the 29 patients with a detectable viral load. For cellular viral DNA, useful PR and RT sequences were obtained for 96.6% and 93.1% of the whole-blood-cell samples and for 93.1% and 93.1% of the DBS samples, respectively. For the 31 patients with an undetectable viral load, PR and RT sequences were obtained for 67.7% and 61.3% of the whole-blood-cell DNA preparations and for 54.8% and 58.1% of the DBS DNA preparations, respectively. A good correlation between RNA and DNA sequences was found; most discordances were caused by the detection of mixed amino acids. Of the RT drug-resistant mutations, 13 (38.2%) were seen in RNA only, 6 (17.6%) in DNA only, and 15 (44.1%) in both. Repeated amplification and sequencing of DNA extracts revealed a lack of reproducibility for the detection of drug resistance mutations in a number of samples, indicating a possible founder effect. In conclusion, this study shows the feasibility of genotypic drug resistance testing on whole blood cells or DBS and its possible usefulness for HIV-1 subtyping or examining the overall distribution of drug resistance in a population. For individual patients, RNA sequencing was shown to be superior to DNA sequencing, especially for patients who experienced early treatment failure. The use of DNA extracted from whole blood or DBS for the detection of archived drug resistance mutations deserves further study.

Identification of HIV-1 infected infants and young children using real-time RT PCR and dried blood spots from Uganda and Cameroon

Serodiagnosis of HIV infection in infants born to HIV-infected mothers is problematic due to the prolonged presence of maternal antibodies in infants. Nucleic acid-based amplification assays have been used to overcome this problem. Here a simplified, one-tube, real-time, duplex reverse transcription PCR (RT PCR) assay is shown to detect HIV-1 total nucleic acid (TNA) isolated from dried blood spots. The detection of TNA, as opposed to DNA alone, increases the HIV target molecules and thus makes the assay more robust. This method was used to detect HIV from the DBS collected from HIV-1 exposed infants and young children in Uganda (n=128) and Cameroon (n=315). The gold-standards used were a plasma viral assay in Uganda and Amplicor DNA assay in Cameroon. The concordance of this real-time assay and the gold standards was 99.2% (127/128) and 99.4% (313/315) with the Ugandan and Cameroonian samples, respectively. This simple and cost-effective assay is potentially useful for the diagnosis of pediatric HIV infection and for evaluating programs to reduce mother-to-child transmission of HIV-1.

Evaluation of dried whole blood spots obtained by heel or finger stick as an alternative to venous blood for diagnosis of human immunodeficiency virus type 1 infection in vertically exposed infants in the routine diagnostic laboratory

The diagnostic accuracy of the Roche Amplicor human immunodeficiency virus type 1 DNA PCR assay (version 1.5) on DNA extracted from pediatric heel prick dried blood spots using Roche MagNA Pure nucleic acid purification technology was evaluated. The methodologies transfer successfully from the labor-intensive research laboratory to the high-throughput automated routine laboratory.

False-positive results of enzyme immunoassays for human immunodeficiency virus in patients with uncomplicated malaria

Malaria may impact upon human immunodeficiency virus (HIV) test results. We evaluated two HIV enzyme immunoassays (EIAs) by testing 1,965 Ugandans with malaria. We found poor positive predictive values (53% and 76%), particularly with younger age. Combining EIAs eliminated false positives but missed 21% of true positives. Performance of HIV EIAs in malaria may be unsatisfactory.

Diagnosis of pediatric human immunodeficiency virus infection in resource-constrained settings

The majority of children infected with human immunodeficiency virus live in resource-constrained settings and die without an established diagnosis. Definitive laboratory diagnosis in children younger than 12-18 months requires virologic testing; however, antibody testing is often the only option available. Antibody testing provides a definitive diagnosis in older children but is frequently not used. Children meeting clinical criteria should be treated regardless of availability of laboratory diagnoses.

HIV-1 viral load assays for resource-limited settings

The authors discuss studies on the low-cost viral load assays that are currently available and their potential for use in resource-limited settings.

Polymerase chain reaction for diagnosis of human immunodeficiency virus infection in infancy in low resource settings

BACKGROUND

Diagnosis of human immunodeficiency virus (HIV) is essential for accessing treatment. Current HIV diagnostic protocols for infants require adaptation and validation before they can be implemented in the developing world. The timing and type of HIV assays will be dictated by country-specific circumstances and experience from similar settings. The performance of an HIV-1 DNA polymerase chain reaction (PCR) test, and in particular a single test at 6 weeks of age, in diagnosing HIV subtype C infection acquired in utero or peripartum was assessed.

METHODS

A retrospective review of 1825 Amplicor HIV-1 DNA PCR version 1.5 tests performed between 2000 and 2004 in 2 laboratories in Johannesburg, South Africa on 769 effectively non-breast-fed infants from 3 clinically well characterized cohorts was undertaken. The HIV status of each infant was used as the standard against which the HIV PCR results were compared.

RESULTS

The overall sensitivity and specificity of the HIV PCR test were 99.3 and 99.5% respectively. A single test was 98.8% sensitive and 99.4% specific in the 627 infants tested at 6 weeks of age (58 HIV-infected and 569 HIV-uninfected). Repeat testing of all positive HIV PCR tests minimized false positive results.

CONCLUSIONS

In resource-poor settings where HIV PCR testing in an environment of good laboratory practice is feasible, a single 6-week HIV DNA PCR test can increase identification of HIV-infected children substantially from current levels. Further operational research on how best to implement and monitor such a diagnostic protocol in specific local settings, especially in breast-fed infants, is necessary.

Usage of dried blood spots for molecular diagnosis and monitoring HIV-1 infection

The usage of dried blood spots as specimens for diagnosis and monitoring of HIV-1 infection in Thailand was evaluated. EDTA blood samples, which were collected from 100 HIV seronegative and 109 HIV seropositive individuals, were tested on dried blood spots; Whatman, Schleicher and Schuell (S&S) No. 903 and S&S IsoCode filter paper. Nucleic acid was extracted and used as a template for HIV-1 proviral DNA detection by an "in-house" multiplex PCR and a commercial Amplicor HIV-1 PCR test (Roche, version 1.0). HIV-1 RNA qualitative (QL) and quantitative (QT) detection was determined by Nucleic Acid Sequence Based Amplification (NASBA). The average DNA per blood spot recovered from Whatman and S&S IsoCode was not statistically different (p = 0.512) with a range of 218.9+/-46.84 and 225.63+/-88.33 microg, respectively. The concordance of HIV-1 proviral DNA detection by PCR from dried blood spots Whatman and S&S IsoCode was 94% versus 89.4% for sensitivity and 100% versus 100% for specificity. The sensitivity and specificity of HIV-1 RNA QL detection in dried blood spots was 89.7 and 97.5%, respectively. The HIV-1 RNA QT from dried blood spots showed a good correlation in paired dried blood spots and plasma with Pearson correlation, r = 0.817 (R2 = 0.667, P < 0.05). The data showed that dried blood spots could be used for the diagnosis and monitoring of HIV-1 infection.

Detection of human immunodeficiency virus type 1 DNA in dried blood spots by a duplex real-time PCR assay

A dried blood spot (DBS) is a well-accepted means for the collection, transport, and storage of blood samples for various epidemiologic, serologic, and molecular assays for human immunodeficiency virus (HIV) studies. It is particularly important for mother-to-infant-transmission studies of affected individuals living in remote areas. We have developed a real-time PCR method to detect HIV type 1 (HIV-1) DNA in dried blood spots. A cellular gene, RNase P, was coamplified with the HIV-1 DNA in the same tube to monitor the DNA extraction efficiency and the overall assay performance. Our assay is a one-tube, single-step closed-system assay and uses a dUTP/uracil DNA glycosidase anti-PCR contamination control. The HIV-1 primers and probe were derived from a conserved region of the long terminal repeat. The detection of RNase P is attenuated by lowering the forward and reverse primer concentrations so that its amplification will not overwhelm the HIV-1 amplification and yet will provide a semiquantitative measurement of the quality of the isolated DBS DNA. We examined 103 HIV-1-seropositive and 56 seronegative U.S. adults and found that our assay has a sensitivity of 98.1% (95% confidence interval [CI], 95.5% to 100%) and specificity of 100% (95% CI, 99% to 100%). The positive and negative predictive values are 100% and 96.6%, respectively. This duplex PCR assay may be useful in identifying HIV-1-infected persons, particularly infants born to seropositive mothers in remote areas of the world.

Dried blood spots improve access to HIV diagnosis and care for infants in low-resource settings

Effective health care delivery to the majority of perinatally exposed infants worldwide, including those enrolled in prevention of mother-to-child transmission programs, is hampered by lack of access to an HIV diagnosis in infancy. Dried blood spot collection from young infants for centralized HIV polymerase chain reaction (PCR) testing is attainable in low-resource settings, provided PCR methodology suitable for routine laboratory service is available. The accuracy of the Roche Amplicor HIV-1 DNA test version 1.5 (Branchburg, NJ) performed on dried blood spots collected prospectively on ordinary Whatman filter paper from a cohort of 300 6-week-old infants born to HIV-infected women in Johannesburg, South Africa, was assessed. Anonymous analysis of the blood spots using a unique DNA extraction procedure was performed in a routine diagnostic laboratory and the results compared with HIV DNA and RNA PCR liquid blood tests at age 6 weeks, and the HIV status of the infant. Dried blood spots were available for 288 infants (96%) of whom 25 (8.7%) were HIV infected. The Roche Amplicor assay yielded a sensitivity of 100% and a specificity of 99.6%. HIV DNA PCR tests on dried blood spots have the potential to improve health care delivery to HIV-affected children in low-resource settings right now.