Optimization of polymerase chain reaction for detection of HIV type 2 DNA.

The aim of this study was to increase the sensitivity of an earlier version of an HIV-2 nested PCR assay based on primers in the gag, pol, LTR, and env regions. The assay was first optimized with regard to concentrations of dNTP, MgCl2, and primers, using a method that allowed optimization of all three parameters in only two test runs. We then designed and optimized new primer sets in the LTR, gag, and gag/pol regions that were based on more isolates than were the former (old) primer sets. Samples from 57 HIV-2 antibody-positive individuals were tested with the four old primer sets as well as with the three new primer sets. Five primer sets from this run (new gag, new gag/pol, old LTR, old env, and new LTR) were then tested with 35 more samples, giving a total number of 92 tested samples from HIV-2-infected individuals. At initial testing of the 92 samples a combination of primer sets from two different regions yielded a sensitivity ranging from 93.5 to 98.9%. After repeated testing the sensitivity ranged from 96.7 to 100% for the different primer combinations. The specificity was 100% for all primer sets except old LTR, which had a specificity of 97%. In conclusion, it is possible to create a more sensitive PCR assay by optimizing the different PCR parameters as well as by including primer sets based on more isolates.

Comparison of in-house and commercial sample preparation and PCR amplification systems for detection of human immunodeficiency virus type 1 DNA in blood samples from Tanzanian adults.

This study compared the performance of several in-house nested PCR systems and the Amplicor human immunodeficiency virus type 1 (HIV-1) PCR kit in the detection of HIV-1 DNA in Tanzanian samples prepared by two different methods. All six of the in-house primer sets evaluated had a higher sensitivity for HIV DNA detection in samples prepared by the Amplicor PCR sample preparation method than in those prepared by the Ficoll-Isopaque (FIP) density gradient centrifugation method. A sensitivity of 100% was achieved by combining two in-house primer sets. The sensitivity of the standard Amplicor HIV-1 PCR kit was only 59%, whereas a modified Amplicor HIV-1 PCR test had a sensitivity of 98%. Our data show that Tanzanian samples prepared by the Amplicor preparation method are more suitable for HIV-1 PCR testing than samples prepared by the FIP method. The modified, but not the standard, Amplicor HIV-1 PCR kit provides an alternative to the nested in-house PCR technique for the diagnosis of HIV infection.

PIP: Blood samples were collected from 73 pregnant mothers attending an antenatal clinic and from 14 adult females recruited into ongoing studies of the incidence and natural history of HIV-1 infection in Dar es Salaam, Tanzania. Study subjects were asymptomatic for HIV infection, but 65 tested HIV-positive. The authors compared the performance of several in-house nested polymerase chain reaction (PCR) systems and the Amplicor HIV-1 PCR kit in detecting HIV-1 DNA in the seropositive samples prepared by two different methods. All six of the in-house primer sets evaluated were more sensitive for HIV DNA detection in samples prepared by the Amplicor PCR sample preparation method than in those prepared by the Ficoll-Isopaque (FIP) density gradient centrifugation method. A sensitivity of 100% was achieved by combining two in-house primer sets. The sensitivity of the standard Amplicor HIV-1 PCR kit was only 59%, while a modified Amplicor HIV-1 PCR test had a sensitivity of 98%. These data indicate that Tanzanian samples prepared by the Amplicor preparation method are more suitable for HIV-1 PCR testing than samples prepared by the FIP method.

Nested PCR assays with novel primers yield greater sensitivity to Tanzanian HIV-1 samples than a commercial PCR detection kit.

To investigate the efficacy of the SK431/SK145 primer pair and two nested primer assays in amplifying African HIV-1 samples, a total of 35 Tanzanian PBMC samples were examined. These were assayed by two HIV-1 specific nested in-house PCR assays and a commercial HIV-1 PCR kit (GeneAmp) using SK431/SK145 as the primer pair. One of the nested PCR assays has been evaluated previously (old assay), whereas the modified assay was constructed from the HIV-1 sequence alignment released in August 1993. The modified nested primer assay showed increased sensitivity in the gag and env regions compared to the old nested primer assay. However, both the old and the modified nested primer assays displayed higher sensitivity for the detection of Tanzanian HIV-1 proviruses than the GeneAmp assay. When two regions were used (gag and env) as targets for the amplification, the modified nested primer assay detected 97.1% (34/35) of the proteinase K lysed samples, compared to 68.6% (24/35) using the SK431/SK145 primer pair (P < 0.01**). The results indicate that the SK431/SK145 primer pair may be less suitable when HIV-1 samples from Africa are analysed. The results also show that continuous modification of primer sequences can improve and maintain high sensitivity for the detection of highly divergent HIV-1 strains.

Early diagnosis of HIV-1 infection in infants in Dar es Salaam, Tanzania.

OBJECTIVES: To evaluate two simple methods, an immune complex dissociation (ICD) p24 antigen assay and an HIV-1-specific IgA antibody assay, for the early demonstration of HIV-1 infection in infants, using the polymerase chain reaction (PCR) as the reference method. DESIGN AND SETTING: Group A: 143 HIV-1-seropositive and 134 -seronegative mothers and their infants were recruited at delivery at the main hospital in Dar es Salaam, Tanzania. Group B: 26 HIV-PCR-positive hospitalized children in Dar es Salaam, 3-15 months old and suspected of having an HIV-related illness. METHODS: Blood samples were taken from mothers and infants in group A at intervals during the children's first 24 months and once from each of the children in group B. Peripheral blood mononuclear cells were tested by nested PCR for viral DNA. Plasma samples were tested by the Coulter p24 antigen (ag) enzyme-linked immunosorbent assay (ELISA) after acid dissociation of p24 antigen-antibody complexes. All p24-ag-positive reactions were confirmed by neutralization. Viral specific IgA antibodies were demonstrated in plasma by a modified ELISA. RESULTS: One hundred and sixty-three of 174 samples from seropositive mothers were PCR-positive (sensitivity 93.7%) and 612 of 614 samples from seronegative mothers and children of seronegative mothers were PCR-negative (specificity 99.7%). Twenty-nine of 145 (20.0%) children born to seropositive mothers were positive by PCR when tested during the first year of life. By use of both the p24 ag ELISA and the IgA antibody ELISA in combination, HIV-1 infection was detected in 9 of 17 (53%) PCR-positive children 1-8 weeks old, in 15 of 18 (83%) PCR-positive children 9-26 weeks old and in 23 of 24 (96%) PCR-positive children 27-52 weeks old. The specificities of the p24 ag ELISA and the IgA ELISA were 100%. CONCLUSIONS: The p24 ag assay and the IgA antibody ELISA, when used in combination, had a high sensitivity and specificity for detection of HIV-1 infection in infants, especially in those above the age of 6 months.

Predictive markers for mother-to-child transmission of HIV-1 in Dar es Salaam, Tanzania.

The aim of this study was to determine immunological factors associated with increased risk of mother-to-child transmission of HIV-1 that could be used as predictive markers in Tanzanian women. One hundred and thirty-eight HIV-1-seropositive and 117-seronegative mothers and their newborns were recruited at delivery and followed up at Muhimbili Medical Centre in Dar es Salaam, Tanzania. Blood specimens from the mothers were analyzed for HIV-1 p24 antigen, beta 2-microglobulin (B2M), T-lymphocyte subsets, and presence of viral DNA in blood mononuclear cells by the polymerase chain reaction (PCR). Among 138 seropositive mothers, 30 (21.7%) had transmitted HIV-1 to their children, as shown by a positive PCR in the child. The vertical transmission rate was significantly higher in women with a percentage of CD4 lymphocytes < or = 20 (eight of 24, 33%) or a level of B2M > or = 2 mg/L (21 of 62, 34%) than in women with a higher percentage of CD4 lymphocytes (10 of 73, 14%) or a lower level of B2M (eight of 57, 14%) (p = 0.034 and 0.018, respectively). In eight of 18 (44%) transmitting mothers the percentage of CD4 lymphocytes was < or = 20, and in 21 of 29 (72%) transmitting mothers the B2M level was > or = 2 mg/L. In women with both a low percentage of CD4 lymphocytes (< or = 20) and a high level of B2M (> or = 2 mg/L), the vertical transmission rate was 54%.(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of nephropathia epidemica virus RNA in patient samples using a nested primer-based polymerase chain reaction.

A nested primer-based polymerase chain reaction was constructed for the detection of Puumala virus RNA in patient samples. Puumala virus RNA was detected in cells from the urinary and the respiratory tracts and in peripheral blood mononuclear cells of patients with nephropathia epidemica. After inoculation with nephropathia epidemica patient material on Vero E6 cells and propagation for nine passages (4 months), Puumala virus RNA was detected at every passage. Hybridization under high-stringency conditions revealed that the overall nucleotide homology between the different patient isolates and the prototype strain (Puumala) is high. Using cDNA from Hällnäs B1 strain as a probe, hybridization occurred only under low-stringency conditions.

Improved detection of HIV-2 DNA in clinical samples using a nested primer-based polymerase chain reaction.

A two-step polymerase chain reaction (PCR), with four double (nested) primer pairs, used for the detection of HIV-2 in clinical samples is described. With these four nested primer pairs we could detect HIV-2 DNA in 17 of 17 virus isolates and in blood mononuclear cell samples from 31 of 37 (83.7%) seropositive individuals after ethidium bromide staining of the amplified DNA. The nested primer PCR was also compared with a single primer pair-based PCR followed by hybridization. The sensitivities of the two methods were almost equal, but the nested primer PCR offered obvious technical advantages.

Selection of primers of optimal sensitivity for the detection of HIV-1 from Africa and Europe by polymerase chain reaction.

In order to facilitate the detection of integrated HIV-1 proviral DNA from African as well as European patients, four new primer pairs for use in the polymerase chain reaction (PCR), localised in the gag, pol, vif and env genes of HIV-1, were constructed. The primer pairs were compared to all accessible HIV-1 sequences from African and European isolates and to some of the earlier published and most commonly used primer pairs. HIV-1 DNA was detected in blood drawn from 13 out of 13 individuals infected in Africa, in three out of three Tanzanian HIV-1 isolates and in three out of three asymptomatic Swedes infected in Europe. The new selection of primer pairs can be used as an alternative to enhance the detection of HIV-1 of different origins.

PIP: In order to facilitate the detection of integrated HIV-1 proviral DNA from African as well as European patients, 4 new primer pairs for use in the polymerase chain reaction (PCR), localized in the gag, pool, vif, and env genes of HIV-1, were constructed. The primer pairs were compared to all accessible HIV-1 sequences from African and European isolates and to some of the earlier published and most commonly used primer pairs. HIV-1 DNA was detected in blood drawn from 13 infected individuals in Africa, in 3 Tanzanian HIV-1 isolates, and in the 3 asymptomatic Swedes infected in Europe. The new selection of primer parts can be used as an alternative to enhance the detection of HIV-1 of different origins.