Low human immunodeficiency virus type 1 (HIV-1) DNA burden as a major cause for failure to detect HIV-1 DNA in clinical specimens by PCR

Generalist host species drive Trypanosoma cruzi vector infection in oil palm plantations in the Orinoco region, Colombia

BACKGROUND

Oil palm plantation establishment in Colombia has the potential to impact Chagas disease transmission by increasing the distribution range of Rhodnius prolixus. In fact, previous studies have reported Trypanosoma cruzi natural infection in R. prolixus captured in oil palms (Elaeis guineensis) in the Orinoco region, Colombia. The aim of this study is to understand T. cruzi infection in vectors in oil palm plantations relative to community composition and host dietary specialization by analyzing vector blood meals and comparing these results to vectors captured in a native palm tree species, Attalea butyracea.

METHODS

Rhodnius prolixus nymphs (n = 316) were collected from A. butyracea and E. guineensis palms in Tauramena, Casanare, Colombia. Vector blood meals from these nymphs were determined by amplifying and sequencing a vertebrate-specific 12S rRNA gene fragment.

RESULTS

Eighteen vertebrate species were identified and pigs (Sus scrofa) made up the highest proportion of blood meals in both habitats, followed by house mouse (Mus musculus) and opossum (Didelphis marsupialis). Individual bugs feeding only from generalist mammal species had the highest predicted vector infection rate, suggesting that generalist mammalian species are more competent hosts for T. cruzi infection .

CONCLUSIONS

Oil palm plantations and A. butyracea palms found in altered areas provide a similar quality habitat for R. prolixus populations in terms of blood meal availability. Both habitats showed similarities in vector infection rate and potential host species, representing a single T. cruzi transmission scenario at the introduced oil palm plantation and native Attalea palm interface.

Field evaluation of HIV point-of-care testing for early infant diagnosis in Cape Town, South Africa

Background

Early infant HIV diagnosis (EID) coverage and uptake remains challenging. Point-of-care (POC) testing may improve access and turn-around-times, but, while several POC technologies are in development there are few data on their implementation in the field.

Methods

We conducted an implementation study of the Alere q Detect POC system for EID at two public sector health facilities in Cape Town. HIV-exposed neonates undergoing routine EID testing at a large maternity hospital and a primary care clinic received both laboratory-based HIV PCR testing per local protocols and a POC test. We analysed the performance of POC versus laboratory testing, and conducted semi-structured interviews with providers to assess acceptability and implementation issues.

Results

Overall 478 specimens were taken: 311 tests were performed at the obstetric hospital (median child age, 1 days) and 167 six-week tests in primary care (median child age, 42 days). 9.0% of all tests resulted in an error with no differences by site; most errors resolved with retesting. POC was more sensitive (100%; lower 95% CI, 39.8%) and specific (100%, lower 95% CI, 98%) among older children tested in primary care compared with birth testing in hospital (90.0%, 95% CI, 55.5–99.8% and 100.0%, lower 95% CI, 98.4%, respectively). Negative predictive value was high (>99%) at both sites. In interviews, providers felt the device was simple to use and facilitated decision-making in the management of infants. However, many wanted clarity on the cause of errors on the POC device to help guide repeat testing.

Conclusions

POC EID testing performs well in field implementation in health care facilities and appears highly acceptable to health care providers.

False-negative post-18-month confirmatory HIV tests in HIV DNA PCR-positive children: a retrospective analysis

OBJECTIVE

The WHO guidelines for children less than 18 months old diagnosed with HIV based on presumptive clinical diagnosis or one virologic test recommend confirmatory HIV antibody testing after 18 months of age. This study describes post-18-month HIV test results following this WHO-recommended confirmatory testing strategy.

DESIGN

Case series and retrospective review of routine program data.

METHODS

Children enrolled at the Baylor Children's Clinical Center of Excellence, a pediatric and family HIV clinic in Maseru, Lesotho from December 2005 through January 2009 with a positive HIV DNA PCR at less than 18 months of age and HIV rapid test results after 18 months of age were included. Post-18-month confirmatory HIV test results are described. Factors associated with non-positive confirmatory rapid tests were determined using binary logistic regression.

RESULTS

Of the 109 children meeting inclusion criteria, 22 (20.2%) had negative and 27 (24.8%) discordant confirmatory rapid tests. Forty-six of these 49 were on antiretroviral therapy (ART). Among these 49, 11 of 24 post-18-month HIV DNA PCRs were negative, whereas nine of 10 post-18-month HIV ELISAs were positive; 29 were definitively and 17 probably HIV-infected, two were uninfected, and one had undetermined status. Only age less than 9 months at ART initiation (odds ratio 4.25, P = 0.002) was associated with non-positive rapid tests.

CONCLUSION

False-negative post-18-month confirmatory rapid tests and HIV DNA PCRs in children on ART are common, associated with early ART initiation, and may lead to inappropriate ART discontinuation and discharge from care of truly HIV-infected children.

Discrepant test findings in early infant diagnosis of HIV in a national reference laboratory in Kenya: challenges and opportunities for programs

BACKGROUND

In Kenya, the availability of a cheap diagnostic service for HIV-exposed infants has helped scale-up access to treatment, and provided a means by which programs that support Prevention of Mother to Child Transmission of HIV can be evaluated. As expected for any large testing program, discrepant and indeterminate results present a significant challenge.

METHODS

Dried Blood Spots were collected from health centers countrywide and couriered to four laboratories for tests. Results were dispatched either by email, telephone, GSM SMS printer or courier. Between 2006 and 2009, tests were conducted with the Manual Roche v. 1.5 Assay. In 2010 the labs switched fully to the Cobas® AmpliPrep/ Cobas® TaqMan® HIV-1 Qual automated Roche Test.

RESULTS

Between 2006 and 2010, the KEMRI CVR EID Lab conducted 64 591 HIV tests in on children <18 months of age. HIV tests (38 834) used the manual assay, while 17 133 tests used the automated assay. Overall, 10.7% (6915) of the samples tested positive, while 86.6% (55 967) tested negative. A total of 1.6% (1041) tested indeterminate and required a re-bleed of the infant. Two hundred positive tests by the manual assay were retrieved randomly and retested using the automated assay. Among them, 192 (96%) remained positive, 5 (2.5%) were negative while 3 (1.5%) failed. A total of 160 negative samples by the manual assay were retrieved and retested with the automated assay. Among them, 154 (96.24%) remained negative, 3 (1.88%) tested positive while 3 (1.88%) failed. A total of 215 samples that gave indeterminate results by the manual assay were retested using the automated system. Among them, 62 (28.8%) gave positive results, 144 (66.97%) negative and 6 (2.8%) samples still gave discrepant results. Three (1.4%) did not amplify successfully. A few infants who were apparently positive appeared to test HIV negative with age.

CONCLUSIONS

Indeterminate results are a significant challenge for HIV diagnostic services, as seen in the Kenyan EID Program. In our experience, they are more often negative than they are positive. False positive and false negative results can arise from clerical error, contamination and limitations of the technologies available. To forestall the consequences of such outcomes, the sensitivity and specificity of available assays must be further improved. All HIV positive samples should be retested for confirmation, and if confirmed, a new sample must be drawn and tested for DNA at the time the infant receives their initial results or starts antiretroviral therapy. Viral clearance is a phenomenon that requires further studies.

Rapid detection of human immunodeficiency virus type 1 group M by a reverse transcription-loop-mediated isothermal amplification assay

A rapid one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the pol-integrase gene was developed to detect human immunodeficiency virus type 1 (HIV-1) group M. This HIV-1 RT-LAMP assay is simple and rapid, and amplification can be completed within 35min under isothermal conditions at 60 degrees C. The 100% detection limit of HIV-1 RT-LAMP was determined using a standard strain (WHO HIV-1 [97/656]) in octuplicate and found to be 120 copies/ml. The RT-LAMP assay was evaluated for use for clinical diagnosis using plasma samples collected from 57 HIV-1-infected and 40 uninfected individuals in Cameroon, where highly divergent HIV-1 strains are prevalent. Of the 57 samples from infected individuals, 56 harbored group-M HIV-1 strains, such as subtypes A, B, G, F2, and circulating recombinant forms (CRFs) _01, _02, _09, _11, _13; all were RT-LAMP positive. One sample harboring group-O HIV-1 and the 40 HIV-1-uninfected samples were RT-LAMP negative. These findings indicate that HIV-1 RT-LAMP can detect HIV-1 group-M RNA from plasma samples rapidly and with high sensitivity and specificity. These data also suggest that this RT-LAMP assay can be useful for confirming HIV diagnosis, particularly in resource-limited settings.

Assessment of mother-to-child HIV-1 and HIV-2 transmission: an AIDS reference laboratory collaborative study

OBJECTIVE

A prospective study was carried out to assess HIV-1 and HIV-2 mother-to-child transmission (MTCT) rates in Portugal between 1999 and 2005 by analysing the proportion of diagnosed infected children born to HIV-positive mothers.

MATERIALS AND METHODS

Serial blood samples were collected from 1315 children at risk of HIV-1 infection, 131 children at risk of HIV-2 infection and six children at risk of both HIV-1 and HIV-2 infections attending 25 Health Institutions. HIV proviral DNA was detected by nested polymerase chain reaction (PCR) and statistical analysis was performed using spss.

RESULTS

DNA PCR using HIV-1 and HIV-2 long terminal repeat (LTR) primers amplified 92.5% and 75% of maternal HIV infections, respectively. Overall, MTCT occurred in 3.4% [95% confidence interval (CI) 2.5-4.6%] of HIV-1 and 1.5% (95% CI 0.2-5.4%) of HIV-2 mother-child pairs. A significant decrease in HIV-1 MTCT was observed with time, from 7.0% (95% CI 2.6-14.6%) in 1999 to 0.5% (95% CI 0.0-2.5%) in 2005. HIV MTCT was associated with an absence of antiretroviral therapy in infected pregnant women (P<0.0001). Of the 48 infected children (46 with HIV-1 and two with HIV-2), the schedule of blood sample collection was followed for only 26 children. In 14 (53.8%) of those 26 children the infections were diagnosed in the first sample collected before they were 48 h old, suggesting in utero transmission. Despite the national recommendations for antenatal HIV testing, a high overall proportion (22.2% for HIV-1 and 44.3% for HIV-2) of mothers did not access any MTCT prevention measures, mostly because of late diagnosis in pregnancy. A small but significant proportion of HIV-2 infection was found in mothers with no identifiable link with West Africa.

CONCLUSION

HIV-2 transmission rates are low (1.5% in this study), and this may have led to a lower uptake of interventions, but in the absence of interventions transmission does occur. HIV-1 transmission was also associated with a lack of intervention, mostly as a result of late presentation. Use of primers restricted to a single sequence led to false-negative maternal results in a significant proportion of cases. In part this may have been attributable to very low HIV DNA loads as well as primer template mismatches. HIV infection was not documented in children born to mothers with negative HIV DNA PCR results.

Prevalence of skin allograft discards as a result of serological and molecular microbiological screening in a regional skin bank in Italy

BACKGROUND

Postmortem skin is widely used in the treatment of patients with severe burns. Skin specimens must be screened for transmissible agents including human immunodeficiency virus (HIV), hepatitis B (HBV) and C (HCV) virus, human T-cell lymphotropic virus (HTLV), cytomegalovirus (CMV) and Treponema pallidum.

METHODS

Four hundred and sixty-one cadaveric donors underwent serological and molecular microbiological (polymerase chain reaction, PCR) screening at Siena Skin Bank between 2000 and 2004.

RESULTS

74/461 donors (16.1%) were found ineligible under current regulations.

CONCLUSIONS

These results are interesting in a local context and underline the importance of screening involving both routine serological procedures and molecular microbiological investigation. The latter has not been uniformly introduced in many countries and very limited data is available to assess its cost-benefit ratio in the field of skin donor screening.

Comparison of polymerase chain reaction-dependent methods for determining the presence of human immunodeficiency virus and hepatitis C virus in washed sperm

OBJECTIVE(S)

To evaluate the effectiveness of sperm washes by double capacitation in patients with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) and to compare between polymerase chain reaction (PCR)-dependent methods to determine viral presence after the procedure.

DESIGN

Controlled prospective clinical trial.

SETTING

Private and university-affiliated setting.

PATIENT(S)

Thirty-four HIV-positive men attending our center for assisted reproduction with their partners.

INTERVENTION(S)

Forty-one semen samples from seropositive males were obtained and washed through density gradients and swim-up and analyzed for the presence of HIV and HCV with either nested or one-round PCR. Qualitative and quantitative detection of DNA and RNA of HIV and RNA of HCV.

RESULT(S)

Of all the semen samples that were analyzed after washing, seven out of 41 samples tested positive for one or both viruses by nested PCR. The confirmation of these results with the currently used commercial methods of quantitative PCR (one-round PCR) resulted in all negatives.

CONCLUSION(S)

Sperm wash with nested PCR is the appropriate method to use in the assisted reproduction techniques that are offered to serodiscordant couples. The detection limits exhibited by one-round PCR do not offer a sufficient guarantee that transmission of all viral particles will be avoided since both viruses can be present in amounts lower than the detection threshold of this technique.

Performance of the Amplicor human immunodeficiency virus type 1 PCR and analysis of specimens with false-negative results

Over a 4-year period, the Roche Amplicor kit was used in a United Kingdom reference laboratory for the detection or confirmation of human immunodeficiency virus (HIV) type 1 infection, particularly in infants born to HIV-infected mothers. Of 408 specimens from adults and older children tested, the 122 seronegative specimens were all Amplicor negative. Of the 286 seropositive specimens, 268 were Amplicor positive. On the basis of these results, the Amplicor assay has a specificity of 100% and a sensitivity of 93.7%. In addition, for 247 specimens from infants and young children, serological results may not have been diagnostic because of placental transfer of maternal antibodies. Forty-eight were Amplicor positive, and of the 199 Amplicor-negative specimens, 19 were assumed to be false negative on the basis of clinical data, serological markers (including p24 antigen), and/or results for previous or follow-up specimens. This represents a sensitivity of 75% for the Amplicor test for specimens from patients under 2 years of age. Of these 37 false-negative specimens plus 2 specimens from other laboratories, 31 could be characterized by amplifying extracted material from them by an in-house nested gag PCR spanning the Amplicor target region. The amplicons were sequenced and found to represent subtypes A (35.5%), B (22.6%), C (22.6%), D (16.1%), and G (3.2%). False-negative results by the Amplicor assay may be ascribed to low-target copy number, the physical behavior of one primer (SK462), and sequence variation in the target region of the other primer (SK431).

A multicentre quality assessment study to monitor the performance of HIV-1 PCR

Eleven German laboratories and one Swiss laboratory initiated a quality assessment study to evaluate the specificity and sensitivity of their polymerase chain reaction (PCR) for detection of HIV-1 DNA. Following its own PCR protocols, each laboratory tested a panel of ten coded samples consisting of cell pellets containing 0, 0.1, 1, 10, 10(2), 10(3) and 10(4) ACH-2 cells per 1.5 x 10(5) uninfected peripheral blood mononuclear cells. Of the twelve participating laboratories, three reported correct results for the dilution series as well as for uninfected specimens. One or more classification errors were recorded for 12% of the samples for which the diagnosis was expected to be positive or negative. Samples containing 10 copies of the target template were correctly reported by eleven of the twelve participants. The average sensitivity was 97%. The results of the study revealed no significant differences between the Amplicor kit and in-house procedures. Most of the classification errors occurred in specimens from HIV-negative samples. Out of 36 negative samples, 5 were reported false positive, showing that contamination remains a problem for some laboratories, regardless of the PCR test performed. Careful laboratory techniques and internal as well as external quality control procedures will help avoiding carryover contamination.

Concordance between polymerase chain reaction and antibody detection in the diagnosis of human immunodeficiency virus type 1 infection

A highly sensitive nested polymerase chain reaction (PCR) protocol was used to detect human immunodeficiency virus type 1 (HIV-1) DNA in peripheral blood mononuclear cells from 271 HIV-1-seropositive patients, 240 HIV-1-seronegative subjects at increased risk for HIV-1 infection, 51 serologically indeterminate individuals, and 120 healthy blood donors. PCR was carried out in a multiplex nested configuration with pol and env region primer sets. HIV-1 DNA was detected in all of the HIV-1 seropositive patients. In contrast, HIV-1 DNA was not detected in any of the either seronegative or serologically indeterminate subjects. Only one of 37 seronegative regular sexual partners of HIV-1-infected patients who were followed longitudinally was found to seroconvert to HIV-1. However, HIV-1 DNA and antibody results were concordant in the four samples obtained from this subject prior to and after seroconversion. These results show an excellent concordance between HIV-1 DNA and antibody detection for diagnosis of HIV-1 infection and suggest that long-term HIV-1 infection in the absence of detectable antibody is likely to occur at a very low frequency.

Increased reliability of selective PCR by using additionally mutated primers and a commercial Taq DNA polymerase enhancer

A reliable selective PCR procedure that combines the use of additionally mutated primers with the specificity-enhancing properties of a commercial preparation (Perfect Match, Stratagene) is described. The human immunodeficiency virus type 1 pol gene point mutations known to confer in vitro resistance to azidothymidine were examined as a model for optimization of the assay. The usual strategy of deliberately introducing an additional mismatch 1 residue from the 3' end in the wild-type and mutant primers did not allow reproducible discrimination between wild-type and mutant target sequences. Addition of minimal amounts of Perfect Match to the same PCR mixtures resulted in a significantly enlarged range of selective annealing temperatures, providing a valuable and cost-effective means for reliable detection of known mutations by selective PCR.