Evaluation of a prototype Amplicor PCR assay for detection of human immunodeficiency virus type 1 DNA in blood samples from Tanzanian adults infected with HIV-1 subtypes A, C and D

Country of Birth of Children With Diagnosed HIV Infection in the United States, 2008-2014

BACKGROUND

Diagnoses of HIV infection among children in the United States have been declining; however, a notable percentage of diagnoses are among those born outside the United States. The impact of foreign birth among children with diagnosed infections has not been examined in the United States.

METHODS

Using the Centers for Disease Control and Prevention National HIV Surveillance System, we analyzed data for children aged <13 years with diagnosed HIV infection ("children") in the United States (reported from 50 states and the District of Columbia) during 2008-2014, by place of birth and selected characteristics.

RESULTS

There were 1516 children [726 US born (47.9%) and 676 foreign born (44.6%)]. US-born children accounted for 70.0% in 2008, declining to 32.3% in 2013, and 40.9% in 2014. Foreign-born children have exceeded US-born children in number since 2011. Age at diagnosis was younger for US-born than foreign-born children (0-18 months: 72.6% vs. 9.8%; 5-12 years: 16.9% vs. 60.3%). HIV diagnoses in mothers of US-born children were made more often before pregnancy (49.7% vs. 21.4%), or during pregnancy (16.6% vs. 13.9%), and less often after birth (23.7% vs. 41%). Custodians of US-born children were more often biological parents (71.9% vs. 43.2%) and less likely to be foster or nonrelated adoptive parents (10.4% vs. 55.1%). Of 676 foreign-born children with known place of birth, 65.5% were born in sub-Saharan Africa and 14.3% in Eastern Europe. The top countries of birth were Ethiopia, Ukraine, Uganda, Haiti, and Russia.

CONCLUSIONS

The increasing number of foreign-born children with diagnosed HIV infection in the United States requires specific considerations for care and treatment.

Prevalence of genotypic resistance to antiretroviral drugs in treatment-naive youths infected with diverse HIV type 1 subtypes and recombinant forms in Dar es Salaam, Tanzania

As human immunodeficiency virus (HIV) diversity may have an impact on both vaccine efficacy and drug resistance, it is important to have knowledge of circulating genetic variants. With widespread use of antiretroviral (ARV) drugs in Africa, one of the major potential challenges is the risk of emergence of ARV drug-resistant HIV strains. This study aimed to determine the circulating HIV subtypes and recombinant forms, as well as the prevalence of ARV drug resistance mutations, among 75 treatment-naive HIV-infected youths in Dar es Salaam, Tanzania. Gag (n = 48), partial pol (n = 44), and partial env (n = 35) sequencing was performed; all three regions were sequenced in 26 samples. Evidence of infection with recombinant viruses was found in 12 (46%) participants; AC recombinants were the most commonly detected and they were identified in six (23%) participants. Of individuals infected with nonrecombinant strains, subtype A was most commonly detected in seven (27%) participants, followed by subtype C detected in six (23%) participants and subtype D detected in one (4%) participant. Among the pol sequences from 44 individuals, three (7%) had resistance to nucleoside reverse transcriptase (RT) inhibitors and four (9%) had nonnucleoside RT inhibitor resistance mutations. Of these, three (7%) individuals were infected with viruses with cross-resistance mutations to both classes of RT inhibitors. These resistant mutations were all associated with drugs currently used in first-line therapy and in the prevention of vertical transmission. This high prevalence of resistance mutations is of considerable concern in apparently drug-naive populations as it may result in treatment failure and the spread of ARV-resistant strains.

Early HIV-1 diagnosis using in-house real-time PCR amplification on dried blood spots for infants in remote and resource-limited settings

BACKGROUND

In resource-limited settings, most perinatally HIV-1-infected infants do not receive timely antiretroviral therapy because early HIV-1 diagnosis is not available or affordable.

OBJECTIVE

To assess the performance of a low-cost in-house real-time polymerase chain reaction (PCR) assay to detect HIV-1 DNA in infant dried blood spots (DBS).

METHODS

One thousand three hundred nineteen DBS collected throughout Thailand from non-breast-fed infants born to HIV-1-infected mothers were shipped at room temperature to a central laboratory.In-house real-time DNA PCR results were compared with Roche Amplicor HIV-1 DNA test (Version 1.5) results. In addition, we verified the Roche test performance on DBS sampled from 1218 other infants using as reference HIV serology result at 18 months of age.

RESULTS

Real-time DNA PCR and Roche DNA PCR results were 100% concordant. Compared with HIV serology results, the Roche test sensitivity was 98.6% (95% confidence interval: 92.6% to 100.0%) and its specificity at 4 months of age was 99.7% (95% confidence interval: 99.2% to 99.9%).

CONCLUSIONS

In-house real-time PCR performed as well as the Roche test in detecting HIV-1 DNA on DBS in Thailand. Combined use of DBS and real-time PCR assays is a reliable and affordable tool to expand access to early HIV-1 diagnosis in remote and resource-limited settings, enabling timely treatment for HIV-1-infected infants.

Evolution of human immunodeficiency virus type 1 serotypes in northern Tanzania: a retrospective study

The HIV-1 epidemic in Tanzania is characterized by the circulation of heterogeneous virus subtypes. A retrospective study was conducted to determine the changing pattern of circulating HIV-1 subtypes in northern Tanzania. A peptide-binding enzyme immunoassay (PEIA) was employed to analyse 305 HIV-1 positive serum and plasma samples collected between 1985 and 2005. Samples were serotyped using synthetic peptides representing HIV-1 genotypes A-E derived from consensus gp120 V3 sequences. Plasma samples collected in 2005 were V3 genotyped for comparison with PEIA results. In 1985, serotypes A and D were co-circulating while serotype C was first detected in 1990. In 2001 and 2005, serotype C was the most prevalent, serotype A was stable, and serotype D was declining. PEIA is relatively rapid and simple to perform compared to molecular approaches, and is a valuable epidemiological tool in regions with limited resources. HIV-1 classification into serotypes based on antigenic V3 diversity may be a useful screening tool for the identification of HIV-1 variants with regard to diagnosis, treatment, disease progression and candidate vaccine development.

Infant human immunodeficiency virus diagnosis in resource-limited settings: issues, technologies, and country experiences

Diagnosing human immunodeficiency virus (HIV) infection in infants is difficult because maternal HIV antibodies cross the placenta, causing positive serologic tests in HIV-exposed infants for the first several months of life. Early definitive diagnosis of HIV requires virologic testing such as polymerase chain reaction (PCR), which is the diagnostic standard in resource-rich settings but has been too complex and expensive for widespread use in most countries with high HIV prevalence. Early PCR testing can help HIV-infected infants access treatment, provide psychosocial benefits for families of uninfected infants, and help programs for prevention of mother-to-child transmission of HIV monitor their effectiveness. HIV testing, including PCR, is increasingly available for infants in resource-limited settings, but there are many barriers and complex policy decisions that need to be addressed before universal early testing can become standard. This paper reviews challenges and progress in the field and suggests ways to facilitate early infant testing in resource-limited settings.

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.

Evaluation of HIV antibody and antigen/antibody combination ELISAs for use in an alternative confirmatory HIV testing strategy in Dar es Salaam, Tanzania

The aim of this study was to evaluate the performance of two antibody enzyme-linked immunosorbent assays (ELISAs) [Vironostika Uni-Form II plus O and Enzygnost anti-HIV-1/2 Plus], and two antigen/antibody combination ELISAs [Murex and Vironostika HIV Uni-Form II] for use in an alternative confirmatory HIV diagnostic testing strategy in Dar es Salaam, Tanzania. Altogether, 1380 serum samples were included. All ELISA reactive samples were tested using the Inno-Lia antibody assay and discrepant samples were tested on the Innotest p24 antigen assay. Three hundred and one (21.8%) samples were confirmed HIV-1 antibody positive by Inno-Lia including 27/508 (5.3%) from blood donors, 65/511 (12.7%) from pregnant women and 209/361 (57.9%) from hospital patients. The sensitivity at initial testing was 100% (95% CI; 98.8-100%) for all assays except Vironostika Uni-Form II plus O (99.7%; 95% CI; 98.2-99.9%) which showed one false negative sample at initial testing but 100% sensitivity after repeat testing. The final specificity at repeat testing was 100% (95% CI; 99.7-100%) for Enzygnost anti-HIV-1/2 Plus, 99.4% (95% CI; 98.8-99.8%) for each of the antigen/antibody combination ELISAs and 97.9% (95% CI; 96.8-98.6%) for Vironostika plus O ELISA. An alternative confirmatory HIV testing strategy based on initial testing on any of the two antigen/antibody assays followed by testing of reactive samples on the Enzygnost anti-HIV-1/2 Plus assay gave 100% specificity (95% CI; 99.7-100%).

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.

Rate of decline of absolute number and percentage of CD4 T lymphocytes among HIV-1-infected adults in Dar es Salaam, Tanzania

OBJECTIVE

To determine the rate of decline of CD4 T lymphocytes among HIV-1-infected individuals.

DESIGN AND SETTING

A prospective open cohort study of workers in three hotels in Dar es Salaam.

METHODS

The workers were seen yearly during the study. CD4 T lymphocyte counts were determined using flow cytometry. The CD4 T-lymphocyte slopes were determined using a linear regression model.

RESULTS

During the 9-year study period 682 subjects were selected for lymphocyte subset determinations. Of these, 94 HIV-1-seroprevalent (72%), 77 HIV-1-seroincident (67%) and 325 seronegative (75%) individuals had three or more CD4 T-cell determinations, and were used for calculations of CD4 cell slopes with a mean follow-up period of 71.4, 52.9 and 86.0 months, respectively. The median yearly decline of the CD4 T-lymphocyte counts and percentages among seroprevalent individuals was -21.5 cells/microl and -1.3%; among the seroincident individuals the median decline was -22.0 cells/microl and -1.5%. In seroincident individuals the mean duration to a CD4 T-lymphocyte level corresponding to a definition of AIDS was 13.3 years or 11.8 years for CD4 cell counts or percentages, respectively. HIV-1-seropositive subjects who died had significantly steeper CD4 cell slopes than those who survived.

CONCLUSION

The rates of CD4 T-lymphocyte decline in HIV-1-infected individuals in our population are similar to those reported in Europe and north America.

Among 46 near full length HIV type 1 genome sequences from Rakai District, Uganda, subtype D and AD recombinants predominate

The impact of HIV-1 genetic diversity on candidate vaccines is uncertain. To minimize genetic diversity in the evaluation of HIV-1 vaccines, vaccine products must be matched to the predominant subtype in a vaccine cohort. To that end, full genome sequencing was used to detect and characterize HIV-1 subtypes and recombinant strains from individuals in Rakai District, Uganda. DNA extracted from peripheral blood mononuclear cells (PMBC) was PCR amplified using primers in the long terminal repeats (LTRs) to generate nearly full length genomes. Amplicons were directly sequenced with dye terminators and automated sequencers. Sequences were phylogenetically analyzed and recombinants were detected and mapped with distance scan and bootscan. Among 46 sequences, 54% were subtype D, 15% were subtype A, and 30% were recombinant. All recombinants were individually unique, and most combined subtypes A and D. Subtype D comprised more than 70% of all the HIV-1 genomes in Rakai when both pure subtypes and recombinants were considered. Candidate vaccines based on HIV-1 subtype D would be appropriate for evaluation in Rakai District, Uganda.

Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants

OBJECTIVE

To further define the genetic diversity of HIV-1 in Kenya using approaches that clearly distinguish subtypes from inter-subtype recombinants.

DESIGN

Near full genome sequencing and analysis were used, including sensitive new tools for detection and mapping of recombinants.

METHODS

Purified peripheral blood mononuclear cell DNA from 41 HIV-1 positive blood donations collected from six hospitals across southern Kenya was used to amplify near full-length genomes by nested PCR. These were sequenced on an ABI 3100 automated sequencer and analyzed phylogenetically.

RESULTS

Among 41 near full-length genomes, 25 were non-recombinant (61%) and 16 were recombinant (39%). Of the 25 pure subtypes, 23 were subtype A, one was subtype C and one was subtype D. Most recombinants consisted of subtype A and either subtype C or subtype D; a few contained A2, a recently identified sub-subtype. Two A2/D recombinants had identical breakpoints and may represent a circulating recombinant form. A third A2/D recombinant had the same structure as a previously described Korean isolate, and these may constitute a second A2-containing circulating recombinant form.

CONCLUSIONS

In Kenya, 93% of HIV-1 genomes were subtype A or A-containing recombinant strains. Almost 40% of all strains were recombinant. Vaccine candidates tested in Kenya should be based on subtype A strains, but the methods used for evaluation of breakthrough infections during future vaccine trials should be capable of identifying non-A subtypes, the A2 sub-subtype, and recombinants.

Efficacy of three short-course regimens of zidovudine and lamivudine in preventing early and late transmission of HIV-1 from mother to child in Tanzania, South Africa, and Uganda (Petra study): a randomised, double-blind, placebo-controlled trial

BACKGROUND

Large reductions in transmission of HIV-1 from mother to child have been achieved in more-developed countries due to the use of antiretrovirals. Short-course regimens, suitable for resource-poor countries, have also been shown to significantly reduce peripartum HIV-1 transmission. We assessed the efficacy of short-course regimens with zidovudine and lamivudine in a predominantly breastfeeding population.

METHODS

We did a randomised, double-blind, placebo-controlled trial in South Africa, Uganda, and Tanzania. Between June, 1996, and January, 2000, HIV-1-infected mothers were randomised to one of four regimens: A, zidovudine plus lamivudine starting at 36 weeks' gestation, followed by oral intrapartum dosing and by 7 days' postpartum dosing of mothers and infants; B, as regimen A, but without the prepartum component; C, intrapartum zidovudine and lamivudine only; or placebo. From Feb 18, 1998, onward, women were only randomised to one of the active treatment groups. Primary outcomes were HIV-1 infection and child mortality at week 6 and month 18 after birth. Analysis was by intention to treat of those randomised before Feb 18, 1998.

FINDINGS

1797 HIV-1-infected women were identified. Week 6 HIV-1 transmission rates were 5.7% for group A, 8.9% for group B, 14.2% for group C, and 15.3% for the placebo group. Respective relative risks for HIV-1 transmission in the treatment groups compared with placebo were 0.37 (95% CI 0.21-0.65), 0.58 (0.36-0.94), and 0.93 (0.62-1.40). For the combined endpoint of HIV-1 infection and infant mortality at week 6 rates were 7.0%, 11.6%, 17.5%, and 18.1%, respectively, with relative risks of 0.39 (0.24-0.64), 0.64 (0.42-0.97), and 0.97 (0.68-1.38). 1081 (74%) of the women analysed initiated breastfeeding. Based on an interval-censored survival analysis, HIV-1 infection rates at month 18 were 15% (95% CI 9-23), 18% (12-26), 20% (13-30) and 22% (16-30), respectively.

INTERPRETATION

Although at week 6 after birth, regimens A and B were effective in reducing HIV-1 transmission, benefits have diminished considerably after 18 months of follow-up. Introduction of short-course regimens to prevent mother-to-child transmission of HIV-1 in less-developed countries should be accompanied by interventions to minimise the risk of subsequent transmission via breastfeeding.

Evaluation of an alternative confirmatory strategy for the diagnosis of HIV infection in Dar Es Salaam, Tanzania, based on simple rapid assays

Alternative confirmatory strategies for detection of antibodies to HIV using enzyme-linked immunosorbent assays (ELISAs) have been shown to be useful in laboratories with limited resources. Three simple and rapid HIV antibody detection assays (Capillus, Serocard and Determine) were evaluated using 1412 fresh serum samples in order to formulate an alternative confirmatory strategy for the diagnosis of HIV infection. All sera were also tested by an anti-HIV ELISA and all sera reactive by any of the assays were tested by a second ELISA as well as by Western blot. Three hundred and eighty-three sera were found to be HIV-1 antibody positive, while 1017 sera were HIV antibody negative; 12 sera which were reactive by one or more of the simple assays had indeterminate Western blot results and these were considered HIV seronegative during the analysis. All assays had a sensitivity of 100%. The initial specificity of the assays were 98.7, 98.2 and 97.9% for Capillus, Serocard and Determine, respectively. In an alternative confirmatory strategy the use of Capillus followed by Serocard or Determine gave a specificity of 99.9 and 99.8%, respectively. Serocard followed by Determine gave a specificity of 99.3%. A testing strategy with 100% specificity (95% CI; 99.6-100%) could be achieved by the sequential use of all three simple/rapid assays or by repeat testing by Capillus followed by Serocard.

Principles of molecular microbiology testing methods

Molecular testing methods have the potential to replace many conventional microbiology laboratory assays. Recent refinements in technology have resulted in more user-friendly testing platforms. These platforms are automated and have lowered risks for contamination, decreased costs, and are faster than older platforms. The success of these technologies depends on their successful application to patient care. Quality issues include appropriate specimens for analysis, performance characteristics of different analytical methods, optimal specimen processing, the effects of PCR inhibitors, and false-positive results caused by contaminating nucleic acids. Quality control guidelines for molecular microbiologic diagnostic assays are in their infancy and require further development. Additionally, the problem of "too much" sensitivity (brought on by the extreme sensitivity of these techniques coupled with the potential presence of small numbers of pathogenic organisms in asymptomatic individuals) should be considered. Potential problems when monitoring therapy (because molecular detection techniques do not generally have the ability to determine whether an organism is dead or alive) can also occur. Cost-effective test use, pathogen- or disease-targeted algorithms, and standardized methods will be necessary for the true value of these technologies to be realized. This is especially important, because, unlike traditional culture methods, most molecular microbiology methods are pathogen-specific. Clinicians familiar with the reasons why "pan-culture" (i.e., requesting all culture possibilities at once) is inadvisable should not use the same irrational approach when requesting molecular tests. The clinical usefulness of molecular testing will be maximized as targeted algorithms are developed and an understanding of molecular test ordering patterns is realized. Laboratory technicians and physicians must continue to apply and combine theories of traditional microbiology, clinical chemistry, and general medicine to the understanding and application of molecular diagnostics.

High proportion of unrelated HIV-1 intersubtype recombinants in the Mbeya region of southwest Tanzania

BACKGROUND

In Mbeya, a rural region of southwest Tanzania, HIV-1 subtypes A, C and D have been co-circulating since the early 1990s.

OBJECTIVE

To define to what extent the co-existence of subtypes has led to recombinant HIV-1 strains and whether there is evidence for epidemic spread of any circulating recombinant form.

METHODS

Nine HIV-1-seropositive young adults from Mbeya Town with no evident high-risk behaviour contributed peripheral blood mononuclear cells for this study. Nine virtually full-length-genome-sequences were amplified from this DNA and phylogenetically analysed.

RESULTS

Out of the nine samples, two were subtype A (22%), two were subtype C (22%) and five were recombinants (56%): four A/C recombinants and one C/D recombinant. None of the recombinants were related to each other; all of them had different mosaic structures. Most of the genome in the recombinants was subtype C.

CONCLUSION

A high proportion of unrelated intersubtype recombinants, none of them apparently spreading in the population, may be present in southwest Tanzania.