Assessment of the performance of the plasma separation card for HIV-1 viral load monitoring in South Africa

Scaling up of newer innovations that address the limitations of the dried blood spot and the logistics of plasma monitoring is needed. We employed a multi-site, cross-sectional assessment of the plasma separation card (PSC) on blood specimens collected from all consenting adults, assenting young and pediatric patients living with HIV from 10 primary healthcare clinics in South Africa. Venous blood for EDTA-plasma samples was collected and analyzed according to the standard of care assay, while collected capillary blood for the PSC samples was analyzed using the Roche COBAS AmpliPrep/Cobas TaqMan (CAP/CTM) HIV-1 Test at the National Reference laboratories. McNemar tests assessed the differences in concordance between the centrifuged plasma and dried plasma spots. The usability of PSC by blood spotting, PSC preparation, and pre-analytical work was assessed by collecting seven-point Likert-scale data from healthcare and laboratory workers. We enrolled 538 patients, mostly adults [n = 515, 95.7% (95% CI: 93.7%-97.1%)] and females [n = 322, 64.2% (95% CI: 60.0%-68.1%)]. Overall, 536 paired samples were collected using both PSC- and EDTA-plasma diagnostics, and 502 paired PSC- and EDTA-plasma samples assessed. Concordance between the paired samples was obtained for 446 samples. Analysis of these 446 paired samples at 1,000 copies per milliliter threshold yielded an overall sensitivity of 87.5% [95% CI: 73.2%-95.8%] and specificity of 99.3% [95% CI: 97.9%-99.8%]. Laboratory staff reported technical difficulties in most tasks. The usability of the PSC by healthcare workers was favorable. For policymakers to consider PSC scale-up for viral load monitoring, technical challenges around using PSC at the clinic and laboratory level need to be addressed.

IMPORTANCE

Findings from this manuscript emphasize the reliability of the plasma separation card (PSC), a novel diagnostic method that can be implemented in healthcare facilities in resource-constrained settings. The agreement of the PSC with the standard of care EDTA plasma for viral load monitoring is high. Since the findings showed that these tests were highly specific, we recommend a scale-up of PSC in South Africa for diagnosis of treatment failure.

Mortality Among Children Aged <5 Years Living with HIV Who Are Receiving Antiretroviral Treatment - U.S. President's Emergency Plan for AIDS Relief, 28 Supported Countries and Regions, October 2020-September 2022

Globally, children aged <5 years, including those living with HIV who are not receiving antiretroviral treatment (ART), experience disproportionately high mortality. Global mortality among children living with HIV aged <5 years receiving ART is not well described. This report compares mortality and related clinical measures among infants aged <1 year and children aged 1-4 years living with HIV with those among older persons aged 5-14, 15-49, and ≥50 years living with HIV receiving ART services at all clinical sites supported by the U.S. President's Emergency Plan for AIDS Relief. During October 2020-September 2022, an average of 11,980 infants aged <1 year and 105,510 children aged 1-4 years were receiving ART each quarter; among these infants and children receiving ART, 586 (4.9%) and 2,684 (2.5%), respectively, were reported to have died annually. These proportions of infants and children who died ranged from four to nine times higher in infants aged <1 year, and two to five times higher in children aged 1-4 years, than the proportions of older persons aged ≥5 years receiving ART. Compared with persons aged ≥5 years living with HIV, the proportions of children aged <5 years living with HIV who experienced interruptions in treatment were also higher, and the proportions who had a documented HIV viral load result or a suppressed viral load were lower. Prioritizing and optimizing HIV and general health services for children aged <5 years living with HIV receiving ART, including those recommended in the WHO STOP AIDS Package, might help address these disproportionately poorer outcomes.

Resistance is common in paediatric patients failing ART in South Africa

BACKGROUND

Minimal data exist on HIV drug resistance patterns and prevalence among paediatric patients failing ART in resource-limited settings. We assessed levels of HIV drug resistance in children with virological failure.

METHODS

This cross-sectional study, performed from March 2017 to March 2019 in South Africa, enrolled HIV-positive children aged ≤19 years, receiving ART through public health facilities with recent evidence suggestive of virological failure (at least one viral load ≥1000 copies/mL), across 45 randomly selected high-volume clinics from all nine provinces. Resistance genotyping was performed using next-generation sequencing technologies. Descriptive analysis taking into account survey design was used to determine outcomes.

RESULTS

Among 899 participants enrolled, the adjusted proportion of HIV drug resistance among children with virological failure was 87.5% (95% CI 83.0%-90.9%). Resistance to NNRTIs was detected in 77.4% (95% CI 72.5%-81.7%) of participants, and resistance to NRTIs in 69.5% (95% CI 62.9%-75.4%) of participants. Overall, resistance to PIs was detected in 7.7% (95% CI 4.4%-13.0%) of children.

CONCLUSIONS

HIV drug resistance was highly prevalent in paediatric patients failing ART in South Africa, with 9 in 10 patients harbouring resistance to NNRTIs and/or NRTIs. PI-based regimens are predicted to be highly efficacious in achieving virological suppression amongst patients failing NNRTI-based regimens. Scaling up resistance testing amongst patients would facilitate access to second- and third-line regimens in South Africa.

HIV Viral Load Scale-up Among Children and Adolescents: Trends in Viral Load Suppression, Sample Type and Processing in 7 PEPFAR Countries, 2015-2018

HIV-positive children and adolescents face gaps in viral load (VL) testing. To understand trends in pediatric/adolescent VL testing, 7 countries collected data from Laboratory Information Management Systems. Results showed increasing proportion of VL tests done through dried blood spot (DBS) and decreased sample rejection rates for DBS compared with plasma, supporting use of DBS VL when skilled phlebotomy is unavailable.

Health facility users' knowledge, perceptions, and practices about infant feeding in the context of option B+ in South Africa: a qualitative study

BACKGROUND

HIV and sub-optimal infant feeding practices remain important threats to child growth, development, and survival in low- and middle-income countries. To our knowledge, few studies have explored health service users' perspective of infant feeding in the context of WHO Option B+ policy to prevent vertical HIV transmission (PMTCT). This paper is a sub-analysis of qualitative data from a mixed-methods multi-level process evaluation of Option B+ implementation in South Africa (SA). In this study we explored health facility users' infant feeding knowledge, perceptions, and practices one year after SA adopted the 2016 updated World Health Organization prevention of mother-to-child transmission of HIV Option B+ infant feeding guidelines.

METHODS

Nineteen focus group discussions (FGDs) were held with six groups of men and women whose infants were aged < 6 months. Participants were attending randomly selected primary health care facilities within six purposively selected priority districts. The six groups included in the FGDs were: (i) adolescent girls and young women living with HIV (WHIV), (ii) adolescent girls and young women not living with HIV (WNHIV), (iii) older postnatal WHIV (iv) older postnatal WNHIV (v) pregnant women, and (vi) men. Data collection took place between April and December 2018. Data analysis involved coding and thematic framework analysis.

RESULTS

Women and men have suboptimal knowledge of the recommended breastfeeding duration and exclusive breastfeeding, especially for HIV-exposed infants. Most women received sub-optimal infant feeding counselling and mixed messages from health care workers. Fewer WHIV initiated breastfeeding at birth compared to WNHIV. Most parents believed that HIV-exposed infants should be breastfed for 6 months and many postnatal women on antiretroviral drugs and younger mothers lacked confidence to breastfeed beyond 6 months. Mixed feeding was predominant among all women due to individual, family, and socio-structural barriers. Many men were supportive on infant feeding; however, they lacked the appropriate information and skills to influence their partners' infant feeding decisions.

CONCLUSIONS

Differences in breastfeeding practices between WHIV and WNHIV are highly influenced by the lack of knowledge of infant feeding policy recommendations. Multiple-level factors deter many mothers from adhering to recommended guidelines. Appropriate ongoing infant feeding counselling and breastfeeding support are required for women and their partners.

Use of Epidemiology Surge Support to Enhance Robustness and Expand Capacity of SARS-CoV-2 Pandemic Response, South Africa

As COVID-19 cases increased during the first weeks of the pandemic in South Africa, the National Institute of Communicable Diseases requested assistance with epidemiologic and surveillance expertise from the US Centers for Disease Control and Prevention South Africa. By leveraging its existing relationship with the National Institute of Communicable Diseases for >2 months, the US Centers for Disease Control and Prevention South Africa supported data capture and file organization, data quality reviews, data analytics, laboratory strengthening, and the development and review of COVID-19 guidance This case study provides an account of the resources and the technical, logistical, and organizational capacity leveraged to support a rapid response to the COVID-19 pandemic in South Africa.

Tuberculosis prevalence, incidence and prevention in a south african cohort of children living with HIV

BACKGROUND

We describe tuberculosis (TB) disease among antiretroviral treatment (ART) eligible children living with HIV (CLHIV) in South Africa to highlight TB prevention opportunities.

METHODS

In our secondary analysis among 0- to 12-year-old ART-eligible CLHIV in five Eastern Cape Province health facilities from 2012 to 2015, prevalent TB occurred 90 days before or after enrollment; incident TB occurred >90 days after enrollment. Characteristics associated with TB were assessed using logistic and Cox proportional hazards regression with generalized estimating equations.

RESULTS

Of 397 enrolled children, 114 (28.7%) had prevalent TB. Higher-income proxy [adjusted odds ratio (aOR) 1.8 [95% confidence interval (CI) 1.3-2.6] for the highest, 1.6 (95% CI 1.6-1.7) for intermediate]; CD4+ cell count <350 cells/µl [aOR 1.6 (95% CI 1.1-2.2)]; and malnutrition [aOR 1.6 (95% CI 1.1-2.6)] were associated with prevalent TB. Incident TB was 5.2 per 100 person-years and was associated with delayed ART initiation [hazard ratio (HR) 4.7 (95% CI 2.3-9.4)], malnutrition [HR 1.8 (95% CI 1.1-2.7)] and absence of cotrimoxazole [HR 2.3 (95% CI 1.0-4.9)]. Among 362 children with data, 8.6% received TB preventive treatment.

CONCLUSIONS

Among these CLHIV, prevalent and incident TB were common. Early ART, cotrimoxazole and addressing malnutrition may prevent TB in these children.

Investigating the quality of HIV rapid testing practices in public antenatal health care facilities, South Africa

Monitoring HIV prevalence using antenatal HIV sentinel surveillance is important for efficient epidemic tracking, programme planning and resource allocation. HIV sentinel surveillance usually employs unlinked anonymous HIV testing which raises ethical, epidemiological and public health challenges in the current era of universal test and treat. The World Health Organization (WHO) recommends that countries should consider using routine prevention of mother-to-child transmission of HIV (PMTCT) data for surveillance. We audited antenatal care clinics to assess the quality of HIV rapid testing practices as the first step to assess whether South Africa is ready to utilize PMTCT programme data for antenatal HIV surveillance. In 2017, we conducted a cross-sectional survey in 360 randomly sampled antenatal care clinics using the adapted WHO Stepwise-Process-for-Improving-the-Quality-of-HIV-Rapid-Testing (SPI-RT) checklist. We calculated median percentage scores within a domain (domain-specific median score), and across all domains (overall median percentage scores). The latter was used to classify sites according to five implementation levels; (from 0:<40% to 4: 90% or higher). Of 346 (96.1%) facilities assessed, an overall median percentage score of 62.1% (inter-quartile range (IQR): 50.8–71.9%) was obtained. The lowest domain-specific median percentage scores were obtained under training/certification (35% IQR: 10.0–50.0%) and external quality assurance (12.5% IQR: 0.0–50.0%), respectively. The majority (89%) of sites had an overall median score at level 2 or below; of these, 37% required improvement in specific areas and 6.4% in all areas. Facilities in districts implementing the HIV Rapid Test Quality Improvement Initiative and supported by the President’s Emergency Plan for AIDS Relief (PEPFAR) had significantly higher median overall scores (65.6% IQR: 53.9–74.2%) (P-value from rank sum test: <0.001) compared with non–PEPFAR–supported facilities (56.6% IQR:47.7–66.0%). We found sub-optimal implementation of HIV rapid testing practices. We recommend the expansion of the PEPFAR-funded Rapid Test Continuous Quality Improvement (RTCQI) support to all antenatal care testing sites.

A risk measurement tool for targeted HIV prevention measures amongst young pregnant and lactating women in South Africa

Background

We aimed to develop and validate a tool to identify which pregnant/lactating young South African women (≤ 24 years) are at risk of HIV infection.

Methods

Data from three national South African Prevention of Mother-to-Child Transmission (PMTCT) evaluations were used to internally validate three HIV acquisition risk models for young postpartum women. We used univariate and multivariable logistic regression analysis to determine which risk factors were significant. Model coefficients were rounded and stratified into risk groups and the area under the receiver operating curve (AUROC) was computed. Models were developed to determine which risk factors provided the most predictive accuracy whilst remining clinically meaningful.

Results

Data from 9 456 adult and 4 658 young pregnant and lactating women were included in the development and validation data sets, respectively. The optimal model included the following risk factors: age (20–24 years old), informal house structure, two or more pregnancies, mothers who had knowledge of when they received their last HIV test result, no knowledge of the infant’s father’s HIV status, no knowledge of breastfeeding as a mode of MTCT and knowledge of PMTCT programme. The mean AUROC was 0.71 and 0.72 in the development and validation datasets respectively. The optimum cut off score was ≥ 27, having 84% sensitivity, 44% specificity, and identifying 44% of high-risk women eligible for PrEP.

Conclusion

The optimal model to be used as a possible risk scoring tool to allow for early identification of those pregnant/lactating women most at-risk of HIV acquisition included both statistically as well as clinically meaningful risk factors. A field-based study is needed to test and validate the effectiveness of this targeted approach.

HIV drug resistance profile in South Africa: Findings and implications from the 2017 national HIV household survey

BACKGROUND

HIV drug resistance (HIVDR) testing was included in the 2017 South African national HIV household survey. We describe the prevalence of HIVDR by drug class, age, sex and antiretroviral drugs (ARV) status.

METHODS

Dried blood were spots tested for HIV, with Viral load (VL), exposure to ARVs and HIVDR testing among those HIV positive. HIVDR testing was conducted on samples with VL ≥1000 copies/ml using Next Generation Sequencing. Weighted percentages of HIVDR are reported.

RESULTS

697/1,105 (63%) of HIV positive samples were sequenced. HIVDR was detected in samples from 200 respondents (27.4% (95% confidence interval (CI) 22.8-32.6)). Among these 130 (18.9% (95% CI 14.8-23.8)), had resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) only, 63 (7.8% (95% CI 5.6-10.9)) resistance to NNRTIs and nucleoside reverse transcriptase inhibitors, and 3 (0.5% (95% CI 0.1-2.1)) resistance to protease inhibitors. Sixty-five (55.7% (95% CI 42.6-67.9) of ARV-positive samples had HIVDR compared to 112 (22.8% (95% CI 17.7-28.7)), in ARV-negative samples. HIVDR was found in 75.6% (95% CI 59.2-87.3), n = 27, samples from respondents who reported ARV use but tested ARV-negative, and in 15.3% (95% CI 6.3-32.8), n = 7, respondents who reported no ARV use and tested ARV-negative. There were no significant age and sex differences in HIVDR.

CONCLUSION

27% of virally unsuppressed respondents had HIVDR, increasing to 75% among those who had discontinued ARV. Our findings support strengthening first-line ARV regimens by including drugs with a higher resistance barrier and treatment adherence strategies, and close monitoring of HIVDR.

Longitudinal adherence to maternal antiretroviral therapy and infant Nevirapine prophylaxis from 6 weeks to 18 months postpartum amongst a cohort of mothers and infants in South Africa

BACKGROUND

Despite improved policies to prevent mother-to-child HIV transmission (MTCT), adherence to maternal antiretroviral therapy (ART) and infant Nevirapine prophylaxis (NVP) is low in South Africa. We describe ART adherence amongst a cohort of HIV-positive mothers and HIV-exposed but uninfected infants from 6 weeks until 18 months post-delivery and identify risk factors for nonadherence.

METHODS

Data were collected in 2012-2014 through a nationally representative survey of PMTCT effectiveness. Mother-infant pairs were enrolled during the infant's first immunization visit at 6 weeks. Mothers and HIV-exposed infants (2811 pairs) were followed to 18 months at 3-month intervals. Mothers who self-reported being on ART at 6 weeks postpartum (N = 1572 (55.9%)) and infants on NVP at 6 weeks (N = 2370 (84.3%)) were eligible for this analysis and information about their adherence was captured at each interview they attended thereafter. We defined nonadherence within each 3-month interval as self-report of missing > 5% of daily ART/NVP doses, estimated adherence using a Cox survival curve with Andersen & Gill setup for recurring events, and identified risk factors for nonadherence with an extended Cox regression model (separately for mothers and infants) in Stata 13. Results are not nationally representative as this is a subgroup analysis of the follow-up cohort.

RESULTS

Amongst mothers on ART at 6 weeks postpartum, cumulative adherence to maternal ART until 18 months was 63.4%. Among infants on NPV at 6 weeks postpartum, adherence to NVP was 74.5%.. Risk factors for nonadherence to maternal ART, controlling for other factors, included mother's age (16-24 years vs. ≥34 years, adjusted Hazard Ratio (aHR): 1.9, 95% CI: 1.4-2.5), nondisclosure of HIV status to anyone (nondisclosure vs. disclosure: aHR: 1.7, 95% CI: 1.3-2.1), and timing of ART initiation (initiated ART after delivery vs. initiated ART before delivery: aHR: 1.6, 95% CI: 1.3-2.0). Provincial variation was seen in nonadherence to infant NVP, controlling for other factors.

CONCLUSION

Maintaining ART adherence until 18 months postpartum remains a crucial challenge, with maternal ART adherence among the six week maternal ART cohort below 65% and infant NVP adherence among breastfeeding infants in this cohort below 75%.This is gravely concerning, given the global policy shift to lifelong ART amongst pregnant and lactating women, and the need for extended infant prophylaxis amongst mothers who are not virally suppressed. Our findings suggest that young mothers and mothers who do not disclose their status should be targeted with messages to improve adherence, and that late maternal ART initiation (after delivery) increases the risk of maternal nonadherence.

Pharmacokinetics and safety of rifabutin in young HIV-infected children receiving rifabutin and lopinavir/ritonavir

Objectives

Co-treatment of HIV and TB in young children is complicated by limited treatment options and complex drug–drug interactions. Rifabutin is an alternative to rifampicin for adults receiving a ritonavir-boosted PI. We aimed to evaluate the short-term safety and pharmacokinetics of rifabutin when given with lopinavir/ritonavir in children.

Patients and methods

We conducted an open-label study of rifabutin dosed at 5 mg/kg three times a week in HIV-infected children ≤5 years of age receiving lopinavir/ritonavir. Intensive steady-state pharmacokinetic sampling was conducted after six doses. The Division of AIDS 2004, clarification 2009, table for grading severity of adverse events was used to classify drug toxicities. The study was registered with ClinicalTrials.gov, number NCT01259219.

Results

Six children completed the study prior to closure by institutional review boards. The median (range) AUC_0–48 of rifabutin was 6.91 (3.52–8.67) μg · h/mL, the median (range) C_max of rifabutin was 0.39 (0.19–0.46) μg/mL, the median (range) AUC_0–48 of 25-O-desacetyl rifabutin was 5.73 (2.85–9.13) μg · h/mL and the median (range) C_max of 25-O-desacetyl rifabutin was 0.17 (0.08–0.32) μg/mL. The neutrophil count declined in all children; two children experienced grade 4 neutropenia, which resolved rapidly without complications. There was strong correlation between AUC_0–48 measures and neutrophil counts.

Conclusions

Rifabutin dosed at 5 mg/kg three times per week resulted in lower AUC_0–48, AUC_0–24 and C_max values for rifabutin and 25-O-desacetyl rifabutin compared with adults receiving 150 mg of rifabutin daily, the current recommended dose. We observed high rates of severe transient neutropenia, possibly due to immaturity of CYP3A4 in young children. It remains unclear whether a safe and effective rifabutin dose exists for treatment of TB in children receiving lopinavir/ritonavir.

Effect of nutritional supplementation of breastfeeding HIV positive mothers on maternal and child health: findings from a randomized controlled clinical trial

BACKGROUND

It has been well established that breastfeeding is beneficial for child health, however there has been debate regarding the effect of lactation on maternal health in the presence of HIV infection and the need for nutritional supplementation in HIV positive lactating mothers.

AIMS

To assess the effect of nutritional supplementation to HIV infected lactating mothers on nutritional and health status of mothers and their infants.

METHODS

A randomized controlled clinical trial to study the impact of nutritional supplementation on breastfeeding mothers. Measurements included anthropometry; body composition indicators; CD4 count, haemoglobin and albumin; as well as incidence rates of opportunistic infections; depression and quality of life scores. Infant measurements included anthropometry, development and rates of infections.

RESULTS

The supplement made no significant impact on any maternal or infant outcomes. However in the small group of mothers with low BMI, the intake of supplement was significantly associated with preventing loss of lean body mass (1.32 kg vs. 3.17 kg; p = 0.026). There was no significant impact of supplementation on the infants.

CONCLUSIONS

A 50 g daily nutritional supplement to breastfeeding mothers had no or limited effect on mother and child health outcomes.

CLINICAL TRIAL REGISTRATION

ISRCTN68128332 (http://www.controlled-trials.com/ISRCTN68128332).

Prevention is better than cure – the art of avoiding non-adherence to antiretroviral treatment

The much-used phrase ‘prevention is better than cure’ is applicable to many circumstances, including human immunodeficiency virus (HIV) infection. In recent years suggestions have been made for a move towards treatment strategies that emphasise prevention of foreseeable adherence problems on a patient-by-patient basis, through focused patient preparation before commencing antiretroviral therapy (ART). This is well elucidated in a statement made in 2004 by Coetzee et al.:1 ‘As it is difficult to ascertain robust predictors of adherence, there has been a move to concentrate on patient preparation before the initiation of ART rather than the use of non-clinical predictors of adherence or selection criteria. A paradigm focused on preparation rather than selection is better suited to the aggressive targets for the scaling up of ART in countries with large epidemics (such as in South Africa), where the view of ART as a very expensive rationed intervention is rapidly changing.’

The effect of nutritional support on weight gain of HIV-infected children with prolonged diarrhoea

AIM

To examine the effect on growth and immunity of enhanced calorie and protein provision to HIV-infected children presenting with prolonged diarrhoea.

METHODS

A total of 169 HIV-infected children aged 6-36 months with diarrhoea for 7 days or more were randomly assigned to either standard nutrition support for children with prolonged diarrhoea or an enhanced diet started during hospitalisation and continued after discharge. The change in weight between enrolment and 8, 14 and 26 weeks and changes in plasma HIV-RNA and CD4 cell count at 8 and 26 weeks were estimated.

RESULTS

Children receiving enhanced nutrition achieved significantly more weight gain (p < 0.001) between enrolment and 8 weeks than children on the standard diet (median increase in weight-for-age standard deviation score +1.02 vs. +0.01). After 8 weeks median weight velocity was normal and similar in both groups. The change in median CD4 count was similar in both groups. The 26-week mortality rate was high in both groups (standard support: 22%, enhanced support: 29%).

CONCLUSIONS

Nutrition support of children with advanced HIV infection and prolonged diarrhoea resulted in significant and sustained weight gain, but did not improve CD4 counts or survival. These results support integrated nutrition interventions for HIV-infected children.

The impact of human immunodeficency virus 1 on largyngeal airway obstruction in children

Children with laryngeal airway obstruction (LAO) require admission to the intensive care unit (ICU). The unresolved ethical dilemma of ICU access for HIV infected children in resource poor settings requires further scientific data to help guide triaging. Of 38 children with LAO, 19 had HIV infection. The mortality, need for supportive management, duration of intubation, intermittent positive pressure ventilation, and ICU and hospitalisation stay were similar in the HIV infected group compared to the HIV uninfected group. Episodes of laryngotracheobronchitis were equally distributed between both groups (31.6% v 31.3%), while oropharyngeal/laryngeal candidiasis (26.3%), tuberculosis (15.8%), and benign lymphoid hyperplasia (15.8%) were commonly seen in the HIV infected group.

Analysis of sequence diversity at the highly polymorphic Cpgp40/15 locus among Cryptosporidium isolates from human immunodeficiency virus-infected children in South Africa

Cryptosporidium sp. is a significant cause of diarrheal disease, particularly in human immunodeficiency virus (HIV)-infected patients in developing countries. We recently cloned and sequenced several alleles of the highly polymorphic single-copy Cryptosporidium parvum gene Cpgp40/15. This gene encodes a precursor protein that is proteolytically cleaved to yield mature cell surface glycoproteins gp40 and gp15, which are implicated in zoite attachment to and invasion of enterocytes. The most-striking feature of the Cpgp40/15 alleles and proteins is their unprecedented degree of sequence polymorphism, which is far greater than that observed for any other gene or protein studied in C. parvum to date. In this study we analyzed nucleic acid and amino acid sequence polymorphism at the Cpgp40/15 locus of 20 C. parvum isolates from HIV-infected South African children. Fifteen isolates exhibited one of four previously identified genotype I alleles at the Cpgp40/15 locus (Ia, Ib, Ic, and Id), while five displayed a novel set of polymorphisms that defined a new Cpgp40/15 genotype I allele, designated genotype Ie. Surprisingly, only 15 of these isolates exhibited concordant type I alleles at the thrombospondin-related adhesive protein of Cryptosporidium and Cryptosporidium oocyst wall protein loci, while five isolates (all of which displayed Cpgp40/15 genotype Ic alleles) displayed genotype II alleles at these loci. Furthermore, the last five isolates also manifested chimeric genotype Ic/Ib or Ic/II alleles at the Cpgp40/15 locus, raising the possibility of sexual recombination within and between prototypical parasite genotypes. Lastly, children infected with isolates having genotype Ic alleles were significantly older than those infected with isolates displaying other genotype I alleles.