Contribution of PEPFAR-Supported HIV and TB Molecular Diagnostic Networks to COVID-19 Testing Preparedness in 16 Countries.

The US President's Emergency Plan for AIDS Relief (PEPFAR) supports molecular HIV and tuberculosis diagnostic networks and information management systems in low- and middle-income countries. We describe how national programs leveraged these PEPFAR-supported laboratory resources for SARS-CoV-2 testing during the COVID-19 pandemic. We sent a spreadsheet template consisting of 46 indicators for assessing the use of PEPFAR-supported diagnostic networks for COVID-19 pandemic response activities during April 1, 2020, to March 31, 2021, to 27 PEPFAR-supported countries or regions. A total of 109 PEPFAR-supported centralized HIV viral load and early infant diagnosis laboratories and 138 decentralized HIV and TB sites reported performing SARS-CoV-2 testing in 16 countries. Together, these sites contributed to >3.4 million SARS-CoV-2 tests during the 1-year period. Our findings illustrate that PEPFAR-supported diagnostic networks provided a wide range of resources to respond to emergency COVID-19 diagnostic testing in 16 low- and middle-income countries.

HIV Viral Load Monitoring Among Patients Receiving Antiretroviral Therapy - Eight Sub-Saharan Africa Countries, 2013-2018.

One component of the Joint United Nations Programme on HIV/AIDS (UNAIDS) goal to end the HIV/AIDS epidemic by 2030, is that 95% of all persons receiving antiretroviral therapy (ART) achieve viral suppression.† Thus, testing all HIV-positive persons for viral load (number of copies of viral RNA per mL) is a global health priority (1). CDC and other U.S. government agencies, as part of the U.S. President's Emergency Plan for AIDS Relief (PEPFAR), together with other stakeholders, have provided technical assistance and supported the cost for multiple countries in sub-Saharan Africa to expand viral load testing as the preferred monitoring strategy for clinical response to ART. The individual and population-level benefits of ART are well understood (2). Persons receiving ART who achieve and sustain an undetectable viral load do not transmit HIV to their sex partners, thereby disrupting onward transmission (2,3). Viral load testing is a cost-effective and sustainable programmatic approach for monitoring treatment success, allowing reduced frequency of health care visits for patients who are virally suppressed (4). Viral load monitoring enables early and accurate detection of treatment failure before immunologic decline. This report describes progress on the scale-up of viral load testing in eight sub-Saharan African countries from 2013 to 2018 and examines the trajectory of improvement with viral load testing scale-up that has paralleled government commitments, sustained technical assistance, and financial resources from international donors. Viral load testing in low- and middle-income countries enables monitoring of viral load suppression at the individual and population level, which is necessary to achieve global epidemic control. Although there has been substantial achievement in improving viral load coverage for all patients receiving ART, continued engagement is needed to reach global targets.

Using queueing models as a decision support tool in allocating point-of-care HIV viral load testing machines in Kisumu County, Kenya.

Point-of-care (POC) technologies-including HIV viral load (VL) monitoring-are expanding globally, including in resource-limited settings. Modelling could allow decision-makers to consider the optimal strategy(ies) to maximize coverage and access, minimize turnaround time (TAT) and minimize cost with limited machines. Informed by formative qualitative focus group discussions with stakeholders focused on model inputs, outputs and format, we created an optimization model incorporating queueing theory and solved it using integer programming methods to reflect HIV VL monitoring in Kisumu County, Kenya. We modelled three scenarios for sample processing: (1) centralized laboratories only, (2) centralized labs with 7 existing POC 'hub' facilities and (3) centralized labs with 7 existing and 1-7 new 'hub' facilities. We calculated total TAT using the existing referral network for scenario 1 and solved for the optimal referral network by minimizing TAT for scenarios 2 and 3. We conducted one-way sensitivity analyses, including distributional fairness in each sub-county. Through two focus groups, stakeholders endorsed the provisionally selected model inputs, outputs and format with modifications incorporated during model-building. In all three scenarios, the largest component of TAT was time spent at a facility awaiting sample batching and transport (scenarios 1-3: 78.7%, 89.9%, 91.8%) and waiting time at the testing site (18.7%, 8.7%, 7.5%); transportation time contributed minimally to overall time (2.6%, 1.3%, 0.7%). In scenario 1, the average TAT was 39.8 h (SD: 2.9), with 1077 h that samples spent cumulatively in the VL processing system. In scenario 2, the average TAT decreased to 33.8 h (SD: 4.8), totalling 430 h. In scenario 3, the average TAT decreased nearly monotonically with each new machine to 31.1 h (SD: 8.4) and 346 total hours. Frequency of sample batching and processing rate most impacted TAT, and inclusion of distributional fairness minimally impacted TAT. In conclusion, a stakeholder-informed resource allocation model identified optimal POC VL hub allocations and referral networks. Using existing-and adding new-POC machines could markedly decrease TAT, as could operational changes.

HIV-1 Transmission Cluster in Injection Drug Users in Nairobi City, Kenya.

Background: While there is a striking increase in the prevalence of HIV in injection drug users, information on envelope-gene subtypes and transmission clusters in injection drug users is scarce. Method: In a cross-sectional study, 247 injection drug users were recruited via out-rich method. Deoxyribonucleic acid was extracted from dry blood spot samples, amplified by Polymerase Chain Reaction and sequenced. Subtyping was performed using COntext-based Modeling for Expeditious Typing (COMET) and Recombinant Identification Program (RIP) tools. Phylogenetic diversity and Transmission clusters were identified using MEGA version 6.0 and TreeLink, respectively. Results: Overall, 42 (17.0%) injection drug users were sero-positive for HIV-1. Of the 37 samples successfully sequenced, 29 (78.4%) sequences were identified as A1, 6 (16.2%) as AG while 1 (2.7%) as A1/G/AE and A1/C recombinants. The HIV subtypes formed clusters with little genetic diversity. Conclusion: The high HIV prevalence was associated with transmission clusters and diversity in subtypes indicating ongoing local transmission. Therefore, there is need for comprehensive HIV care tailored to this population.

Retrospective longitudinal analysis of low-level viremia among HIV-1 infected adults on antiretroviral therapy in Kenya.

Background: HIV low-level viremia (LLV) (51-999 copies/mL) can progress to treatment failure and increase potential for drug resistance. We analyzed retrospective longitudinal data from people living with HIV (PLHIV) on antiretroviral therapy (ART) in Kenya to understand LLV prevalence and virologic outcomes. Methods: We calculated rates of virologic suppression (≤50 copies/mL), LLV (51-999 copies/mL), virologic non-suppression (≥1000 copies/mL), and virologic failure (≥2 consecutive virologic non-suppression results) among PLHIV aged 15 years and older who received at least 24 weeks of ART during 2015-2021. We analyzed risk for virologic non-suppression and virologic failure using time-dependent models (each viral load (VL) <1000 copies/mL used to predict the next VL). Findings: Of 793,902 patients with at least one VL, 18.5% had LLV (51-199 cp/mL 11.1%; 200-399 cp/mL 4.0%; and 400-999 cp/mL 3.4%) and 9.2% had virologic non-suppression at initial result. Among all VLs performed, 26.4% were LLV. Among patients with initial LLV, 13.3% and 2.4% progressed to virologic non-suppression and virologic failure, respectively. Compared to virologic suppression (≤50 copies/mL), LLV was associated with increased risk of virologic non-suppression (adjusted relative risk [aRR] 2.43) and virologic failure (aRR 3.86). Risk of virologic failure increased with LLV range (aRR 2.17 with 51-199 copies/mL, aRR 3.98 with 200-399 copies/mL and aRR 7.99 with 400-999 copies/mL). Compared to patients who never received dolutegravir (DTG), patients who initiated DTG had lower risk of virologic non-suppression (aRR 0.60) and virologic failure (aRR 0.51); similarly, patients who transitioned to DTG had lower risk of virologic non-suppression (aRR 0.58) and virologic failure (aRR 0.35) for the same LLV range. Interpretation: Approximately a quarter of patients experienced LLV and had increased risk of virologic non-suppression and failure. Lowering the threshold to define virologic suppression from <1000 to <50 copies/mL to allow for earlier interventions along with universal uptake of DTG may improve individual and program outcomes and progress towards achieving HIV epidemic control. Funding: No specific funding was received for the analysis. HIV program support was provided by the President's Emergency Plan for AIDS Relief (PEPFAR) through the United States Centers for Disease Control and Prevention (CDC).

HIV Incidence, Recent HIV Infection, and Associated Factors, Kenya, 2007-2018.

Nationally representative surveys provide an opportunity to assess trends in recent human immunodeficiency virus (HIV) infection based on assays for recent HIV infection. We assessed HIV incidence in Kenya in 2018 and trends in recent HIV infection among adolescents and adults in Kenya using nationally representative household surveys conducted in 2007, 2012, and 2018. To assess trends, we defined a recent HIV infection testing algorithm (RITA) that classified as recently infected (<12 months) those HIV-positive participants that were recent on the HIV-1 limiting antigen (LAg)-avidity assay without evidence of antiretroviral use. We assessed factors associated with recent and long-term (≥12 months) HIV infection versus no infection using a multinomial logit model while accounting for complex survey design. Of 1,523 HIV-positive participants in 2018, 11 were classified as recent. Annual HIV incidence was 0.14% in 2018 [95% confidence interval (CI) 0.057-0.23], representing 35,900 (95% CI 16,300-55,600) new infections per year in Kenya among persons aged 15-64 years. The percentage of HIV infections that were determined to be recent was similar in 2007 and 2012 but fell significantly from 2012 to 2018 [adjusted odds ratio (aOR) = 0.31, p < .001]. Compared to no HIV infection, being aged 25-34 versus 35-64 years (aOR = 4.2, 95% CI 1.4-13), having more lifetime sex partners (aOR = 5.2, 95% CI 1.6-17 for 2-3 partners and aOR = 8.6, 95% CI 2.8-26 for ≥4 partners vs. 0-1 partners), and never having tested for HIV (aOR = 4.1, 95% CI 1.5-11) were independently associated with recent HIV infection. Although HIV remains a public health priority in Kenya, HIV incidence estimates and trends in recent HIV infection support a significant decrease in new HIV infections from 2012 to 2018, a period of rapid expansion in HIV diagnosis, prevention, and treatment.

Progress in scale up of HIV viral load testing in select sub-Saharan African countries 2016-2018.

INTRODUCTION: We assessed progress in HIV viral load (VL) scale up across seven sub-Saharan African (SSA) countries and discussed challenges and strategies for improving VL coverage among patients on anti-retroviral therapy (ART). METHODS: A retrospective review of VL testing was conducted in Côte d'Ivoire, Kenya, Lesotho, Malawi, Namibia, Tanzania, and Uganda from January 2016 through June 2018. Data were collected and included the cumulative number of ART patients, number of patients with ≥ 1 VL test result (within the preceding 12 months), the percent of VL test results indicating viral suppression, and the mean turnaround time for VL testing. RESULTS: Between 2016 and 2018, the proportion of PLHIV on ART in all 7 countries increased (range 5.7%-50.2%). During the same time period, the cumulative number of patients with one or more VL test increased from 22,996 to 917,980. Overall, viral suppression rates exceeded 85% for all countries except for Côte d'Ivoire at 78% by June 2018. Reported turnaround times for VL testing results improved in 5 out of 7 countries by between 5.4 days and 27.5 days. CONCLUSIONS: These data demonstrate that remarkable progress has been made in the scale-up of HIV VL testing in the seven SSA countries.

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.

Impact of nucleos(t)ide reverse transcriptase inhibitor resistance on dolutegravir and protease-inhibitor-based regimens in children and adolescents in Kenya.

We assessed the impact of using dolutegravir or a protease inhibitor with an inactive nucleoside-reverse transcriptase inhibitor (NRTI) in children and adolescents. We observed high-levels of viral suppression among those on tenofovir-lamivudine-dolutegravir even in presence of an inactive NRTI backbone but lower levels among those on protease inhibitors, especially those retained on an inactive abacavir. Although tenofovir may be recycled with dolutegravir, more studies are needed to determine if abacavir can be reused with dolutegravir or protease inhibitors.

Costs of Point-of-Care Viral Load Testing for Adults and Children Living with HIV in Kenya.

BACKGROUND: The number of people living with HIV (PLHIV) in need of treatment monitoring in low-and-middle-income countries is rapidly expanding, straining existing laboratory capacity. Point-of-care viral load (POC VL) testing can alleviate the burden on centralized laboratories and enable faster delivery of results, improving clinical outcomes. However, implementation costs are uncertain and will depend on clinic testing volume. We sought to estimate the costs of decentralized POC VL testing compared to centralized laboratory testing for adults and children receiving HIV care in Kenya. METHODS: We conducted microcosting to estimate the per-patient costs of POC VL testing compared to known costs of centralized laboratory testing. We completed time-and-motion observations and stakeholder interviews to assess personnel structures, staff time, equipment costs, and laboratory processes associated with POC VL administration. Capital costs were estimated using a 5 year lifespan and a 3% annual discount rate. RESULTS: We estimated that POC VL testing cost USD $24.25 per test, assuming a clinic is conducting 100 VL tests per month. Test cartridge and laboratory equipment costs accounted for most of the cost (62% and 28%, respectively). Costs varied by number of VL tests conducted at the clinic, ranging from $54.93 to $18.12 per test assuming 20 to 500 VL tests per month, respectively. A VL test processed at a centralized laboratory was estimated to cost USD $25.65. CONCLUSION: POC VL testing for HIV treatment monitoring can be feasibly implemented in clinics within Kenya and costs declined with higher testing volumes. Our cost estimates are useful to policymakers in planning resource allocation and can inform cost-effectiveness analyses evaluating POC VL testing.

From Sequence Data to Patient Result: A Solution for HIV Drug Resistance Genotyping With Exatype, End to End Software for Pol-HIV-1 Sanger Based Sequence Analysis and Patient HIV Drug Resistance Result Generation.

INTRODUCTION: With the rapid scale-up of antiretroviral therapy (ART) to treat HIV infection, there are ongoing concerns regarding probable emergence and transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to lead to an increased need for routine HIVDR testing to inform the clinical decision on a regimen switch. Although the majority of wet laboratory processes are standardized, slow, labor-intensive data transfer and subjective manual sequence interpretation steps are still required to finalize and release patient results. We thus set out to validate the applicability of a software package to generate HIVDR patient results from raw sequence data independently. METHODS: We assessed the performance characteristics of Hyrax Bioscience's Exatype (a sequence data to patient result, fully automated sequence analysis software, which consolidates RECall, MEGA X and the Stanford HIV database) against the standard method (RECall and Stanford database). Exatype is a web-based HIV Drug resistance bioinformatic pipeline available at sanger.exatype.com. To validate the exatype, we used a test set of 135 remnant HIV viral load samples at the National HIV Reference Laboratory (NHRL). RESULT: We analyzed, and successfully generated results of 126 sequences out of 135 specimens by both Standard and Exatype software. Result production using Exatype required minimal hands-on time in comparison to the Standard (6 computation-hours using the standard method versus 1.5 Exatype computation-hours). Concordance between the 2 systems was 99.8% for 311,227 bases compared. 99.7% of the 0.2% discordant bases, were attributed to nucleotide mixtures as a result of the sequence editing in Recall. Both methods identified similar (99.1%) critical antiretroviral resistance-associated mutations resulting in a 99.2% concordance of resistance susceptibility interpretations. The Base-calling comparison between the 2 methods had Cohen's kappa (0.97 to 0.99), implying an almost perfect agreement with minimal base calling variation. On a predefined dataset, RECall editing displayed the highest probability to score mixtures accurately 1 vs. 0.71 and the lowest chance to inaccurately assign mixtures to pure nucleotides (0.002-0.0008). This advantage is attributable to the manual sequence editing in RECall. CONCLUSION: The reduction in hands-on time needed is a benefit when using the Exatype HIV DR sequence analysis platform and result generation tool. There is a minimal difference in base calling between Exatype and standard methods. Although the discrepancy has minimal impact on drug resistance interpretation, allowance of sequence editing in Exatype as RECall can significantly improve its performance.

Phenotypic and Genotypic Antibiotic Resistant diarrheagenic Escherichia coli pathotypes isolated from Children with Diarrhea in Nairobi City, Kenya.

BACKGROUND: The marked genome plasticity of diarrheagenic Escherichia coli promotes emergence of pathotypes displaying unique phenotypic and genotypic resistance. This study examined phenotypic and genotypic antibiotic resistant diarrheagenic Escherichia coli pathotypes among children in Nairobi City, Kenya. METHODS: In a cross-sectional study, diarrheagenic Escherichia coli pathotypes were isolated from stool samples and their phenotypic and genotypic resistance against eight antimicrobial agents assayed. RESULTS: Diarrheagenic Escherichia coli was detected in 136(36.4%) children. Most of diarrheagenic Escherichia coli that were resistant to ampicillin, ceftriaxone, streptomycin, gentamycin, ciprofloxacin, chloramphenicol, erythromycin and tetracycline, harbored citm, bla CMY, aadA1, aac(3)-IV, qnr, catA, ere(A) and tet(A) corresponding resistant genes. CONCLUSION: Antimicrobial-resistant genes are highly prevalent among phenotypic resistant ETEC pathotypes indicating a possibility of horizontal gene transfer in spreading antibiotic resistant genes among E. coli pathotypes.

Point-of-Care Early Infant Diagnosis Improves Adherence to the Testing Algorithm in Kenya.

INTRODUCTION: We determine the level of adherence to the revised Kenya early infant diagnosis (EID) algorithm during implementation of a point-of-care (POC) EID project. METHODS: Data before (August 2016 to July 2017) and after (August 2017 to July 2018) introduction of POC EID were collected retrospectively from the national EID database and registers for 33 health facilities. We assessed the number of HIV-infected infants who underwent confirmatory testing and received baseline viral load test and proportion of infants with an initial negative result who had a subsequent test. RESULTS AND DISCUSSION: Significantly higher number of infants accessed confirmatory testing (94.2% versus 38.6%; P < .0001) with POC EID. Baseline viral load test and follow-up testing at 6 months, although higher with POC EID, were not significantly different from the pre-POC EID intervention period. CONCLUSION: The POC EID implementation has the potential to increase proportion of infants who receive confirmatory testing, thus reducing the risk of false-positive results.

Undisclosed HIV infection and antiretroviral therapy use in the Kenya AIDS indicator survey 2012: relevance to national targets for HIV diagnosis and treatment.

OBJECTIVES: This analysis assessed the impact of undisclosed HIV infection and antiretroviral therapy (ART) on national estimates of diagnosed HIV and ART coverage in Kenya. METHODS: HIV-positive dried blood spot samples from Kenya's second AIDS Indicator Survey were tested for an antiretroviral biomarker by liquid chromatography-tandem mass spectrometry. Weighted estimates of diagnosed HIV and ART coverage based on self-report were compared with those corrected for undisclosed HIV infection and ART use based on antiretroviral test results. Multivariate analysis determined factors associated with undisclosed HIV infection and ART use among persons on ART. RESULTS: The antiretroviral biomarker was detected in 42.5% [confidence interval (CI) 37.4-47.7] of HIV-infected persons. Antiretroviral drugs were present in 90.7% (CI 86.1-95.2) of HIV-infected persons reporting HIV-positive status and receiving ART, 66.7% (CI 59.9-73.4) reporting HIV-positive status irrespective of ART use, 21.0% (CI 13.4-28.6) reporting HIV-negative status, and 19.3% (CI 9.0-29.5) reporting no previous HIV test. After correcting for undisclosed HIV infection and ART use, diagnosed HIV increased from 46.9 to 57.2% and ART coverage increased from 31.8 to 42.8%. Undisclosed HIV infection while on ART was associated with being aged 25-39 years and not visiting a health provider in the past year, while younger age and higher wealth were associated with undisclosed ART use. CONCLUSION: Substantial levels of undisclosed HIV infection and ART use among persons on ART were observed, resulting in diagnosed HIV underestimated by approximately 112000 persons and ART coverage by approximately 131000 persons. Supplementing self-reported ART status with objective measures of ART use in national population-based serosurveys can improve monitoring of HIV diagnosis and treatment targets in countries.

Quarantine stressing voluntary compliance.

A 1-day table-top exercise in San Diego, California, in December 2004 emphasized voluntary compliance with home quarantine to control an emerging infectious disease outbreak. The exercise heightened local civilian-military collaboration in public health emergency management. Addressing concerns about lost income by residents in quarantine was particularly challenging.