Building Integrated Testing Programs for Infectious Diseases.

In the past 2 decades, testing services for diseases such as human immunodeficiency virus (HIV), tuberculosis, and malaria have expanded dramatically. Investments in testing capacity and supportive health systems have often been disease specific, resulting in siloed testing programs with suboptimal capacity, reduced efficiency, and limited ability to introduce additional tests or respond to new outbreaks. Emergency demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing overcame these silos and demonstrated the feasibility of integrated testing. Moving forward, an integrated public laboratory infrastructure that services multiple diseases, including SARS-CoV-2, influenza, HIV, tuberculosis, hepatitis, malaria, sexually transmitted diseases, and other infections, will help improve universal healthcare delivery and pandemic preparedness. However, integrated testing faces many barriers including poorly aligned health systems, funding, and policies. Strategies to overcome these include greater implementation of policies that support multidisease testing and treatment systems, diagnostic network optimization, bundled test procurement, and more rapid spread of innovation and best practices across disease programs.

The network approach to laboratory procurement and supply chain management: Addressing the system issues to enhance HIV viral load scale-up.

Investment in viral load scale-up in order to control the HIV epidemic and meet the Joint United Nations Programme on HIV and AIDS (UNAIDS) '90-90-90' goals has prompted the President's Emergency Plan for AIDS Relief and countries to increase their investment in viral load and infant virological testing. This has resulted in the increased procurement of molecular-based instruments, with many countries having challenges to effectively procure and place these products. In response to these challenges, the global laboratory stakeholder community has developed an informed 'network approach' to guide placement strategies. This article defines and describes the 'network approach' for laboratory procurement and supply chain management to assist countries in developing a strategic instrument procurement and placement strategy. The four key pillars of the approach should be performed in a stepwise fashion, with regular reviews. The approach is comprised of (1) laboratory network optimisation, (2) forecasting and supply planning, (3) the development of effective procurement and strategic sourcing to develop 'all-inclusive' contracts that provide transparent pricing, and the establishment of clear service and maintenance expectations and key performance indicators and (4) performance management to increase communication and planning, and promote issue resolution. Investments in the network approach will enable countries to strengthen laboratory systems and ready them for future laboratory needs. These disease-agnostic networks will be poised to improve overall national disease surveillance and assist countries in responding to disease outbreaks and other chronic diseases.

A Commitment to HIV Diagnostic Accuracy - a comment on "Towards more accurate HIV testing in sub-Saharan Africa: a multi-site evaluation of HIV RDTs and risk factors for false positives 'and' HIV misdiagnosis in sub-Saharan Africa: a performance of diagnostic algorithms at six testing sites".

As part of the global response to the HIV/AIDS epidemic, the U.S. President's Emergency Plan for AIDS Relief (PEPFAR) is committed to the provision of high-quality services and ensuring testing accuracy. Two recently published papers focusing on HIV testing and misdiagnosis in sub-Saharan Africa by Kosack et al. report on evaluations of HIV rapid diagnostic tests (RDTs) and found lower than expected specificity and sensitivity on some tests when used in certain geographic locations. The magnitude of PEPFAR's global HIV response has been possible due to the extensive use of RDTs, which have made HIV diagnosis accessible all over the world. We take the opportunity to address concerns raised about the potential implications that these findings could have on real-world HIV testing accuracy. PEPFAR supported countries adhere to the normative guidance by World Health Organization (WHO) supporting algorithms which require sequential positive tests for diagnostic accuracy. An analysis of Médecins Sans Frontières (MSF) RDT site-specific data applied to PEPFAR in-country protocols demonstrate a variation in the diagnostic accuracy of the testing algorithms, but with a very small population-level effect. The data demonstrate, with the use of these algorithms, that the RDT outcomes found in the study by Kosack et al. would be largely mitigated and would not be expected to have a significant impact on diagnostic accuracy and overall programming in most countries. Avoiding any misdiagnosis is a priority for PEPFAR, and it remains vital to gain a deeper understanding of the causes and the extent of diagnostic errors and any misclassification. Extensive quality control mechanisms and continued research are essential. With a focus on epidemic control and ensuring diagnostic accuracy, PEPFAR recommends that all countries use WHO pre-qualified RDTs within the recommended strategies and algorithms for HIV testing. We also support validation of HIV testing algorithms using in-country specimens to determine optimal performance, and the reverification testing of all people diagnosed with HIV prior to starting treatment as an essential quality assurance measure.

The Critical Role of Supply Chains in Preventing Human Immunodeficiency Virus Drug Resistance in Low- and Middle-Income Settings.

The functioning of the supply chain may be a driving factor behind the development of human immunodeficiency virus (HIV) drug resistance (HIVDR) in many low- and middle-income countries (LMICs). Additionally, the effectiveness of supply chains will likely impact the scale-up of both viral-load monitoring and HIVDR testing. This article describes the complexities of global supply chains relevant for LMICs and presents early data on stock-outs and drug substitutions in several countries supported by the US President's Emergency Plan for AIDS Relief. Supply chain systems will need to be strengthened to minimize interruptions as new antiretroviral therapy regimens are introduced and to facilitate adoption of new laboratory technologies.

Next-Generation Human Immunodeficiency Virus Sequencing for Patient Management and Drug Resistance Surveillance.

High-quality, simplified, and low-cost human immunodeficiency virus (HIV) drug resistance tests that are able to provide timely actionable HIV resistance data at individual, population, and programmatic levels are needed to confront the emerging drug-resistant HIV epidemic. Next-generation sequencing technologies embedded in automated cloud-computing analysis environments are ideally suited for such endeavor. Whereas NGS can reduce costs over Sanger sequencing, automated analysis pipelines make NGS accessible to molecular laboratories regardless of the available bioinformatic skills. They can also produce highly structured, high-quality data that could be examined by healthcare officials and program managers on a real-time basis to allow timely public health action. Here we discuss the opportunities and challenges of such an approach.

Progress with Scale-Up of HIV Viral Load Monitoring - Seven Sub-Saharan African Countries, January 2015-June 2016.

The World Health Organization (WHO) recommends viral load testing as the preferred method for monitoring the clinical response of patients with human immunodeficiency virus (HIV) infection to antiretroviral therapy (ART) (1). Viral load monitoring of patients on ART helps ensure early diagnosis and confirmation of ART failure and enables clinicians to take an appropriate course of action for patient management. When viral suppression is achieved and maintained, HIV transmission is substantially decreased, as is HIV-associated morbidity and mortality (2). CDC and other U.S. government agencies and international partners are supporting multiple countries in sub-Saharan Africa to provide viral load testing of persons with HIV who are on ART. This report examines current capacity for viral load testing based on equipment provided by manufacturers and progress with viral load monitoring of patients on ART in seven sub-Saharan countries (Côte d'Ivoire, Kenya, Malawi, Namibia, South Africa, Tanzania, and Uganda) during January 2015-June 2016. By June 2016, based on the target numbers for viral load testing set by each country, adequate equipment capacity existed in all but one country. During 2015, two countries tested >85% of patients on ART (Namibia [91%] and South Africa [87%]); four countries tested <25% of patients on ART. In 2015, viral suppression was >80% among those patients who received a viral load test in all countries except Côte d'Ivoire. Sustained country commitment and a coordinated global effort is needed to reach the goal for viral load monitoring of all persons with HIV on ART.

Progress in Harmonizing Tiered HIV Laboratory Systems: Challenges and Opportunities in 8 African Countries.

In 2014, the Joint United Nations Programme on HIV/AIDS released its 90-90-90 targets, which make laboratory diagnostics a cornerstone for measuring efforts toward the epidemic control of HIV. A data-driven laboratory harmonization and standardization approach is one way to create efficiencies and ensure optimal laboratory procurements. Following the 2008 "Maputo Declaration on Strengthening of Laboratory Systems"-a call for government leadership in harmonizing tiered laboratory networks and standardizing testing services-several national ministries of health requested that the United States Government and in-country partners help implement the recommendations by facilitating laboratory harmonization and standardization workshops, with a primary focus on improving HIV laboratory service delivery. Between 2007 and 2015, harmonization and standardization workshops were held in 8 African countries. This article reviews progress in the harmonization of laboratory systems in these 8 countries. We examined agreed-upon instrument lists established at the workshops and compared them against instrument data from laboratory quantification exercises over time. We used this measure as an indicator of adherence to national procurement policies. We found high levels of diversity across laboratories' diagnostic instruments, equipment, and services. This diversity contributes to different levels of compliance with expected service delivery standards. We believe the following challenges to be the most important to address: (1) lack of adherence to procurement policies, (2) absence or limited influence of a coordinating body to fully implement harmonization proposals, and (3) misalignment of laboratory policies with minimum packages of care and with national HIV care and treatment guidelines. Overall, the effort to implement the recommendations from the Maputo Declaration has had mixed success and is a work in progress. Program managers should continue efforts to advance the principles outlined in the Maputo Declaration. Quantification exercises are an important method of identifying instrument diversity, and provide an opportunity to measure efforts toward standardization.

Cost analysis of integrating the PrePex medical device into a voluntary medical male circumcision program in Zimbabwe.

BACKGROUND: Fourteen African countries are scaling up voluntary medical male circumcision (VMMC) for HIV prevention. Several devices that might offer alternatives to the three WHO-approved surgical VMMC procedures have been evaluated for use in adults. One such device is PrePex, which was prequalified by the WHO in May 2013. We utilized data from one of the PrePex field studies undertaken in Zimbabwe to identify cost considerations for introducing PrePex into the existing surgical circumcision program. METHODS AND FINDINGS: We evaluated the cost drivers and overall unit cost of VMMC at a site providing surgical VMMC as a routine service ("routine surgery site") and at a site that had added PrePex VMMC procedures to routine surgical VMMC as part of a research study ("mixed study site"). We examined the main cost drivers and modeled hypothetical scenarios with varying ratios of surgical to PrePex circumcisions, different levels of site utilization, and a range of device prices. The unit costs per VMMC for the routine surgery and mixed study sites were $56 and $61, respectively. The two greatest contributors to unit price at both sites were consumables and staff. In the hypothetical scenarios, the unit cost increased as site utilization decreased, as the ratio of PrePex to surgical VMMC increased, and as device price increased. CONCLUSIONS: VMMC unit costs for routine surgery and mixed study sites were similar. Low service utilization was projected to result in the greatest increases in unit price. Countries that wish to incorporate PrePex into their circumcision programs should plan to maximize staff utilization and ensure that sites function at maximum capacity to achieve the lowest unit cost. Further costing studies will be necessary once routine implementation of PrePex-based circumcision is established.

Optimising the laboratory supply chain: The key to effective laboratory services.

BACKGROUND: The Supply Chain Management System (SCMS) is a contract managed under the Partnership for Supply Chain Management (PFSCM) consortium by the United States Agency for International Development (USAID). SCMS procures commodities for programmes supported by the US President's Emergency Plan for AIDS Relief (PEPFAR). From 2005 to mid-2012, PEPFAR, through SCMS, spent approximately $384 million on non-pharmaceutical commodities. Of this, an estimated $90m was used to purchase flow cytometry technology, largely for flow cytometry platforms and reagents. OBJECTIVES: The purpose of this paper is to highlight the cost differences between low, medium and high utilisation rates of common CD4 testing instruments that have been procured though PEPFAR funding. METHOD: A scale of costs per test as a function of test volume through the machine was calculated for the two most common CD4 testing machines used in HIV programmes: Becton Dickinson (BD) FACSCount™ and BD FACSCalibur™. Instrument utilisation data collected at the facility level in three selected countries were then used to calculate the onsite cost-per-test experienced in each country. RESULTS: Cost analyses indicated that a target of at least 40% utilisation for FACSCount™ and 15% utilisation for FACSCalibur™, respectively, closely approach maximal per-test cost efficiency. The average utilisation rate for CD4 testing instruments varies widely by country, level of laboratory and partner (0% - 68%). CONCLUSION: Our analysis indicates that, because cost-per-test is related inversely to sample throughput, the underutilisation of flow cytometry machines is resulting in an increase in average cost-per-test for many instruments.

Voluntary medical male circumcision: logistics, commodities, and waste management requirements for scale-up of services.

BACKGROUND: The global HIV prevention community is implementing voluntary medical male circumcision (VMMC) programs across eastern and southern Africa, with a goal of reaching 80% coverage in adult males by 2015. Successful implementation will depend on the accessibility of commodities essential for VMMC programming and the appropriate allocation of resources to support the VMMC supply chain. For this, the United States President's Emergency Plan for AIDS Relief, in collaboration with the World Health Organization and the Joint United Nations Programme on HIV/AIDS, has developed a standard list of commodities for VMMC programs. METHODS AND FINDINGS: This list of commodities was used to inform program planning for a 1-y program to circumcise 152,000 adult men in Swaziland. During this process, additional key commodities were identified, expanding the standard list to include commodities for waste management, HIV counseling and testing, and the treatment of sexually transmitted infections. The approximate costs for the procurement of commodities, management of a supply chain, and waste disposal, were determined for the VMMC program in Swaziland using current market prices of goods and services. Previous costing studies of VMMC programs did not capture supply chain costs, nor the full range of commodities needed for VMMC program implementation or waste management. Our calculations indicate that depending upon the volume of services provided, supply chain and waste management, including commodities and associated labor, contribute between US$58.92 and US$73.57 to the cost of performing one adult male circumcision in Swaziland. CONCLUSIONS: Experience with the VMMC program in Swaziland indicates that supply chain and waste management add approximately US$60 per circumcision, nearly doubling the total per procedure cost estimated previously; these additional costs are used to inform the estimate of per procedure costs modeled by Njeuhmeli et al. in "Voluntary Medical Male Circumcision: Modeling the Impact and Cost of Expanding Male Circumcision for HIV Prevention in Eastern and Southern Africa." Program planners and policy makers should consider the significant contribution of supply chain and waste management to VMMC program costs as they determine future resource needs for VMMC programs.

Dengue virus utilizes a novel strategy for translation initiation when cap-dependent translation is inhibited.

Viruses have developed numerous mechanisms to usurp the host cell translation apparatus. Dengue virus (DEN) and other flaviviruses, such as West Nile and yellow fever viruses, contain a 5' m7GpppN-capped positive-sense RNA genome with a nonpolyadenylated 3' untranslated region (UTR) that has been presumed to undergo translation in a cap-dependent manner. However, the means by which the DEN genome is translated effectively in the presence of capped, polyadenylated cellular mRNAs is unknown. This report demonstrates that DEN replication and translation are not affected under conditions that inhibit cap-dependent translation by targeting the cap-binding protein eukaryotic initiation factor 4E, a key regulator of cellular translation. We further show that under cellular conditions in which translation factors are limiting, DEN can alternate between canonical cap-dependent translation initiation and a noncanonical mechanism that appears not to require a functional m7G cap. This DEN noncanonical translation is not mediated by an internal ribosome entry site but requires the interaction of the DEN 5' and 3' UTRs for activity, suggesting a novel strategy for translation of animal viruses.

End-to-end communication in the modulation of translation by mammalian RNA viruses.

A 5'-3' end interaction leading to stimulation of translation has been described for many cellular and viral mRNAs. Enhancement of viral translational efficiency mediated by 5' and 3' untranslated regions (UTRs) has been shown to occur via RNA-RNA interactions or novel RNA-protein interactions. Mammalian RNA viruses make use of end-to-end communication in conjunction with both viral and cellular factors to regulate multiple processes including translation initiation and the switch between translation and RNA synthesis during the viral lifecycle.

Molecular biology of flaviviruses.

Flaviviruses are enveloped viruses with a single-stranded, 10.7kb positive-sense RNA genome. The genomic RNA, which has a 5' cap but no poly(A) tail, is translated as a single polyprotein that is then cleaved into three structural proteins and seven non-structural (NS) proteins by both viral and host proteases. The NS proteins include an RNA-dependent RNA polymerase (NS5), a helicase/protease (NS3), and other proteins that form part of the viral replication complex. Sequences and structures in the 5' and 3' untranslated regions (UTR) and capsid gene, including the cyclization sequences, the upstream AUG region, and the terminal 3' stem-loop, regulate translation, RNA synthesis and viral replication. We have also found that an RNA hairpin structure in the capsid coding region (cHP) influences start codon selection and viral replication of the flavivirus dengue virus (DENV). Peptide-conjugated phosphorodiamidate morpholino oligomers (P-PMOs) were used to further dissect the role of conserved regions of the 5' and 3' UTRs; several P-PMOs were shown to specifically inhibit DENV translation and/or RNA synthesis and, hence, are potentially useful as antiviral agents. Regarding the mechanism of DENV translation, we have shown that DENV undergoes canonical cap-dependent translation initiation as well as a non-canonical mechanism when cap-dependent translation is suppressed. Although much remains to be elucidated about the molecular biology of flavivirus infection, progress is being made towards defining the cis and trans factors that regulate flavivirus translation and replication.

Translation efficiency determines differences in cellular infection among dengue virus type 2 strains.

We have investigated the molecular basis for differences in the ability of natural variants of dengue virus type 2 (DEN2) to replicate in primary human cells. The rates of virus binding, virus entry, input strand translation, and RNA stability of low-passage Thai and Nicaraguan and prototype DEN2 strains were compared. All strains exhibited equivalent binding, entry, and uncoating, and displayed comparable stability of positive strand viral RNA over time in primary cells. However, the low-passage Nicaraguan isolates were much less efficient in their ability to translate viral proteins. Sequence analysis of the full-length low-passage Nicaraguan and Thai viral genomes identified specific differences in the 3' untranslated region (3'UTR). Substitution of the different sequences into chimeric RNA reporter constructs demonstrated that the changes in the 3'UTR directly affected the efficiency of viral translation. Thus, differences in infectivity among closely related DEN2 strains correlate with efficiency of translation of input viral RNA.

Complete nucleotide sequence analysis of a Brazilian dengue virus type 2 strain.

In the last decade, dengue fever (DF) in Brazil has been recognized as an important public health problem, and an increasing number of dengue haemorrhagic fever (DHF) cases have been reported since the introduction of dengue virus type 2 (DEN-2) into the country in 1990. In order to analyze the complete genome sequence of a DEN-2 Brazilian strain (BR64022/98), we designed primers to amplify contiguous segments of approximately 500 base pairs across the entire sequence of the viral genome. Twenty fragments amplified by reverse transcriptase-PCR were cloned, and the complete nucleotide and the deduced amino acid sequences were determined. This constitutes the first complete genetic characterization of a DEN-2 strain from Brazil. All amino acid changes differentiating strains related to the Asian/American-Asian genotype were observed in BR64022/98, indicating the Asiatic origin of the strain.

Complete nucleotide sequence analysis of a Brazilian dengue virus type 2 strain

In the last decade, dengue fever (DF) in Brazil has been recognized as an important public health problem, and an increasing number of dengue haemorrhagic fever (DHF) cases have been reported since the introduction of dengue virus type 2 (DEN-2) into the country in 1990. In order to analyze the complete genome sequence of a DEN-2 Brazilian strain (BR64022/98), we designed primers to amplify contiguous segments of approximately 500 base pairs across the entire sequence of the viral genome. Twenty fragments amplified by reverse transcriptase-PCR were cloned, and the complete nucleotide and the deduced amino acid sequences were determined. This constitutes the first complete genetic characterization of a DEN-2 strain from Brazil. All amino acid changes differentiating strains related to the Asian/American-Asian genotype were observed in BR64022/98, indicating the Asiatic origin of the strain