In a recent study published in Emerging infectious diseasesthe researchers described the ways in which national-level programs have exploited PEPFAR [president’s emergency plan for acquired immunodeficiency syndrome (AIDS) relief]assisted laboratory resources for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing during coronavirus disease 2019 (COVID-19).

Study: Contribution of PEPFAR-supported HIV and TB molecular diagnostic networks to COVID-19 testing readiness in 16 countries.  Image credit: tilialucida/Shutterstock
Study: Contribution of PEPFAR-supported HIV and TB molecular diagnostic networks to COVID-19 testing readiness in 16 countries. Image credit: tilialucida/Shutterstock

Background

The United States (US) PEPFAR assists molecular human immunodeficiency virus (HIV) and tuberculosis (TB) diagnostic networks and data management systems among LMICs (low- and middle-income countries). With the availability of SARS-CoV-2 testing assays, PEPFAR-assisted LMICs developed customized testing strategies using existing laboratory facilities, human resources, signaling, instrumentation, referrals, standardized and supply chains for COVID-19 testing.

The strategies used for COVID-19 testing by each nation were unique. They had to strike a balance between existing capabilities for SARS-CoV-2 testing and testing needs for which nations used either efficient centralized laboratory setups with large testing capacities or low-efficiency decentralized laboratory setups located near test points. COVID- 19 patient care.

About the studio

In the present cross-sectional, retrospective study, researchers quantified existing PEPFAR-assisted population health laboratories used during the SARS-CoV-2 pandemic.

The team sent Microsoft Excel spreadsheets including 46 indicators evaluating the utilization of PEPFAR-assisted molecular diagnostic networks during the SARS-CoV-2 outbreak between April 1, 2020 and March 31, 2021 to 27 regions or countries assisted by PEPFAR. The spreadsheets were also sent electronically as open requests to Centers for Disease Control and Prevention (CDC) PEPFAR laboratory consultants in 24 countries and three regions in Asia, the Americas and Africa.

Broadly speaking, three categories were identified which were: (i) Centralized HIV EID (early diagnosis of the child) and VL (viral load) and instrumentation for COVID-19 testing; (ii) PEPFAR-assisted laboratory information systems (LIS) to manage COVID-19 data; and (iii) decentralized HIV and tuberculosis resources and instrumentation for COVID-19 testing. The data was obtained by CDC National Laboratory Consultants between June and August 2021, followed by verification by staff at the CDC Headquarters in Georgia.

Country-wide COVID-19 testing volumes were obtained from the Our World in Data database. Centralized laboratories were those equipped with efficient testing platforms used for regular EID and HIV testing and could be used for COVID-19 testing. Decentralized laboratories were those with PEPFAR-aided equipment of any generation capacity for HIV and/or TB testing.

The team obtained country-specific information on the counts of decentralized and centralized laboratories supported by PEPFAR; laboratories involved in COVID-19 testing; laboratory instrumentation; TB, laboratory test volumes for HIV, COVID-19, and EID; and PEPFAR-assisted staff use, laboratory reporting, training, LIS, and supplies for COVID-19 testing at two levels of laboratories.

Results

In total, active COVID-19 testing was documented for 109 PEPFAR-assisted centralized HIV EID and VL testing laboratories and 138 decentralized laboratories located in 16 countries. Collectively, the testing regions contributed more than three million COVID-19 tests in 12 months.

Eleven nations implemented PEPFAR-assisted LIS for COVID-19 testing management in 121 decentralized and centralized laboratories between March and December 2020, and all 11 nations documented that rep LIS contributed to SARS-CoV-2 surveillance . Among the 11 nations, 3,341,592 COVID-19 tests were performed during the reporting period, accounting for 42.0% of testing volumes nationwide.

The Dominican Republic, Ethiopia and Zambia have performed more than 500,000 COVID-19 tests in PEPFAR-supported laboratories, representing 50%, 27% and 49% of testing volumes nationwide, respectively. Additionally, the three nations documented the highest number of COVID-19 tests performed at PEPFAR-assisted centralized laboratories compared to HIV EID and VL testing ranging from 96% (Dominican Republic) to 37% (Zambia).

Mozambique, Kenya, Nigeria and Uganda performed 208,000 to 402,000 COVID-19 tests, representing 80%, 70%, 30% and 33% respectively of COVID-19 testing volumes nationwide. Out of 16 countries, 14, 13, 12 and 10 countries respectively used PEPFAR-assisted laboratory reports, staff, reference networks and training materials for COVID-19 testing.

Eleven countries have integrated SARS-CoV-2 into HIV and TB diagnostic services at 138 PEPFAR-assisted decentralized sites. Notably, none of the nations performed decentralized COVID-19 testing before June 2020. South Sudan (100%), Dominican Republic (64%), Malawi (39%), Democratic Republic of Congo (11%) and Zimbabwe (27 %) documented most of the use of PEPFAR-assisted decentralized laboratory instruments for COVID-19 testing.

Lower rates for GeneXpert usage were documented by nations such as Zambia, Nigeria, Uganda, and Ethiopia (250 to 400 instruments) that supported larger networks. The majority of COVID-19 testing has been documented from Nigeria, Zambia, Lesotho, Malawi, Mozambique and Zimbabwe, while COVID-19 testing volumes have been minimal for Eswatini and the Dominican Republic.

PEPFAR-assisted decentralized regions contributed only 2.5% of test volumes due to less efficient instrumentation. COVID-19 testing products have been supplied to eight countries. In addition, seven nations have used PEPFAR-backed diagnostic connectivity solutions to report COVID-19 test results to surveillance programs or healthcare professionals.

Conclusion

Overall, the study results showed that PEPFAR-assisted diagnostic networks provided a wealth of resources for COVID-19 diagnostic testing at 16 LMICs.

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