The EVD outbreak in Liberia began in March 2014 and has had a devastating impact on the health system. The health system was ill equipped to effectively respond to the epidemic. The laboratory diagnostic service was one of the health services which was affected by the EVD outbreak . During the outbreak, laboratory services like other health services component had to come to a standstill. This was mainly due to the lack of laboratory reagents and consumables. The laboratory system of Liberia in the pre- Ebola era was weak and lagged behind the other component of the health services. Even though the National Diagnostic Unit of Liberia was established in 2009 and laboratory policy was developed in 2011, the laboratory subunits in the Ministry of Health including the National Reference Laboratory, the National Diagnostics Unit and the National Blood Safety Program, were not well coordinated and operated as separate units. The laboratory testing service was limited to hospitals, health centers and clinics. There was no specialized and molecular testing capacity at the national reference laboratory which was providing limited testing services for epidemic-prone diseases such as measles, rubella and yellow fever [2, 3].
The lack of in-country molecular and specialized testing capacity critically affected the epidemic prone disease testing as well as specialized clinical testing in Liberia. Some of the services which were affected by the lack of the molecular testing capacity were HIV viral load, HIV early infant diagnosis testing, TB, Lassa fever, Dengue, Marburg and other hemorrhagic fevers. It was only at the end of 2013 that the first molecular testing capacity was established at the national reference laboratory of Liberia. Prior to 2013, Liberia used to send HIV 1 specimens to South Africa for polymerase chain reaction molecular testing. The average Turnaround Time (TAT) was 30 to 45 days. The first molecular testing capacity was initiated at the national reference laboratory of Liberia by the coordinated effort of Clinton Health Access Initiative (CHAI) Liberia office and the National AIDS Control Program (NACP) of Liberia. A standard molecular laboratory for specimen extraction, master mixing and amplification /detection was established for HIV molecular testing. This was funded by the Global Fund. The testing service for HIV was interrupted and the laboratory was dedicated for EVD testing; following the Ebola outbreak in March 2014. This was the only molecular laboratory in Liberia that could be potentially used for EVD testing. The dedication of the molecular laboratory for EVD testing interrupted the HIV clinical molecular testing. During the EVD outbreak; the HIV molecular testing was not restored for more than one year. The interrupted molecular tests include HIV 1 early infant diagnosis and HIV viral load testing. Patients on Anti-Retroviral Therapy (ART) should be monitored for treatment response using viral load test . Despite this, developing countries manage patients by CD4 cell counts and clinical staging as result of the expensive equipment and skilled man power required by the current viral load assays .
According to 2013 Liberian Demographic and Health Survey, the prevalence of HIV in the general population aged 15-49 was 2.1% (1.9% HIV 1 and about 0.3% HIV-2). In 2015, an estimated 26,313 adults and 2,339 children were living with HIV respectively. The percentage of eligible people receiving ART were 25.8% only . The lack of capacity for HIV molecular testing, the low testing volume as result of the 2.1% low prevalence of HIV and the poor specimen referral linkage are the fundamental reasons for the adoption of point of care and near point of care devices in Liberia. As a good opportunity to this, the Xpert HIV-1 Viral Load (Cepheid) cartridge was launched in 2014, as a potential point-of-care rapid viral load assay . The release of the EVD and HIV viral load GeneXpert assays from Cepheid in 2014 followed by Ministry of Health of Liberia approval for use in 2015 was a very crucial opportunity for Liberia.
The GeneXpert instrument system is an automated and integrated cartridge-based system for sample purification, nucleic acid amplification and detection of target in clinical specimens using real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR). A number of infectious agents can be detected using the technology and appropriate cartridge including EVD, HIV Viral Load, HIV Early Infant Diagnosis (EID), MTB and rifampicin resistant strains. The GeneXpert platform offers module sizes of 1 to 64 which facilitates placement of the technology across the entire health system tier. The GeneXpert can be used outside of central reference laboratories and is ideal when placed at district and even sub-district levels .
In July 2017, the HIV-1 viral load cartridge received the World Health Organization (WHO) prequalification. The GeneXpert viral load assay is the most needed and market attractive diagnostic tool in resource-constrained setting as result of the minimal training and infrastructure requirement. Country-level validation studies have been conducted on the accuracy of the GeneXpert viral load assays in a variety of settings. All reported correlations between the Xpert HIV-1 viral load assay and gold standard tests were very high and indicated a very high degree of agreement between Xpert viral load and reference standard viral load values . Despite the recommendations put forward by the WHO consolidated guidelines on the use of antiretroviral drugs for treating and preventing HIV infection, viral load monitoring of ART is not routinely performed in Liberia . The national ART guideline of Liberia also recommends viral load testing for monitoring of treatment failure for all patient categories.
EID was initiated in Liberia in 2013 at the national reference laboratory of Liberia using Roche reagent. However, it was interrupted by EVD outbreak as the molecular laboratory used for EID was dedicated for EVD testing. A decentralized EID testing is very critical in low volume and resource constrained setting. The placement of the GeneXpert machines also considered the EID testing. During 2015, a total of 71,891 pregnant women were tested for HIV and 2122 of them were HIV positive. Out of the 1684 infants born from HIV positive mothers, only 346 were EID tested in 2011 .
The GeneXpert MTB/RIF assay on the GeneXpert molecular system, which was endorsed by WHO in 2010, is the first GeneXpert TB assay released for clinical testing in resource-limited settings and the most scaled-up new TB technology . Liberia adopted a 4 modules GeneXpert technology for testing MTB/RIF assay in 2013 with two machines installed at the TB annex hospital and the Ghanta TB/leprosy rehabilitation center. The machines were procured by the Global Fund office in Liberia and the installation and training was conducted by CHAI and the National Diagnostics Unit of Liberia. The GeneXpert technology was introduced as a diagnostic test in individuals suspected of Multi-Drug Resistant (MDR) TB. In 2015, the national TB program TB testing algorism was revised to include GeneXpert for smear negative TB cases and for HIV associated TB. The Tuberculosis culture and drug susceptibility testing laboratory was not fully operational and adoption of MTB/RIF assay was very timely to detect MDR suspected cases in Liberia.
According to the WHO report of 2017; the TB incidence in Liberia for the year 2016 was 308/100,000 population. The total number of patients diagnosed with TB was 7180 in 2016. The percentage pulmonary TB case is 70% of all the notified TB cases and only 60% of the pulmonary cases were bacteriologically confirmed. The MDR-TB burden is unknown in Liberia as there has been no national drug resistance survey conducted. According to the 2017 WHO TB report, the estimated MDR/RR-TB was 2.6% in new cases and 18% in previously treated cases respectively. TB diagnosis in Liberia has been mainly based on sputum smear microscopy . The sensitivity and specificity of sputum microscopy is very low.
To improve the TB diagnosis in Liberia, the introduction of GeneXpert technologies with higher sensitivities and specificities is crucial. The pooled sensitivity of GeneXpert MTB/RIF assay is 88% and 68% when used as an initial diagnostic test replacing smear microscopy and as an add-on test following a negative smear-microscopy result respectively. The pooled specificity is 99% in both cases. When used to detect rifampicin resistance, GeneXpert MTB/RIF assay achieved a pooled sensitivity of 95% and a pooled specificity of 98% .
One of the lessons learnt from the 2014 outbreak of EVD was the importance of rapid and accurate diagnosis of new and re-emerging disease and the challenges around diagnostic testing to address these diseases. Throughout the 2014-2015 outbreak, EVD testing was limited to sophisticated biocontainment laboratory facility, leading to challenges with specimen collection, data management and often a prolonged TAT to final results. At an outbreak setting, it was very difficult to manage the high number of specimens with this setup. Poor specimen referral network, lack of trained manpower and poor result reporting system were some of the challenges faced during the EVD outbreak. As a result of these challenges, the need for rapid test, point-of-care and near point of care EVD testing was evolved . It was with this initiative that the GeneXpert EVD assay was developed for use in 2015.
WHO included Cepheid's GeneXpert Ebola test to its list of Ebola diagnostics with emergency use authorization on the 8th May 2015 . Following the WHO acceptance, The GeneXpert Ebola test also received the United States Food and Drug Association (FDA) approval in March 2015 . The Ministry of Health of Liberia approved the EVD assay in September 2015 with support from WHO, Foundation for Innovative New Diagnostics (FIND), Academic Consortium to Combating Ebola in Liberia (ACCEL), United States Centre for Disease Control and Prevention (CDC) and other stakeholders. The GeneXpert for EVD were used at the modular laboratory at Eternal Love Winning Africa (ELWA) in biosafety level three laboratories during the EVD outbreak .
When Liberia was declared free of EVD, WHO and ACCEL brought additional GeneXpert machines. The EVD GeneXpert machines have been in use for EVD surveillance testing with limited tests per day. The underutilization of these machines as well as the critical molecular testing challenges of HIV and TB program were the driving force for the integrated use of the GeneXpert platform in Liberia. Despite the effort of the NACP to initiate in-country capacity for HIV molecular testing, the dedication of the HIV molecular laboratory for EVD testing and the expiration of the reagents negatively impacted the HIV molecular testing service in Liberia. The TB program as well couldn’t conduct enough tests using the four GeneXpert machines. EID was also considered in the integrated testing as it was interrupted during EVD outbreak. GeneXpert EID testing training was provided together with the HIV viral load GeneXpert training using whole blood but it was not included in our study as there was a prolonged delay in the procurement of HIV EID cartridges, heat block and Dried Blood Spot (DBS) bundles. When EID is fully integrated, DBS will be transported from the 335 prevention of mother to child transmission of HIV sites.
As a result of the above challenges, Liberia started integrated use of the GeneXpert technology in 2015. This was designed with aim of filling the testing gaps of TB and HIV molecular tests and sustain epidemic preparedness and response capabilities for EVD and related outbreak testing. From online search of databases, we realized that our study is the first of its type to evaluate the integrated use of GeneXpert for TB, HIV viral load and EVD. It can be used as a model for using a laboratory platform for multiple disease diagnosis as well as active surveillance for epidemic preparedness. WHO also recommends collaboration and integration as a priority for those countries with currently operational multi-disease testing devices . The objective of this study was to evaluate the impact of integrated use of GeneXpert testing for TB, HIV viral load and EVD and provide recommendations and strategies for scaling up of the services based on the findings of the study.