The last two decades have seen significant progress in the implementation of programs for HIV prevention, care and treatment in several countries in sub-Saharan Africa. In the area of prevention, there are examples of progress that has been made in expanding programs for voluntary counseling and testing [1, 2], Mother-to-child HIV transmission (PMTCT) [3–5] and scaling up programs for safe male circumcision [6–8]. In the area of treatment, antiretroviral therapy is now widely available and has been associated with significant reductions in morbidity and mortality [9, 10].

Despite, the significant progress made, many of these programs have fallen short of their targets. Such targets include the United Nations General Assembly Special Session (UNGASS) goal of 80 % coverage with PMTCT accompanied by significant reductions in new infant infections [11] has not been achieved for many countries. Many PMTCT programs in resource limited settings have not achieved this target and their full potential and impact [12], despite knowledge of the scientific evidence about efficacy and cost effectiveness of interventions [13–15]. In 2010, new infections from mother-to-child transmission contributed to over 90 % of new HIV infections among children globally [16]. Operational issues that present these gaps in achieving program success still exist and need to be addressed [12, 17].

Secondly, the landscape for HIV prevention, care and treatment is constantly changing. For instance clinical trials have now provided evidence for prevention of HIV using circumcision, [18] among HIV discordant couples using pre-exposure prophylaxis [19–22]. These findings present implementation gaps in the contemporary programs designed prior to publication of these findings, or simply designed with resource limited settings in mind. These new findings also prompt changes in policy and guidelines. For instance, the WHO has revised the treatment guidelines [23] and this presents challenges to the health systems in resource limited setting to meet the new targets. The requirement to meet these new targets exposes the gaps in the delivery of HIV services that need to be addressed by programs through implementation.

Implementation science has been defined as ‘a multidisciplinary scientific field that seeks generalizable knowledge about the magnitudes of, determinants and strategies to close the gap between evidence and routine practice for health in real world settings’ [24]. The identification of bottle necks and gaps has been proposed as a first step in a four component approach to implementation science [25]. The other steps in sequence are developing and implementing strategies, measuring effectiveness and efficiency, and lastly utilizing results.

The Strengthening Civil Society for Improved HIV/AIDS and Orphans and Vulnerable Children service delivery in Uganda (SCIPHA) is a 5-year project supported by the Civil Society Fund and aims to increase access and utilization of HIV/AIDS care, treatment and support services while building capacity for Civil Society Organizations (CSOs) to deliver quality HIV prevention, care and treatment services. Within the context of SCIPHA, the aim of this study was to identify gaps in the HIV prevention, care and treatment cascade, in the 19 implementation districts of the program. The aim is to identify interventions that are amenable for evaluation using implementation science, in order to improve the delivery of HIV programs in rural Uganda. Data from this evaluation can be used to inform interventions aiming at more efficient HIV programs and closing the implementation gap.

The results from the analysis fell under nine emerging themes that comprise the gaps and these were Referral mechanisms, low levels of integration of HIV/TB services, low uptake of services for PMTCT services by pregnant women, low coverage of services for most at risk populations (MARPs), HIV coordination structures in the districts, delivery of pediatric HIV/AIDS services, Community support for Orphans and Vulnerable (OVC’s), home based care services and HIV services and support for discordant couples.

The study has showed several gaps in the delivery of HIV/AIDS and these include inadequate linkages and referral among service providers at health facilities and community level. This was further compounded by low levels of integration of HIV/TB services. There is a gap in the PMTCT programs resulting in poor uptake of services. And this is likely to be compounded further as the policy on PMTCT transforms to the Option B+ [29] targeting the elimination of MTCT. Another gap was identified in the coverage of services for MARPs, and inadequate HIV coordination structures at the district. On the care and support front, the study identified gaps in the delivery of pediatric HIV care, community support for OVCs, inadequate home based care and services for discordant couples.

Our data collection identified gaps in the referral mechanisms of patients with HIV. More research should be done to understand clearly how these gaps arise. For instance, an analytical framework of the continuum for prevention and care in Vietnam helped to identify the strengths and weaknesses that contribute to retention [30]. Similar work was done in several other Asia and Pacific countries and was helpful in making recommendations for service decentralization, integration, linkages [31].

The integration of HIV and TB services has been shown to enhance uptake of services and lower the delay in initiating cotrimoxazole and antiretroviral therapy in rural Kenya [32]. In Uganda, integration of these services led to better outcomes in TB treatment [33]. The evidence in support of integration is overwhelming. Delivery of integrated services is challenged by the lack of service delivery policies and guidelines as well as knowledge of how to integrate, inadequate staff numbers and in-service training which makes it difficult for service providers to integrate these services. On a day-to-day basis, health workers are overwhelmed with the work load. Health systems need to be restructured to accommodate a natural integration of services and implementation science could test and try some of the potential interventions from Kenya, Uganda and South Africa [34], that have been shown to work.

Health workers indicated there is low uptake of PMTCT services and this may be attributed to several reasons. There are still challenges in testing pregnant mothers and linking them to care. There are still challenges with availability of drugs and test kits, human resources to deliver these services in rural areas. There also gaps in involvement of men in these programs. Previous studies have indicated women seek permission of their husbands before they can test [35] and rely on them for financial support to meet the costs related to antenatal care [36].

There is a need to design and test community based and culturally appropriate interventions to enable adequate uptake and retention of mothers in these programs. One such intervention that has recently shown success is congregation based randomized trial in Nigeria [37]. Pregnant women who received congregation based counseling were more likely to have HIV testing compared to those who were referred to health facilities for HIV testing. Such novel interventions will need to be developed and tested in the field. Interventions should also be designed to target the barriers and facilitators of male involvement [38].

This study has showed that there are still pockets of the population with in the study districts which are at high risk for HIV infection and yet they are not adequately targeted with HIV prevention, care and treatment services. The populations identified included mobile populations (including truck and bus drivers), commercial sex workers, fishing communities, internally displaced people (IDPs), uniformed services and people with disability. For instance HIV incidence among fishing folk is very high [39, 40] and high risk behavior in this population continues unabated [41].

The district team is central in the delivery of HIV care, and hence coordination at this level is critical. Our data shows challenges in the coordination with occurrence of parallel structures and duplication of roles. Also challenges in the health system were seen in the delivery of pediatric HIV/AIDS services. These challenges were attributed to the long turn-around time for DNA PCR results upcountry and poor mechanism for the districts to hasten transfer of money for transporting the blood samples for DNA-PCR and CD4 from the health facilities to the central laboratories for testing. Recent systematic review of studies on HIV testing and counseling among children and adolescents in sub-Saharan Africa [42] recommends evaluation of testing strategies beyond the health facility, in order to identify and treat persons in their early stages of infection.

The study has showed that OVCs services are provided but on a small scale. OVC indicate a lack of emotional and physical support. There are inadequate community structures and systems that support OVCs. There is a huge gap that needs to be closed. Data from Swaziland, a country with a high burden of HIV and OVCs shows OVCs were less likely to be in school compared to the non-OVCs [43]. The needs of these OVCs are varied in nature and a survey in Nigeria showed over 60 % were living in a dilapidated shelter. More data indicates OVCs are at higher risk for poor social protection, even when care is given in a family setting [44]. Asset ownership among households caring for an orphan has been shown to reduce social vulnerability of these children [45], hence offsetting some potential adverse outcomes. Implementation of interventions of this nature may lead to positive results.

Home based care services have been developed to provide easy access to services and have shown success in increasing uptake of HIV testing [46], adherence to antiretroviral therapy and high probability of viral load suppression [47]. A recent metanalysis has shown home based testing is associated with lower risk of stigma, high risk sexual behavior and intimate partner violence [48]. Home based HIV counseling and testing is also cost effective compared to standard facility based HIV testing [49, 50]. Participants in our study demanded home based services. These services have been shown to be cost effective and should be implemented and evaluated in the local setting.

There are currently very few interventions aiming at preventing HIV transmission between HIV discordant couples. Therefore, there is need for strengthening family centered provider initiated HCT, specifically targeting couples. Future projects should implement activities that accelerate identification of discordant couples and providing pre-exposure prophylaxis to the negative partner. The strength of this study is that we collected data from a large parts of Uganda with varying HIV prevalence and service delivery and therefore data cover wide representation. Our study has some weaknesses; one is the data on the breakdown of the KIs was not captured and this may provide insights into the nature of gaps likely to be faced.

In conclusion, our study has identified several gaps and suggested several interventions that should be tested or implemented. These implementation programs need to be evaluated in order to provide field evidence of effectiveness.