Despite the implementation process of IDSR in Nigeria since 2000 , this study has shown that there is a strong existence of vertical programs on diseases like malaria, tuberculosis, HIV, and NTDs in Nigeria. From our findings, almost all the vertical programs have different reporting forms from the available IDSR system. This resulted in ineffective utilization of data harmonization forums and multiple data reporting.
The study revealed that resources for these vertical programs were separate from those for IDSR including personnel, funding, and materials. This defeats the objective of the IDSR and consequently leads to a waste of resources .
This study also found that developmental partners funded more vertical programs than IDSR. Another finding from this study showed non-integrated supportive supervision involving the vertical programs managers and the state epidemiology unit. These findings are peculiar with donor-funded vertical programs [2, 21].
The major effects from the existence of these vertical programs included the following broad areas: Health information management; Program processes and structure; Donor funding and influence; and Human resources.
Health information management
There was gross poor data management with different reporting mechanisms and data collection tools from the IDSR tools. This defeats the aim of the adopted IDSR. This could also result in poor response to outbreaks without an integrated surveillance system. Also, data reported were mostly on service delivery of the vertical programs and not on surveillance. This is similar to findings in a systematic review in LMIC  despite efforts by member states to integrate surveillance for efficiency.
The study participants recommended the following: quarterly functional disease data consultative fora, provision of surveillance data tools, one health (human and zoonotic) disease data capturing, and harmonization of all reporting forms and channels of reporting. Some studies have also recommended an integrated one health disease data capturing [22, 23] and harmonization of reporting channels  especially in the advent of emerging and re-emerging diseases like Ebola, brucellosis, dengue, and recently COVID 19.
Surveillance and responding to infectious disease outbreaks has been a major public health challenge in Nigeria, given its rapid population growth, increasing movement of people and destruction of infrastructure following the insecurity that has plagued the country in the recent past as well as outbreaks from new and re-emerging pathogens.
Program processes and structure
The vertical programs lacked linkages and synergy and high-level advocacy was recommended for addressing this. All disease programs should be mandated to report through and be collapsed into IDSR. The onus lies on the national health system governance to ensure the integration and coordination of these programs in line with the country’s policy direction. A review on health system strengthening  also revealed that good governance using a multi-stakeholder approach is an important factor in improving health services and outcomes.
Donor funding and influence
Vertical programs development partners fund these programs with no support for already existing programs and this comes with donor-specific terms of references. There is expected to be a pool of funds for integrated disease surveillance and response instead of the reported multiplicity of funds from vertical programs. Donor influence and lack of coordination by the government creates this diversion. There is eventually skewed and poor funding of IDSR programs. This finding is corroborated by a systematic review done in 2015 .
It is recommended that development partners should not undermine one program for another. Better country ownership and oversight of development partners with more intra and intersectoral collaboration (One health) can also further strengthen integrated disease surveillance. Basket funding has been recommended in health programs . Improved funding and equipping of IDSR desk officers is also advocated. Again good governance is required here for implementation.
This study showed a non-integration and lack of cooperation and coordination of personnel in disease surveillance and response. Vertical program officers feel threatened by surveillance officers over whom they claim superiority due to funding allocated to them by partners. This consequently places a low priority on the IDSR priority diseases.
Capacity building and incentives to surveillance personnel is recommended, with increased collaboration between epidemiologists and vertical program officers. A similar recommendation was made in several studies study [21, 27, 28].
Vertical programs affect pillars of the health systems as evident above. Efforts have been made in Nigeria to strengthen the health system through strategies like the National Strategic Health Development Plan (NSHDP) II framework  which was founded on the eight pillars of the health system. A cohesive implementation framework for the NSHDP II was validated by stakeholders in 2017 . This comprises the integration of health services including surveillance of diseases. A lot of effort on the part of leadership and governance is needed for the implementation of health programs including IDSR. Continuous involvement of stakeholders including leadership in the implementation of IDSR is necessary.
A rapid assessment of IDSR performance in 47 African countries between 2014 and 2017 showed that 44 of those countries (98%) were implementing IDSR though the quality of the implementation was not assessed . The study revealed that Nigeria was among the few countries with less than 50 % coverage of IDSR at the subnational level as compared with other African countries with over 90 % coverage like Uganda, Rwanda, Liberia, Senegal and Togo . This low coverage in Nigeria could be due to the vertical program’s surveillance running concurrently with IDSR.
Adoption of the National Technical Guidelines on IDSR has helped some countries in the management of recent outbreaks like Ebola [28, 31]. There is therefore a need for African countries and other LMICs to fully adopt their level National Technical Guidelines on IDSR and other integrated surveillance systems to be better positioned to prepare for and identify outbreaks like Ebola and COVID-19.
This study is not without limitations. Firstly, it only involved a limited number of epidemiologists with over and under-representation of some geopolitical zones thus its findings may not be generalizable to the whole of the country. However, the inclusion of epidemiologists from all geopolitical zones of Nigeria improves its representativeness. As is peculiar to the diversity of the Nigerian context, the States in the different geopolitical zones may have differences in demographic characteristics but they share similar IDSR structures across States. Because the study was based on self-reports, desirability bias may have played a role however this is unlikely because most of our findings have been associated with vertical programs. The additional use of observational checklists is recommended for future studies.