The World Health Organization (WHO) defines fragile, conflict-affected and vulnerable (FCV) countries as those experiencing situations of crises due to protracted emergencies, disruption of governance structures and/or armed conflict [7]. While the WHO nomenclature is slightly different from that of the World Bank Group which uses “violence” instead of “vulnerable”, the WHO classification of FCV countries largely depends on the World Bank Group list [8]. This list currently includes 37 countries out of which 18 are in sub-Saharan Africa.Footnote 1 In the context of this article, the term “fragile” refers to countries who are in unstable situations while “vulnerable” refers to countries who are at risk of multiple public health emergencies and both terms are viewed as distinct.

FCV countries of sub-Saharan Africa face peculiar challenges, such as pervasively weak health system, vulnerability to multiple public health emergencies, increased demand for healthcare services in the face of disrupted or weak routine healthcare delivery systems and inadequate health funding among others. The COVID-19 pandemic has further aggravated these challenges.

First, the COVID-19 pandemic overwhelmed already compromised health systems in these countries, rapidly depleting critical human, financial and material resources and adversely disrupting the delivery of essential health services. In South Sudan, a special survey estimated health workforce density (doctors, nurses and midwives) at 0.76 per 1000 population [unpublished data from the South Sudan Services Availability and Readiness Survey, 2018]—far below the Sustainable Development Goals (SDG) threshold of 4.45 per 1000 population for making progress towards Universal Health Coverage [9]. Within the countries of the WHO African Region, mainly in Sub-Saharan Africa, health workforce density is as low as 1.55 per 1000 population, with only four countries in the region (Mauritius, Seychelles, South Africa and Namibia) above the 4.45 threshold. FCV countries, such as Chad and Central African Republic, are among those with the lowest levels, fewer than 0.5 health workers per 1000 population [10]. For 2020, South Sudan’s Humanitarian Response Plan estimated additional funding needed for COVID-19 at USD 150 million, or 8% of the original amount of $1.9 billion allocated for the overall humanitarian response for the year [11]. For the same year, the South Sudan Health Sector Strategic Plan listed the amount needed for the entire health sector routine programming at $457 million—largely designated for development interventions in the health care sector [unpublished data from the South Sudan Health Sector Strategic Plan 2017–2022]. Based on the 2020 Humanitarian Response Plan, the additional funds needed for COVID-19 response in 2020 alone, was 33% of the entire sector budget for the year.

Second, these countries continue to experience multiple and recurrent emergencies arising from conflicts, natural disasters such as droughts, floods and disease outbreaks, including of wild polio virus (and its vaccine derived variant), yellow fever, cholera, measles, meningitis, among others, due to prevailing poor living conditions and weak health systems. Third, the social, economic and cultural impacts of the pandemic have been particularly severe in these countries, including aggravation of poverty through disruption of livelihoods and of societal structures. Fourth, the current approach to COVID-19 epidemic response, which relies on vertical systems and structures is resource intensive and not sustainable.

We agree with Ali et al. on the need for longer-term, sustainable, cost-effective and integrated responses to the outbreaks in FCV settings [12]. The aims of such an approach are three: to enhance global health security, ensure health system recovery and strengthen health system resilience [13, 14]. We propose policy options to guide transition from the initial emergency public health responses to the COVID-19 pandemic to humanitarian and development programming. We present a case study of South Sudan where health system challenges are enormous, and the complexity of its humanitarian crisis is among the most challenging in sub-Saharan Africa. We next summarize policy options and principles to guide implementation of more sustainable approaches. Then we discuss implications of the changes and summarize early lessons from implementation in South Sudan to inform the transition from emergency (vertical) COVID-19 responses to longer-term approaches integrating COVID -19 into routine care and structures in similar settings.