A step towards reinvigorating the COVID-19 response: an intra-action review of the WHO Regional Office for Africa Incident Management Support Team.

The WHO Regional Office for Africa (AFRO) COVID-19 Incident Management Support Team (IMST) was first established on 21 January 2020 to coordinate the response to the pandemic in line with the Emergency Response Framework and has undergone three modifications based on intra-action reviews (IAR). An IAR of the WHO AFRO COVID-19 IMST was conducted to document best practices, challenges, lessons learnt and areas for improvement from the start of 2021 to the end of the third wave in November 2021. In addition, it was designed to contribute to improving the response to COVID-19 in the Region. An IAR design as proposed by WHO, encompassing qualitative approaches to collecting critical data and information, was used. It employed mixed methods of data collection: document reviews, online surveys, focus group discussions and key informant interviews. A thematic analysis of the data focused on four thematic areas, namely operations of IMST, data and information management, human resource management and institutional framework/governance. Areas of good practice identified, included the provision of guidelines, protocols and technical expertise, resource mobilisation, logistics management, provision of regular updates, timely situation reporting, timely deployment and good coordination. Some challenges identified included a communication gap; inadequate emergency personnel; lack of scientific updates; and inadequate coordination with partners. The identified strong points/components are the pivot for informed decisions and actions for reinvigorating the future response coordination mechanism.

SARS-CoV-2 Omicron variant of concern in the Seychelles: Introduction and spread

Background: The emergence of the Omicron variant of concern in late 2021 led to a resurgence of SARS-CoV-2 infections globally. By September 2022, Seychelles had experienced two major surges of SARS-CoV-2 infections driven by the Omicron variant. Here, we examine the genomic epidemiology of Omicron in the Seychelles between November 2021 and September 2022. Methods: : We analysed 618 SARS-CoV-2 Omicron genomes identified in the Seychelles between November 2021 and September 2022 to infer virus introductions and local transmission patterns using phylogenetics and the ancestral state reconstruction approach. We then evaluated the impact of government coronavirus 2019 (COVID-19) countermeasures on the estimated number of viral introductions during the study period. Results: : The genomes classified into 43 distinct Pango lineages. The first surge in Omicron cases (beginning November 2021 and peaking in January 2022) was predominated by the BA.1.1 lineage (59%) co-circulating with 11 other Omicron lineages. In the second surge (between April and June 2022), four lineages (BA.2, BA.2.10, BA.2.65 and BA.2.9) co-circulated and these were swiftly replaced by BA.5 subvariants in July 2022, which remained predominant through to September 2022. In the latter period, sporadic detections of BA.5 subvariants BQ.1, BE and BF were observed. We estimated 109 independent Omicron importations into Seychelles over the 11-month period, most of which occurred between December 2021 and March 2022 when strict government restrictions (SI>50%) were still in force. The districts Anse Royale, and Baie St. Anne Praslin appeared to be the major dispersal points fuelling local transmission. Conclusions: : Our results suggest that the waves of Omicron infections in the Seychelles were driven by multiple lineages and multiple virus introductions. The introductions were followed by substantial local spread and successive lineage displacement that mirrored the global patterns.

Prevalence of HIV and Viral Hepatitis Markers among Healthcare Workers in the Republic of Guinea.

Healthcare workers are much more likely to be infected with HIV and hepatitis viruses compared to the general population. Although healthcare workers are more aware of HIV and hepatitis viruses, several countries in Africa lack a comprehensive grasp of disease routes and transmission risks. The aim of this study was to assess the prevalence of the serological and molecular biological markers of HIV and viral hepatitis among healthcare workers in the Republic of Guinea. The study material was 74 blood serum samples collected from healthcare workers who received additional training at the Institute of Applied Biological Research of Guinea (IRBAG, Kindia, Republic of Guinea). The markers examined included HBsAg, HBeAg, anti-HBs IgG, anti-HBcore IgG, anti-HCV qualitative determination, anti-HEV IgM and IgG, anti-HAV IgM and IgG, and anti-HIV. For viral DNA and RNA detection, nucleic acids were extracted from blood serum, and viral presence was inferred using real-time PCR with hybridization fluorescence detection. A high prevalence of viral hepatitis B markers was shown, and significantly fewer cases of viral hepatitis C and HIV were detected. Almost all examined medical workers had anti-HAV IgG antibodies, but no antibodies to hepatitis E virus. Apparently, the identified markers depend on the general prevalence of certain pathogens in the region and are associated with the traditions and characteristics of the country's residents.

How prepared is the world? Identifying weaknesses in existing assessment frameworks for global health security through a One Health approach.

The COVID-19 pandemic has exposed faults in the way we assess preparedness and response capacities for public health emergencies. Existing frameworks are limited in scope, and do not sufficiently consider complex social, economic, political, regulatory, and ecological factors. One Health, through its focus on the links among humans, animals, and ecosystems, is a valuable approach through which existing assessment frameworks can be analysed and new ways forward proposed. Although in the past few years advances have been made in assessment tools such as the International Health Regulations Joint External Evaluation, a rapid and radical increase in ambition is required. To sufficiently account for the range of complex systems in which health emergencies occur, assessments should consider how problems are defined across stakeholders and the wider sociopolitical environments in which structures and institutions operate. Current frameworks do little to consider anthropogenic factors in disease emergence or address the full array of health security hazards across the social-ecological system. A complex and interdependent set of challenges threaten human, animal, and ecosystem health, and we cannot afford to overlook important contextual factors, or the determinants of these shared threats. Health security assessment frameworks should therefore ensure that the process undertaken to prioritise and build capacity adheres to core One Health principles and that interventions and outcomes are assessed in terms of added value, trade-offs, and cobenefits across human, animal, and environmental health systems.

Transitioning the COVID-19 response in the WHO African region: a proposed framework for rethinking and rebuilding health systems.

The onset of the pandemic revealed the health system inequities and inadequate preparedness, especially in the African continent. Over the past months, African countries have ensured optimum pandemic response. However, there is still a need to build further resilient health systems that enhance response and transition from the acute phase of the pandemic to the recovery interpandemic/preparedness phase. Guided by the lessons learnt in the response and plausible pandemic scenarios, the WHO Regional Office for Africa has envisioned a transition framework that will optimise the response and enhance preparedness for future public health emergencies. The framework encompasses maintaining and consolidating the current response capacity but with a view to learning and reshaping them by harnessing the power of science, data and digital technologies, and research innovations. In addition, the framework reorients the health system towards primary healthcare and integrates response into routine care based on best practices/health system interventions. These elements are significant in building a resilient health system capable of addressing more effectively and more effectively future public health crises, all while maintaining an optimal level of essential public health functions. The key elements of the framework are possible with countries following three principles: equity (the protection of all vulnerable populations with no one left behind), inclusiveness (full engagement, equal participation, leadership, decision-making and ownership of all stakeholders using a multisectoral and transdisciplinary, One Health approach), and coherence (to reduce the fragmentation, competition and duplication and promote logical, consistent programmes aligned with international instruments).

A Policy Analysis of the Deployment of International EMT in the WHO African Region during the COVID-19 Pandemic

Background/Introduction:The COVID-19 pandemic, especially in Africa, has increased the need for EMTs for surge management, clinical care, and capacity-building support for establishing national EMTs.Objectives:To analyze the implementation of EMTs deployments in the AFRO Region during the COVID-19 pandemic.Method/Description:This is a retrospective policy analysis done from the perspective of the EMT policy implementor using Walt and Gilson’s policy triangle1 (capturing processes, the actors, the context, and the content). Data were collected through document reviews, key informant interviews, semi-structured in-depth interviews, and focus-group discussions. Analysis was done through a priori framework analysis.Results/Outcomes:Overall, 22 countries benefited from international EMT deployments since the onset of COVID-19, with deployment periods varying between six to 24 weeks. Development partners, governments, and local authorities supported deployments. Some deployments were hampered by inadequate knowledge of EMTs processes, bureaucratic and administrative barriers, and slow mobilization of resources. Other challenges were the lack of critical care equipment and teams facing resistance due to cultural differences. Some teams only worked in big cities rather than local regions with low capacity and high morbidities from COVID-19. Collaboration between international and national teams resulted in enhanced capacity building, optimistic volunteerism and resilience, and provision of clinical care in constraint settings to save lives.Conclusion:The deployments were critical in saving lives in under-resourced settings despite the challenges. COVID-19 has provided an impetus to strengthen national public health response by providing training opportunities, twinning or exchange programs, building health infrastructure, and prepositioning supplies and equipment to ensure national reliance and sustainability.

Framing the future of the COVID-19 response operations in 2022 in the WHO African region.

BACKGROUND: With the evolving epidemiological parameters of COVID-19 in Africa, the response actions and lessons learnt during the pandemic's past two years, SARS-COV 2 will certainly continue to circulate in African countries in 2022 and beyond. As countries in the African continent need to be more prepared and plan to 'live with the virus' for the upcoming two years and after and at the same time mitigate risks by protecting the future most vulnerable and those responsible for maintaining essential services, WHO AFRO is anticipating four interim scenarios of the evolution of the pandemic in 2022 and beyond in the region. OBJECTIVE: In preparation for the rollout of response actions given the predicted scenarios, WHO AFRO has identified ten strategic orientations and areas of focus for supporting member states and partners in responding to the COVID-19 pandemic in Africa in 2022 and beyond. METHODS: WHO analysed trends of the transmissions since the first case in the African continent and reviewed lessons learnt over the past months. RESULTS: Establishing a core and agile team solely dedicated to the COVID-19 response at the WHO AFRO, the emergency hubs, and WCOs will improve the effectiveness of the response and address identified challenges. The team will collaborate with the various clusters of the regional office, and other units and subunits in the WCOs supported with good epidemics intelligence. COVID-19 pandemic has afflicted global humanity at unprecedented levels. CONCLUSION: Two years later and while starting the third year of the COVID-19 response, we now need to change and adapt our strategies, tools and approaches in responding timely and effectively to the pandemic in Africa and save more lives.

SARS-CoV-2 infection in Africa: a systematic review and meta-analysis of standardised seroprevalence studies, from January 2020 to December 2021.

INTRODUCTION: Estimating COVID-19 cumulative incidence in Africa remains problematic due to challenges in contact tracing, routine surveillance systems and laboratory testing capacities and strategies. We undertook a meta-analysis of population-based seroprevalence studies to estimate SARS-CoV-2 seroprevalence in Africa to inform evidence-based decision making on public health and social measures (PHSM) and vaccine strategy. METHODS: We searched for seroprevalence studies conducted in Africa published 1 January 2020-30 December 2021 in Medline, Embase, Web of Science and Europe PMC (preprints), grey literature, media releases and early results from WHO Unity studies. All studies were screened, extracted, assessed for risk of bias and evaluated for alignment with the WHO Unity seroprevalence protocol. We conducted descriptive analyses of seroprevalence and meta-analysed seroprevalence differences by demographic groups, place and time. We estimated the extent of undetected infections by comparing seroprevalence and cumulative incidence of confirmed cases reported to WHO. PROSPERO: CRD42020183634. RESULTS: We identified 56 full texts or early results, reporting 153 distinct seroprevalence studies in Africa. Of these, 97 (63%) were low/moderate risk of bias studies. SARS-CoV-2 seroprevalence rose from 3.0% (95% CI 1.0% to 9.2%) in April-June 2020 to 65.1% (95% CI 56.3% to 73.0%) in July-September 2021. The ratios of seroprevalence from infection to cumulative incidence of confirmed cases was large (overall: 100:1, ranging from 18:1 to 954:1) and steady over time. Seroprevalence was highly heterogeneous both within countries-urban versus rural (lower seroprevalence for rural geographic areas), children versus adults (children aged 0-9 years had the lowest seroprevalence)-and between countries and African subregions. CONCLUSION: We report high seroprevalence in Africa suggesting greater population exposure to SARS-CoV-2 and potential protection against COVID-19 severe disease than indicated by surveillance data. As seroprevalence was heterogeneous, targeted PHSM and vaccination strategies need to be tailored to local epidemiological situations.

COVID-19 vaccination rollout in the World Health Organization African region: status at end June 2022 and way forward.

In October 2021, the WHO published an ambitious strategy to ensure that all countries had vaccinated 40% of their population by the end of 2021 and 70% by mid-2022. The end of June 2022 marks 18 months of implementation of coronavirus disease 2019 (COVID-19) vaccination in the African region and provides an opportunity to look back and think ahead about COVID-19 vaccine set targets, demand and delivery strategies. As of 26 June 2022 two countries in the WHO African region have achieved this target (Mauritius and Seychelles) and seven are on track, having vaccinated between 40% and 69% of their population. By the 26 June 2022, seven among the 20 countries that had less than 10% of people fully vaccinated at the end of January 2022, have surpassed 15% of people fully vaccinated at the end of June 2022. This includes five targeted countries, which are being supported by the WHO Regional Office for Africa through the Multi-Partners' Country Support Team Initiative. As we enter the second semester of 2022, a window of opportunity has opened to provide new impetus to COVID-19 vaccination rollout in the African region guided by the four principles: Scale-up, Transition, Consolidation and Communication. Member States need to build on progress made to ensure that this impetus is not lost and that the African region does not remain the least vaccinated global region, as economies open up and world priorities change.

Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021.

Seychelles, an archipelago of 155 islands in the Indian Ocean, had confirmed 24,788 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the 31st of December 2021. The first SARS-CoV-2 cases in Seychelles were reported on the 14th of March 2020, but cases remained low until January 2021, when a surge was observed. Here, we investigated the potential drivers of the surge by genomic analysis of 1056 SARS-CoV-2 positive samples collected in Seychelles between 14 March 2020 and 31 December 2021. The Seychelles genomes were classified into 32 Pango lineages, 1042 of which fell within four variants of concern, i.e., Alpha, Beta, Delta and Omicron. Sporadic cases of SARS-CoV-2 detected in Seychelles in 2020 were mainly of lineage B.1 (lineage predominantly observed in Europe) but this lineage was rapidly replaced by Beta variant starting January 2021, and which was also subsequently replaced by the Delta variant in May 2021 that dominated till November 2021 when Omicron cases were identified. Using the ancestral state reconstruction approach, we estimated that at least 78 independent SARS-CoV-2 introduction events occurred in Seychelles during the study period. The majority of viral introductions into Seychelles occurred in 2021, despite substantial COVID-19 restrictions in place during this period. We conclude that the surge of SARS-CoV-2 cases in Seychelles in January 2021 was primarily due to the introduction of more transmissible SARS-CoV-2 variants into the islands.

COVID-19 in the 47 countries of the WHO African region: a modelling analysis of past trends and future patterns.

BACKGROUND: COVID-19 has affected the African region in many ways. We aimed to generate robust information on the transmission dynamics of COVID-19 in this region since the beginning of the pandemic and throughout 2022. METHODS: For each of the 47 countries of the WHO African region, we consolidated COVID-19 data from reported infections and deaths (from WHO statistics); published literature on socioecological, biophysical, and public health interventions; and immunity status and variants of concern, to build a dynamic and comprehensive picture of COVID-19 burden. The model is consolidated through a partially observed Markov decision process, with a Fourier series to produce observed patterns over time based on the SEIRD (denoting susceptible, exposed, infected, recovered, and dead) modelling framework. The model was set up to run weekly, by country, from the date the first infection was reported in each country until Dec 31, 2021. New variants were introduced into the model based on sequenced data reported by countries. The models were then extrapolated until the end of 2022 and included three scenarios based on possible new variants with varying transmissibility, severity, or immunogenicity. FINDINGS: Between Jan 1, 2020, and Dec 31, 2021, our model estimates the number of SARS-CoV-2 infections in the African region to be 505·6 million (95% CI 476·0-536·2), inferring that only 1·4% (one in 71) of SARS-CoV-2 infections in the region were reported. Deaths are estimated at 439 500 (95% CI 344 374-574 785), with 35·3% (one in three) of these reported as COVID-19-related deaths. Although the number of infections were similar between 2020 and 2021, 81% of the deaths were in 2021. 52·3% (95% CI 43·5-95·2) of the region's population is estimated to have some SARS-CoV-2 immunity, given vaccination coverage of 14·7% as of Dec 31, 2021. By the end of 2022, we estimate that infections will remain high, at around 166·2 million (95% CI 157·5-174·9) infections, but deaths will substantially reduce to 22 563 (14 970-38 831). INTERPRETATION: The African region is estimated to have had a similar number of COVID-19 infections to that of the rest of the world, but with fewer deaths. Our model suggests that the current approach to SARS-CoV-2 testing is missing most infections. These results are consistent with findings from representative seroprevalence studies. There is, therefore, a need for surveillance of hospitalisations, comorbidities, and the emergence of new variants of concern, and scale-up of representative seroprevalence studies, as core response strategies. FUNDING: None.