Influenza Surveillance among Outpatients and Inpatients in Morocco, 1996–2009

There is limited information about the epidemiology of influenza in Africa. We describe the epidemiology and seasonality of influenza in Morocco from 1996 to 2009 with particular emphasis on the 2007-2008 and 2008-2009 influenza seasons. Successes and challenges of the enhanced surveillance system introduced in 2007 are also discussed.Virologic sentinel surveillance for influenza virus was initiated in Morocco in 1996 using a network of private practitioners that collected oro-pharyngeal and naso-pharyngeal swabs from outpatients presenting with influenza-like-illness (ILI). The surveillance network expanded over the years to include inpatients presenting with severe acute respiratory illness (SARI) at hospitals and syndromic surveillance for ILI and acute respiratory infection (ARI). Respiratory samples and structured questionnaires were collected from eligible patients, and samples were tested by immunofluorescence assays and by viral isolation for influenza viruses.We obtained a total of 6465 respiratory specimens during 1996 to 2009, of which, 3102 were collected during 2007-2009. Of those, 2249 (72%) were from patients with ILI, and 853 (27%) were from patients with SARI. Among the 3,102 patients, 98 (3%) had laboratory-confirmed influenza, of whom, 85 (87%) had ILI and 13 (13%) had SARI. Among ILI patients, the highest proportion of laboratory-confirmed influenza occurred in children less than 5 years of age (3/169; 2% during 2007-2008 and 23/271; 9% during 2008-2009) and patients 25-59 years of age (8/440; 2% during 2007-2009 and 21/483; 4% during 2008-2009). All SARI patients with influenza were less than 14 years of age. During all surveillance years, influenza virus circulation was seasonal with peak circulation during the winter months of October through April.Influenza results in both mild and severe respiratory infections in Morocco, and accounted for a large proportion of all hospitalizations for severe respiratory illness among children 5 years of age and younger

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Proportion of patients with laboratory-confirmed influenza by age group and surveillance network, Morocco, 2007–2009.

<p>*from September 2007 to August 2008.</p><p>**from September 2008 to August 2009.</p

Onset peak and duration of influenza seasons, Morocco, 1996–2009.

<p>Onset peak and duration of influenza seasons, Morocco, 1996–2009.</p

Model coefficient, 95% confidence interval and p-value for the Interrupted Time-Series Regression Analysis for the assessment of the impact of the enhanced surveillance system, Morocco, 1996–2009.

<p>*the slope coefficient represent the expected average increase of number of samples in each consecutive year during the pre-intervention period (1996–2006).</p><p>**the slope coefficient represent the expected average increase of number of samples in each consecutive year during the post intervention period (2007–2009).</p

Number of positive influenza samples by type and subtypes and proportion of ILI cases over total consultation in the health unit and private clinic networks by week, Morocco, 2007–2009.

<p>Number of positive influenza samples by type and subtypes and proportion of ILI cases over total consultation in the health unit and private clinic networks by week, Morocco, 2007–2009.</p

Observed and predicted (using the Interrupted Time Series Analysis) numbers of samples during the pre- and post-intervention period, Morocco, 1996–2009.

<p>Observed and predicted (using the Interrupted Time Series Analysis) numbers of samples during the pre- and post-intervention period, Morocco, 1996–2009.</p

Demographic characteristics of influenza-like illness (ILI) and severe acute respiratory illness (SARI) patients, Morocco, 2007–2009.

<p>*from September 2007 to August 2008.</p><p>**from September 2008 to August 2009.</p