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

Introducing a mobile-connected umbilical doppler device (UmbiFlow™) into a primary care maternity setting : does this reduce unnecessary referrals to specialised care? results of a pilot study in Kraaifontein, South Africa

CITATION: Mufenda, J., et al. 2015. Introducing a mobile-connected umbilical doppler device (UmbiFlow™) into a primary care maternity setting : does this reduce unnecessary referrals to specialised care? results of a pilot study in Kraaifontein, South Africa. PLoS ONE, 10(11):1-13, doi:10.1371/journal.pone.0142743.The original publication is available at http://journals.plos.org/plosoneObjectives: UmbiFlow™ is a mobile-connected Doppler device that utilises a continuous waveform to measure resistance in the umbilical artery. The main aim of this pilot study was to determine whether the use of UmbiFlow™ for umbilical artery Doppler in patients with a suspected decreased symphysis fundal (SF) growth could safely lead to a decreased number of patients requiring referral to a more specialised level of care. A secondary aim of the study was to evaluate the effectiveness of UmbiFlow™ Doppler as a screening tool for concealed placental insufficiency in late bookers by using a single screening cut-off value that will be abnormal for any gestation >28 weeks. Methods: The cohort comprised two groups of patients: The first group included all follow-up patients with suspected intra-uterine growth restriction (a decreased symphysis-fundus measurement based on serial assessment) who underwent on-site UmbiFlow™Doppler testing performed by the midwife directly after the clinical examination. The second group included late bookers, where gestation was uncertain; but estimated >28 weeks based on clinical grounds. This group was comprised of unselected patients who report to antenatal care late for the first time and received an UmbiFlow™Doppler test for concealed placental insufficiency. Results: UmbiFlow™Doppler could reduce the number of false referrals to hospital by 55%. A single UmbiFlow™Doppler test in late bookers appeared to identify a group of women at moderate risk of lower birth weight babies.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142743Publisher's versio

Demographic characteristics of the study population.

<p>Demographic characteristics of the study population.</p

Algorithm of participating women in the poor SF group.

<p>Algorithm of participating women in the poor SF group.</p

The UmbiFlow™ setup in a clinic.

<p>The UmbiFlow™ setup in a clinic.</p

Algorithm of participating women in the late bookers group.

<p>Algorithm of participating women in the late bookers group.</p

Results from an UmbiFlow™ Doppler measurement plotted against the gestation.

<p>Results from an UmbiFlow™ Doppler measurement plotted against the gestation.</p

A schematic representation, showing that at any gestation ≥28 weeks, an umbilical artery resistance of >0.8 would be abnormal (≥95th centile) (shaded area).

<p>A schematic representation, showing that at any gestation ≥28 weeks, an umbilical artery resistance of >0.8 would be abnormal (≥95th centile) (shaded area).</p