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

Shell morphometrics and physicochemical conditions during CO2 acidified seawater laboratory experiment and field experiment of flat tree oysters, Isognomon alatus (Gmelin, 1791)

The emission of anthropogenic carbon dioxide leads to the lowering of seawater pH. Ocean acidification is a major problem for marine calcifying organisms. There is a need to study short- and long-term effects of lowered pH on marine organisms such as oysters. Oysters are an important food source and useful for nutrients recycling in the coastal estuarine environments. The coastal estuarine environment such as mangrove ecosystems connected to the Sargasso Sea, Ferry Reach, Bermuda, has a natural variation of pH according to the changes in tidal regime (thus low and high tide activities). The unique environment serves as a model place to carry out the effect of changing pH on a marine organism such as flat tree oysters inhabiting this coastal ecosystem. For the laboratory experiment, a total of 84 specimens of the flat tree oyster, Isognomon alatus, were randomly collected on 21 January 2009 from rocks exposed at low tide in Mullet Bay, an intertidal mudflat, St. George, Bermuda (latitude: 32° 22' 30'' N, longitude: 64° 41' 35''W). An experiment was performed to test the effect of projected future pH decrease in a seawater flow-through system at Bermuda Institute of Ocean Sciences (BIOS) for a short period (February to April 2009). Physicochemical conditions (seawater temperature, salinity, pH and oxygen concentration) in three control tanks (C1, C2, C3, pH = 8.1 - 8.2) and three acidification tanks (T1, T2, T3, pH = 7.8 - 7.9) used for the culture of the oysters were recorded. Changes in shell morphometrics of the oysters were determined. For the field experiment, 42 specimens of I. alatus were randomly placed in 6 tanks (approx. n = 7 oysters/tank). Two tanks were then positioned along the transect at each station (A, B ,C) in Mangrove Bay, Bermuda. The shell parameters of flat tree oysters and physicochemical conditions were monitored biweekly

Seawater carbonate chemistry and shell morphometrics during CO2 acidified seawater laboratory experiment and field experiment of flat tree oysters, Isognomon alatus (Gmelin, 1791)

Seawater changing chemistry has consequences on coastal ecosystems and their living resources. Future projections suggest the pH could drop 0.2-0.3 pH units by the year 2100 under a business-as-usual (BAU) CO2 emission scenario. Marine calcifying organisms such as corals, calcifying algae, crustaceans, mussels, oysters and clams are most likely to be impacted by ocean acidification. The Isognomon alatus (flat tree oyster) is an important species that can be negatively affected by the lowering of seawater pH. Isognomon alatus is an important food source, a substrate for other benthic organisms (e.g., stone crab, Menippe mercenaria) and contribute to nutrients recycling in coastal ecosystems. The study was conducted to test the impacts acidified seawater CO2 on the growth of I. alatus under controlled laboratory conditions as well as field experiment. The Isognomon alatus lost weight and experienced negative growth rates of –0.56 +- 0.36 mg /g/day under average pH values of 7.8 expected by the end of this century compared to a loss of –0.26 +- 0.23 mg/g/day under ambient pH (value 8.1) conditions. In contrast, I. alatus incubated in a field experiment showed a gain in weight and positive growth of 3.30 +- 0.23 mg/g/day despite exposure to pH levels (7.4) during low tide significantly lower than those experienced in the laboratory. Overall, the results showed concern on the impacts of acidification flat tree oyster (Bivalvia:Isognomonidae). A decline of calcifying bivalves populations can impact coastal ecosystems function and indirectly affect the human beings that depend on them as a food source

Seasonal oceanography from Physics to micronekton in the south-west pacific

International audienceTuna catches represent a major economic and food source in the Pacific Ocean, yet are highly variable. This variability in tuna catches remains poorly explained. The relationships between the distributions of tuna and their forage (micronekton) have been mostly derived from model estimates. Observations of micronekton and other mid-trophic level organisms, and their link to regional oceanography, however are scarce and constitute an important gap in our knowledge and understanding of the dynamics of pelagic ecosystems. To fill this gap, we conducted two multidisciplinary cruises (Nectalis1 and Nectalis2) in the New Caledonian Exclusive Economic Zone (EEZ) at the southeastern edge the Coral Sea, in 2011 to characterize the oceanography of the region during the cool (August) and the hot (December) seasons. The physical and biological environments were described by hydrology, nutrients and phytoplankton size structure and biomass. Zooplankton biomass was estimated from net sampling and acoustics and micronecton was estimated from net sampling, the SEAPODYM ecosystem model, a dedicated echosounder and non-dedicated acoustics. Results demonstrated that New Caledonia is located in an oligotrophic area characterized by low nutrient and low primary production which is dominated by a high percentage of picoplankton cyanobacteria Prochlorococcus (>90%). The area is characterized by a large-scale north-south temperature and salinity gradient. The northern area is influenced by the equatorial Warm Pool and the South Pacific Convergence Zone and is characterized by higher temperature, lower salinity, lower primary production and micronekton biomass. The southern area is influenced by the Tasman Sea and is characterized by cooler temperature, higher salinity, higher primary production and micronekton biomass. Interactions between the dynamic oceanography and the complex topography creates a myriad of mesoscale eddies, inducing patchy structures in the frontal area. During the cool season, a tight coupling existed between the ocean dynamics and primary production, while there was a stronger decoupling during the hot season. There was little difference in the composition of mid-trophic level organisms (zooplankton and micronekton) between the two seasons. This may be due to different turn-over times and delays in the transmission of primary production to upper trophic levels. Examination of various sampling gears for zooplankton and micronekton showed that net biomass estimates and acoustic-derived estimates compared reasonably well. Estimates of micronekton from net observations and the SEAPODYM model were in the same range. The non-dedicated acoustics adequately reproduced trends observed in zooplankton from nets, but the acoustics could not differentiate between zooplankton and micronekton and absolute biomasses could not be calculated. Understanding the impact of mesoscale features on higher trophic levels will require further investigation and patchiness induced by eddies raises the question of how to best sample highly dynamic areas via sea experiments

Effects of physical forcing on COastal ZOoplankton community structure: study of the unusual case of a MEDiterranean ecosystem under strong tidal influence (Project COZOMED-MERMEX).

International audienceThe COZOMED-MERMEX project aims at understanding how hydrodynamic forcing (currents, tides, winds)combine with anthropogenic forcing and climate to affect the variability of coastal Mediterranean zooplanktoncommunities under contrasting tidal influence. This study includes (i) a zero state of knowledge via a literaturereview of existing data and (ii) a case study on the system Boughrara lagoon - Gulf of Gabes. This ecosystemgives major services for Tunisia (about 65% of national fish production) but is weakened by its situation in aheavily anthropized area and under influence of urban, industrial and agricultural inputs. Besides this regionis subject to specific climate forcing (Sahelian winds, scorching heat, intense evaporation, flooding) whichpossible changes will be considered. The expected issues are (i) to improve our knowledge of hydrodynamicforcing on zooplankton and ultimately on the functioning of coastal Mediterranean ecosystems impacted byanthropogenic and climatic effects and (ii) to elaborate management tools to help preserving good ecologicalstatus of these ecosystems: hydrodynamic circulation model, mapping of isochrones of residence times, mappingof the areas of highest zooplankton abundances (swarms), and sensitive areas, etc. This project strengthensexisting scientific collaborations within the MERMEX program (The MerMex Group, 2011) and in the frameof an international joint laboratory (COSYS-Med) created in 2014. A first field mulidisciplinary campaign wasperformed in October 2016. The strategy combined measurements of sea level and currents (mooring of ADCP,Argonaute and tidal gauges), hydrological description of water masses (horizontal and vertical transect with aMinibat equipped with CTD, fluorescence and turbidity sensors) and discrete sampling of nutrients, DOC, POC,pico, nano, microphytoplankton and mesozooplankton. The first results allow a description of water currents andshows a good coupling between tidal cycles (ebb-flood and spring tide neap tide) and the dynamics of planktoniccompartments in the lagoon