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

Early Mode of Life and Hatchling Size in Cephalopod Molluscs: Influence on the Species Distributional Ranges

27 pages, 4 figures, 3 tablesCephalopods (nautiluses, cuttlefishes, squids and octopuses) exhibit direct development and display two major developmental modes: planktonic and benthic. Planktonic hatchlings are small and go through some degree of morphological changes during the planktonic phase, which can last from days to months, with ocean currents enhancing their dispersal capacity. Benthic hatchlings are usually large, miniature-like adults and have comparatively reduced dispersal potential. We examined the relationship between early developmental mode, hatchling size and species latitudinal distribution range of 110 species hatched in the laboratory, which represent 13% of the total number of live cephalopod species described to date. Results showed that species with planktonic hatchlings reach broader distributional ranges in comparison with species with benthic hatchlings. In addition, squids and octopods follow an inverse relationship between hatchling size and species latitudinal distribution. In both groups, species with smaller hatchlings have broader latitudinal distribution ranges. Thus, squid and octopod species with larger hatchlings have latitudinal distributions of comparatively minor extension. This pattern also emerges when all species are grouped by genus (n = 41), but was not detected for cuttlefishes, a group composed mainly of species with large and benthic hatchlings. However, when hatchling size was compared to adult size, it was observed that the smaller the hatchlings, the broader the latitudinal distributional range of the species for cuttlefishes, squids and octopuses. This was also valid for all cephalopod species with benthic hatchlings pooled together. Hatchling size and associated developmental mode and dispersal potential seem to be main influential factors in determining the distributional range of cephalopodsFAFA was supported by a predoctoral fellowship (BES-2013-063551) of the Spanish Ministry of Economy and Competiveness; URL: http://www.mineco.gob.es/portal/site/mineco?lang_choosen=en. EAGV was funded by the Brazilian National Research Council – Conselho Nacional de Desenvolvimento Científico e Tecnológico (Grants no. 250017/2013-0; 207680/2014-0); URL: http://www.cnpq.br/. RV was funded by the Spanish Ministry of Education and Culture (Grant no. PRX15/00100); URL: http://www.mecd.gob.es/portada-mecd/ and by the Spanish Ministry of Economy and Competiveness (Grant no. AGL2012-39077, CALOCEAN-2); URL: http://www.mineco.gob.es/portal/site/mineco?lang_choosen=enPeer Reviewe

Cephalopod culture: Current status of main biological models and research priorities

Vidal, Erica A.G. ... et. al.- 98 pages, 23 figures, 3 tablesA recent revival in using cephalopods as experimental animals has rekindled interest in their biology and life cycles, information with direct applications also in the rapidly growing ornamental aquarium species trade and in commercial aquaculture production for human consumption. Cephalopods have high rates of growth and food conversion, which for aquaculture translates into short culture cycles, high ratios of production to biomass and high cost-effectiveness.However, at present, only small-scale culture is possible and only for a few species: the cuttlefish Sepia officinalis, the loliginid squid Sepioteuthis lessoniana and the octopuses Octopus maya and O. vulgaris. These four species are the focus of this chapter, the aims of which are as follows: (1) to provide an overview of the culture requirements of cephalopods, (2) to highlight the physical and nutritional requirements at each phase of the life cycle regarded as essential for successful full-scale culture and (3) to identify current limitations and the topics on which further research is required.Knowledge of cephalopod culture methods is advanced, but commercialization is still constrained by the highly selective feeding habits of cephalopods and their requirement for large quantities of high-quality (preferably live) feed, particularly in the early stages of development. Future research should focus on problems related to the consistent production of viable numbers of juveniles, the resolution of which requires a better understanding of nutrition at all phases of the life cycle and better broodstock management, particularly regarding developments in genetic selection, control of reproduction and quality of eggs and offspring. © 2014 Elsevier Ltd.EAGV was supported by the Brazilian National Research Council (CNPq-Pro. 485653/2012-5). RV was funded by the research project CALOCEAN-2 (AGL2012-39077) from the Ministry of Economy and Competitiveness of Spain (MINECO). [...] IGG is supported by the Japan Science and Technology Agency Grant No. J130000263Peer Reviewe

Yolk utilization, metabolism and growth in reared

To understand the mechanisms that influence recruitment of the commercially important chokka squid Loligo vulgaris reynaudii, knowledge of its early life history is required. This paper evaluates the influence of food supply on yolk utilization, metabolism and growth of paralarvae. Eggs collected on the spawning grounds were incubated and the paralarvae reared in the laboratory under “fed” and “starved” conditions for 22 d at 16 ± 1 °C. Some paralarvae lasted 42 d in the laboratory. Mantle length (ML), wet and dry weights (WW and DW) and yolk weight (YW) were measured daily from samples of ~30 (10−51) paralarvae from each group. Yolk weight was estimated using image analysis to determined yolk volume. Three methods (growth model, O2 consumption rates and yolk utilization rates) were used to estimate metabolic rates. Input parameters included daily mean wet weight of paralarvae and temperature. Mean ML, WW, DW and YW at hatching were found to be 2.3 mm, 1.86 mg, 0.45 mg and 0.21 mg, respectively. The experiment revealed that daily yolk utilization rates were 86 and 95% d−1 for fed and starved paralarvae respectively, and that the yolk reserve was almost exhausted 3−4 d after hatching. Starved paralarvae survived for 6 days (with 80% mortality), while fed paralarvae attained a growth rate of 7.8% body WW d−1 over the first 22 days after hatching. Results illustrate that temperatures on the chokka squid spawning grounds allow paralarvae to grow at the fastest rates possible without being subjected to a growth “slow down” caused by a high temperature dependent imbalance between sustaining high metabolic and commitment high feeding rates

Early mode of life and hatchling size in cephalopods: influence on the species distributional ranges

Cephalopod International Advisory Council (CIAC) Conference, 10-14 November 2015, Hakodate, JapanPeer Reviewe

Towards the identification of the ommastrephid squid paralarvae (Mollusca: Cephalopoda): morphological description of three species and a key to the north‐east Atlantic species

20 pages, 4 figures, 4 tables, supporting information https://doi.org/10.1111/zoj.12496Oceanic squids of the family Ommastrephidae are an important fishing resource worldwide. Although cumulative knowledge exists on their subadult and adult forms, little is known about their young stages. Their hatchlings are among the smaller cephalopod paralarvae. They are characterized by the fusion of their tentacles into a proboscis and are very difficult to identify to species level, especially in areas where more than one species coexist. Seven species are found in the north-east (NE) Atlantic. In this study, mature oocytes of Illex coindetii, Todarodes sagittatus and Todaropsis eblanae were fertilized in vitro to obtain and describe hatchlings. Full descriptions based on morphometric characters, chromatophore patterns, skin sculpture and the structure of proboscis suckers are provided based on live specimens. This information was combined with previous descriptions of paralarvae, not necessarily based on DNA or known parentage, from four other ommastrephid species distributed in the same area and a dichotomous key was developed for the identification of paralarvae of the NE Atlantic. The most useful taxonomic characters were: the relative size of the lateral and medial suckers of the proboscis, the presence/absence of photophores and the arrangement of pegs on the proboscis suckers. This key was successfully used to identify wild collected rhynchoteuthion paralarvae from the NE Atlantic. Reliable identification of wild paralarvae can foster a better understanding of the population dynamics and life cycles of ommastrephid squidsThe Sthenoteuthis pteropus specimen was collected on board the RV Hesperides during the research project MAFIA (CTM2012-39587-C04-03), funded by the Spanish Ministry of Economy and Competitiveness (MINECO). [...] F.A.F.A. was supported by a Predoctoral Fellowship of the MINECO (BES-2013–063551). E.A.G.V was supported by the Brazilian National Research Council-CNPq (grant nos. 207680/2014-0, 250017/2013-0). This study was funded by the research projects CALOCEAN-1 (AGL2009-11546) and CALOCEAN-2 (AGL2012-39077) from the MINECOPeer reviewe

The genus Ommastrephes d’Orbigny 1834: a single species or more than one hidden behind a single name?

Cephalopod International Advisory Council (CIAC) Conference, 10-14 November 2015, Hakodate, JapanThe genus Ommastrephes d'Orbigny, 1834 in 1834–1847 is currently accepted to be formed only by a widely distributed species: O. bartramii (Lesueur, 1821). According to its known antitropical distribution, the species occur in temperate waters of the Atlantic, Pacific and Indian Oceans. Current taxonomic status proposed that O. bartramii is formed by three different populations/subspecies distributed in the North Atlantic, Southern Hemisphere and in the North Pacific, respectively. Here, all the available published cytochrome oxidase I information for ommastrephid squids plus new sequences are integrated, reanalyzed and the reliability for the use of DNA barcoding in the whole family is evaluated. Among ommastrephids, intraspecific p-distances range from 0-2 % and the interspecific from 3.2-23.4 % suggesting the presence of a barcoding gap. The available information for Ommastrephes from both the North and South Pacific waters was compared with recently obtained Atlantic specimens, suggesting the existence of more than one species within this oceanic genusPeer Reviewe

Las primeras etapas de vida de los calamares oceánicos y su estudio a través de fecundación in vitro

9 figures, 1 tableLos cefalópodos (nautilos, calamares, sepias y pulpos) es un grupo de animales con una biología reproductiva dispar: desde animales longevos que realizan varias puestas hasta otros que se reproducen unas pocas veces al final de su fugaz vida. La mayoría de los cefalópodos actuales son representantes de este segundo grupo. Algunos cefalópodos colocan sus huevos en lugares relativamente accesibles para los investigadores, sin embargo, los calamares oceánicos realizan puestas en mar abierto, por lo que estudiar su desarrollo es realmente difícil. Una alternativa al estudio de puestas salvajes es realizar fertilizaciones in vitro y estudiar su descendencia en condiciones controladas de laboratorioFernando Ángel Fernández-Álvarez recibe un Contrato Predoctoral para la Formación de Doctores del Ministerio de Economía y Competitividad (MINECO). La investigación está financiada por el MINECO bajo los proyectos CALOCEAN-1 (AGL2009-11546) y CALOCEAN-2 (AGL2012-39077)Peer Reviewe

Future challenges in cephalopod research

Cephalopods (Mollusca: Cephalopoda) play an important role as keystone invertebrates in various marine ecosystems, as well as being a valuable fisheries resource. At the World Malacological Congress, held 21 - 28 July 2013 in Ponta Delgada, Azores, Portugal, a number of cephalopod experts convened to honour the contribution of the late Malcolm R. Clarke, FRS (1930 - 2013) to cephalopod research. Endorsed by the Cephalopod International Advisory Council (CIAC), the meeting discussed some of the major challenges that cephalopod research will face in the future. These challenges were identified as follows: (1) to find new ways to ascertain the trophic role and food web links of cephalopods using hard tissues, stable isotopes and novel concepts in theoretical ecology; (2) to explore new approaches to the study of cephalopod morphology; (3) to further develop cephalopod aquaculture research; (4) to find new ways to ascertain cephalopod adaptation and response to environmental change; (5) to strengthen cephalopod genetics research; and (6) to develop new approaches for cephalopod fisheries and conservation. The present paper presents brief reviews on these topics, followed by a discussion of the general challenges that cephalopod research is bound to face in the near future. By contributing to initiatives both within CIAC and independent of CIAC, the principle aim of the paper is to stimulate future cephalopod research