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

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Analysis of whistles produced by the Tucuxi Dolphin Sotalia fluviatilis from Sepetiba Bay, Brazil

From July 2001 to June 2002, we recorded a total of 2h55min of Tucuxi Dolphin Sotalia fluviatilis vocalizations from Sepetiba Bay, Brazil (22º35'S-44º03'W). A total of 3350 whistles were analyzed quantitative and qualitatively and were divided into 124 types, by visual inspection of sonograms. The following parameters were measured: Initial Frequency, Final Frequency, Minimum Frequency, Maximum Frequency, Duration, Number of Inflections, Frequency at the Inflection Points, Frequency at 1/2, 1/4, and 3/4 of whistle duration, Presence of Frequency Modulation and Harmonics. Ascending type whistles (N=2719) were most common, representing 82% of the total. Dolphin behavior and average group size observed during recording influenced the whistle's quantitative and qualitative parameters. The results demonstrate the great diversity of whistles emitted and indicate a functional role of these vocalizations during the observed behaviors

Behavioral event occurrence differs between behavioral states in Sotalia guianensis (Cetarctiodactyla: Delphinidae) dolphins: a multivariate approach

Difficulties in quantifying behavioral events can cause loss of information about cetacean behavior, especially behaviors whose functions are still debated. The lack of knowledge is greater for South American species such as Sotalia guianensis (Van Benédén, 1864). Our objective was to contextualize the behavioral events inside behavioral states using a Permutational Multivariate Analysis of Variance (MANOVA). Three events occurred in the Feeding, Socio-Sexual and Travelling states (Porpoising, Side flop, Tail out dive), and five events occurred in the Feeding and Travelling states (Back flop, Horizontal jump, Lobtail, Spy-hop, Partial flop ahead). Three events (Belly exposure, Club, and Heading) occurred exclusively in the Socio-sexual state. Partial Back flop and Head flop occurred exclusively in the Feeding state. For the events that occurred in multiple states, we observed that some events occurred more frequently in one of the states (p < 0.001), such as Lobtail, Tail out dive horizontal Jump, Partial flop ahead and Side flop. Our multivariate analysis, which separated Socio-sexual behavior from Feeding and Travelling, showed that the abundance of behavioral events differs between states. This differentiation indicates that some events are associated with specific behavioral states. Almost 40% of the events observed were exclusively performed in one state, which indicates a high specialization for some events. Proper discrimination and contextualization of behavioral events may be efficient tools to better understand dolphin behaviors. Similar studies in other habitats and with other species, will help build a broader scenario to aid our understanding of the functions of dolphin behavioral events

Coordinated feeding behavior of the Guiana dolphin, Sotalia guianensis (Cetacea: Delphinidae), in southeastern Brazil: a comparison between populations

The coordinated feeding tactics used by delphinids are influenced by differences in the distribution of prey species, season, and opportunities for social learning. In the present study, we compared the coordinated feeding behavior of two populations of the Guiana dolphin, Sotalia guianensis, in southeastern Brazil, and how these feeding tactics vary seasonality and in the presence of calves. We observed eight types of coordinated feeding tactics, which differed in frequency and in the mean number of individuals engaged in them, and between both areas. Feeding tactics used to herd and capture prey were the most frequent and engaged a greater number of individuals, suggesting that these tactics are better for capturing fish that gather in larger schools. Furthermore, the seasons influenced the occurrence of different prey items, which in turn modified the feeding tactics of the dolphins. In the Ilha Grande Bay we observed that bouts lasted longer and larger groups engaged in the feeding tactics, which may be associated with the seasonal spawning of larger schooling fish such as Sardinella brasiliensis (Steindachner, 1879) (Teleostei: Clupeidae). However, in the Sepetiba Bay, we observed longer feeding bouts and a smaller number of individuals engaged in the feeding tactics during autumn-winter. This may be associated with the fact that the most abundant prey species, Micropogonias furnieri (Desmarest, 1823) (Teleostei: Sciaenidae), gathers in small schools. Calves were present in 95% of all coordinated feeding tactics that occurred in the Ilha Grande Bay and in approximately 61% of feeding tactics in the Sepetiba Bay, suggesting that these areas are important for social learning. This study provides more information about feeding tactics and improves knowledge of the coordinated behavior of Sotalia guianensis (Van Benéden, 1864)