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

The Influence of Body Mass Index, Age and Sex on Inflammatory Disease Risk in Semi-Captive Chimpanzees

<div><p>Obesity and ageing are emerging issues in the management of captive primates, including Chimpanzees, <i>Pan troglodytes</i>. Studies on humans show that obesity and old age can independently increase the risk of inflammatory-associated diseases indicated by elevated levels of pro-inflammatory cells and proteins in the blood of older or obese compared to levels in younger or non-obese individuals. In humans, sex can influence the outcomes of these risks. Health management of these problems in chimpanzee populations requires an understanding of similarities and differences of factors influencing inflammatory disease risks in humans and in chimpanzees. We examined the relationship between age, sex and Body Mass Index (BMI) with hematological biomarkers of inflammatory disease risk established for humans which include the neutrophil to lymphocyte ratio (NLR), and neutrophil, white blood cell (WBC), platelet microparticle and platelet counts. We found that higher values of NLR, neutrophil count and platelet microparticle count were associated with higher BMI values and older age indicating increased inflammation risk in these groups; a similar pattern to humans. There was a strong sex by age interaction on inflammation risk, with older males more at risk than older females. In contrast to human studies, total WBC count was not influenced by BMI, but like humans, WBC and platelet counts were lower in older individuals compared to younger individuals. Our findings are similar to those of humans and suggest that further insight on managing chimpanzees can be gained from extensive studies of ageing and obesity in humans. We suggest that managing BMI should be an integral part of health management in captive chimpanzee populations in order to partially reduce the risk of diseases associated with inflammation. These results also highlight parallels in inflammation risk between humans and chimpanzees and have implications for understanding the evolution of inflammation related diseases in apes.</p></div

Coefficients showing the influence of age, BMI and sex on the proportion of lymphocytes.

<p>Coefficients showing the influence of age, BMI and sex on the proportion of lymphocytes.</p

Coefficients showing the influence of age, BMI and sex on platelet microparticles.

<p>Coefficients showing the influence of age, BMI and sex on platelet microparticles.</p

Model coefficients for the influence of age, BMI on the proportion of neutrophils.

<p>Model coefficients for the influence of age, BMI on the proportion of neutrophils.</p

Coefficients showing the influence of age, BMI and sex on blood platelets.

<p>Coefficients showing the influence of age, BMI and sex on blood platelets.</p

Coefficients showing the influence of age, BMI and sex on WBCs.

<p>Coefficients showing the influence of age, BMI and sex on WBCs.</p

Spatio-temporal variation in prevalence of Rift Valley fever : a post-epidemic serum survey in cattle and wildlife in Kenya

BACKGROUND: Rift Valley fever (RVF) is a fatal arthropod-borne zoonotic disease of livestock and humans. Since the identification of RVF in Kenya in the 1930s, repeated epizootics and epidemics coinciding with El Niño events have occurred in several locations in Africa and Saudi Arabia, causing mass deaths of livestock and humans. RVF is of great interest worldwide because of its negative effect on international livestock trade and its potential to spread globally. The latter is due to the increasing incidence of extreme climatic phenomena caused by global warming, as well as to the increase in global trade and international travel. How RVF is maintained and sustained between epidemics and epizootics is not clearly understood, but it has been speculated that wildlife reservoirs and trans-ovarian transmission in the vector may be important. Several studies have examined the role of wildlife and livestock in isolation or in a limited geographical location within the one country over a short time (usually less than a year). In this study, we examined the seroprevalence of anti-RVF antibodies in cattle and several wildlife species from several locations in Kenya over an inter-epidemic period spanning up to 7 years. METHODS: A serological survey of immunoglobulin G (IgG) antibodies to RVF using competitive ELISA was undertaken on 297 serum samples from different wildlife species at various locations in Kenya. The samples were collected between 2008 and 2015. Serum was also collected in 2014 from 177 cattle from Ol Pejeta Conservancy; 113 of the cattle were in close contact with wildlife and the other 64 were kept separate from buffalo and large game by an electric fence. RESULTS: The seroprevalence of RVF virus (RVFV) antibody was 11.6% in wildlife species during the study period. Cattle that could come in contact with wildlife and large game were all negative for RVFV. The seroprevalence was relatively high in elephants, rhinoceros, and buffalo, but there were no antibodies in zebras, baboons, vervet monkeys, or wildebeest. CONCLUSIONS: Diverse species in conservation areas are exposed to RVFV. RVFV exposure in buffalo may indicate distribution of the virus over wide geographical areas beyond known RVFV foci in Kenya. This finding calls for thorough studies on the epizootology of RVFV in specific wildlife species and locations

Shifting reasons for older men remaining uncircumcised: Findings from a pre- and post-demand creation intervention among men aged 25-39 years in western Kenya.

Voluntary medical male circumcision (VMMC) reduces men's risk of acquiring Human immunodeficiency virus (HIV) through vaginal sex. However, VMMC uptake remains lowest among Kenyan men ages 25-39 years among whom the impact on reducing population-level HIV incidence was estimated to be greatest at the start of the study in 2014. We conducted a pre- and post-intervention survey as part of a cluster randomized controlled trial to determine the effect of two interventions (interpersonal communication (IPC) and dedicated service outlets (DSO), delivered individually or together) on improving VMMC uptake among men ages 25-39 years in western Kenya between 2014 and 2016. The study had three intervention arms and a control arm. In arm one, an IPC toolkit was used to address barriers to VMMC. In arm two, men were referred to DSO that were modified to address their preferences. Arm three combined the IPC and DSO. The control arm had standard of care. At baseline, uncircumcised men ranked the top three reasons for remaining uncircumcised. An IPC demand creation toolkit was used to address the identified barriers and men were referred for VMMC at study-designated facilities. At follow-up, those who remained uncircumcised were again asked to rank the top three reasons for not getting circumcised. There was inconsistency in ranking of reported barriers at pre- and post- intervention: 'time/venue not convenient' was ranked third at baseline and seventh at follow-up; 'too busy to go for circumcision' was tenth at baseline but second at follow-up, and concern about 'what I/family will eat' was ranked first at both baseline and follow-up, but the proportion reduced from 62% to 28%. Men ages 25-39 years cited a variety of logistical and psychosocial barriers to receiving VMMC. After exposure to IPC, most of these barriers shifted while some remained the same. Additional innovative interventions to address on-going and shifting barriers may help improve VMMC uptake among older men