The tuberculosis challenge in a rural South African HIV programme.

BACKGROUND: South Africa remains the country with the greatest burden of HIV-infected individuals and the second highest estimated TB incidence per capita worldwide. Within South Africa, KwaZulu-Natal has one of the highest rates of TB incidence and an emerging epidemic of drug-resistant tuberculosis. METHODS: Review of records of consecutive HIV-infected people initiated onto ART between 1st January 2005 and 31st March 2006. Patients were screened for TB at initiation and incident episodes recorded. CD4 counts, viral loads and follow-up status were recorded; data was censored on 5th August 2008. Geographic cluster analysis was performed using spatial scanning. RESULTS: 801 patients were initiated. TB prevalence was 25.3%, associated with lower CD4 (AHR 2.61 p = 0.01 for CD4 25 copies/ml (OR 1.75 p = 0.11). A low-risk cluster for incident TB was identified for patients living near the local hospital in the geospatial analysis. CONCLUSION: There is a large burden of TB in this population. Rate of incident TB stabilises at a rate higher than that of the overall population. These data highlight the need for greater research on strategies for active case finding in rural settings and the need to focus on strengthening primary health care

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

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

Parker_et_al_2012

Linear (mm) measures of the forearm, and weight (mg) of the body and testes of quacking frogs collected from 10 natural populations in Western Australi

Alternation of nest visits varies with experimentally manipulated workload in brood-provisioning great tits

In species with biparental care, the amount of care devoted to offspring is affected by the negotiation rules that the parents adopt. Recently, turn taking in provisioning visits has been proposed as a negotiation rule by which parents respond to their partner's behaviour, which results in a perfect alternation of the nest visits by the parents. Empirical evidence suggests that parents do not strictly alternate their visits, and, so far, this imperfect alternation has received no experimental investigation. In this study, we tested whether alternation of nest visits might be subject to time constraints affecting the ability of parents to strictly take turns. We manipulated the workload of 15 great tit, Parus major, pairs using a short-term brood size manipulation. Parental nest visits alternated more in reduced than control and enlarged broods. To understand whether this variability could be caused by changes in turn taking, we explored the rate and regularity of the parents' intervisit intervals. Treatment differences in alternation were still present when controlling for the rate and regularity of the visits by each of the two parents, suggesting that workload also affected alternation via the temporal sequence of the intervals (e.g. via turn taking). Our results show that alternation of nest visits varies in response to workload and is not merely a by-product of variation in visit rate or regularity.</p

Alternation of nest visits varies with experimentally manipulated workload in brood-provisioning great tits

In species with biparental care, the amount of care devoted to offspring is affected by the negotiation rules that the parents adopt. Recently, turn taking in provisioning visits has been proposed as a negotiation rule by which parents respond to their partner's behaviour, which results in a perfect alternation of the nest visits by the parents. Empirical evidence suggests that parents do not strictly alternate their visits, and, so far, this imperfect alternation has received no experimental investigation. In this study, we tested whether alternation of nest visits might be subject to time constraints affecting the ability of parents to strictly take turns. We manipulated the workload of 15 great tit, Parus major, pairs using a short-term brood size manipulation. Parental nest visits alternated more in reduced than control and enlarged broods. To understand whether this variability could be caused by changes in turn taking, we explored the rate and regularity of the parents' intervisit intervals. Treatment differences in alternation were still present when controlling for the rate and regularity of the visits by each of the two parents, suggesting that workload also affected alternation via the temporal sequence of the intervals (e.g. via turn taking). Our results show that alternation of nest visits varies in response to workload and is not merely a by-product of variation in visit rate or regularity

Insights on dispersal and recruitment paradigms: sex- and age-dependent variations in a nomadic breeder

Correction DOI: 10.1007/s00442-017-4001-6 (WOS:000419477800010)International audienceSex- and age-dependence in recruitment and dispersal are often explained by costs arising from competition for holding a breeding territory over the years-a typical feature of species living in stable habitats. For instance, long-lived birds with male territoriality often exhibit large variation in recruitment age and higher dispersal in females and young individuals. As a corollary, we expected that species with ephemeral habitat suitability, and hence nomadic breeding, would show weak age- and sex-dependence in dispersal and low variation in recruitment age, because territory ownership is not maintained over the years. In addition, the higher cost of reproduction in females might not be (over)compensated for by costs of territoriality in males. Accordingly, females would recruit later than males. We explored these variations using multievent capture-recapture models over 13 years, 3479 (2392 sexed) slender-billed gulls (Chroicocephalus genei) and 45 colony sites along the French Mediterranean coast. As expected, variability in recruitment age was low with males recruiting earlier than females. Nonetheless, dispersal in and out of the study area decreased with age and was slightly higher in males than in females. Decreased dispersal with age might result from foraging benefits associated with increased spatial familiarity. Higher dispersal in males might be explained by a male-biased sex ratio or higher philopatry benefits in females (arising from their higher cost of reproduction). Sex- and age-dependent dispersal and recruitment may thus occur in the absence of year-to-year breeding territory ownership, which stresses the importance of considering other processes in shaping recruitment and dispersal patterns

Data availability and model complexity, generality, and utility: A reply to Lonergan

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