Leprosy in wild chimpanzees

Humans are considered as the main host for Mycobacterium leprae1, the aetiological agent of leprosy, but spillover has occurred to other mammals that are now maintenance hosts, such as nine-banded armadillos and red squirrels2,3. Although naturally acquired leprosy has also been described in captive nonhuman primates4-7, the exact origins of infection remain unclear. Here we describe leprosy-like lesions in two wild populations of western chimpanzees (Pan troglodytes verus) in Cantanhez National Park, Guinea-Bissau and Taï National Park, Côte d'Ivoire, West Africa. Longitudinal monitoring of both populations revealed the progression of disease symptoms compatible with advanced leprosy. Screening of faecal and necropsy samples confirmed the presence of M. leprae as the causative agent at each site and phylogenomic comparisons with other strains from humans and other animals show that the chimpanzee strains belong to different and rare genotypes (4N/O and 2F). These findings suggest that M. leprae may be circulating in more wild animals than suspected, either as a result of exposure to humans or other unknown environmental sources

Stronger maternal social bonds and higher rank are associated with accelerated infant maturation in Kinda baboons

Social relationships are critical components of health and fitness for humans and other animals. For female-philopatric species, affiliative relationships among females (kin and nonkin alike) can influence components of fitness that include individual survival, interbirth interval and offspring survival. Affiliative relationships with males have attracted somewhat less attention, with most studies focusing on female–male relationships as adaptations for infanticide avoidance. Here, we use 8 years of behavioural data on Kinda baboons, Papio kindae, to assess whether maternal social relationships—both among females and between females and males—affect infant survival, interbirth interval and the pace of infant development. Kinda baboons are an ideal system for these analyses because males and females form strong relationships outside of the periovulatory period and in the absence of obvious infanticide threat. We calculated social metrics that reflected dominance status, total social integration and social bond strength and paired these metrics with data on offspring survival, interbirth interval (IBI) duration and infant behavioural maturation. Neither dominance rank nor sociality had a significant effect on interbirth interval or survival, but higher rank and the stronger affiliative relationships between a female and her top female and top male social partners predicted more rapid infant behavioural maturation. These results suggest that maternal dominance and sociality may confer advantages related to infant development and independence that ultimately may permit females to more quickly invest in subsequent offspring and point to advantages of relationships with males outside of lowering infanticide threat

Application of Conservation and Veterinary Tools in the Management of Stray Wildlife in Zambia

In recent years, Zambia has seen an increase in the incidences of conflicts involving stray wild animals with humans. Notable among these animals include the African elephants, buffalo and lion. Consequently, this triggers a response from law enforcement units of both government and the department of national parks to control the animals. Regrettably, most of their responses have involved the shooting down of these animals, rather than taking advantage of conservation and veterinary tools to relocate the animals back into protected areas, and this raises concerns about the welfare of these animals. Therefore, this chapter will bring to light some of the locally available tools that could be used to control stray wildlife in order to contribute towards both conservation and reducing human-wildlife conflicts in Zambia

Yaws Disease Caused by Treponema pallidum subspecies pertenue in Wild Chimpanzee, Guinea, 2019

Yaws-like lesions are widely reported in wild African great apes, yet the causative agent has not been confirmed in affected animals. We describe yaws-like lesions in a wild chimpanzee in Guinea for which we demonstrate infection with Treponema pallidum subsp. pertenue. Assessing the conservation implications of this pathogen requires further research

Luna Virus and Helminths in Wild Mastomys natalensis in Two Contrasting Habitats in Zambia: Risk Factors and Evidence of Virus Dissemination in Semen

Transmission dynamics and the maintenance of mammarenaviruses in nature are poorly understood. Using metagenomic next-generation sequencing (mNGS) and RT-PCR, we investigated the presence of mammarenaviruses and co-infecting helminths in various tissues of 182 Mastomys natalensis rodents and 68 other small mammals in riverine and non-riverine habitats in Zambia. The Luna virus (LUAV) genome was the only mammarenavirus detected (7.7%; 14/182) from M. natalensis. Only one rodent from the non-riverine habitat was positive, while all six foetuses from one pregnant rodent carried LUAV. LUAV-specific mNGS reads were 24-fold higher in semen than in other tissues from males. Phylogenetically, the viruses were closely related to each other within the LUAV clade. Helminth infections were found in 11.5% (21/182) of M. natalensis. LUAV-helminth co-infections were observed in 50% (7/14) of virus-positive rodents. Juvenility (OR = 9.4; p = 0.018; 95% CI: 1.47-59.84), nematodes (OR = 15.5; p = 0.001; 95% CI: 3.11-76.70), cestodes (OR = 10.8; p = 0.025; 95% CI: 1.35-86.77), and being male (OR = 4.6; p = 0.036; 95% CI: 1.10-18.90) were associated with increased odds of LUAV RNA detection. The role of possible sexual and/or congenital transmission in the epidemiology of LUAV infections in rodents requires further study, along with the implications of possible helminth co-infection

Mosquito-Borne Viral Pathogens Detected in Zambia: A Systematic Review

Emerging and re-emerging mosquito-borne viral diseases are a threat to global health. This systematic review aimed to investigate the available evidence of mosquito-borne viral pathogens reported in Zambia. A search of literature was conducted in PubMed and Google Scholar for articles published from 1 January 1930 to 30 June 2020 using a combination of keywords. Eight mosquito-borne viruses belonging to three families, Togaviridae, Flaviviridae and Phenuiviridae were reported. Three viruses (Chikungunya virus, Mayaro virus, Mwinilunga virus) were reported among the togaviruses whilst four (dengue virus, West Nile virus, yellow fever virus, Zika virus) were among the flavivirus and only one virus, Rift Valley fever virus, was reported in the Phenuiviridae family. The majority of these mosquito-borne viruses were reported in Western and North-Western provinces. Aedes and Culex species were the main mosquito-borne viral vectors reported. Farming, fishing, movement of people and rain patterns were among factors associated with mosquito-borne viral infection in Zambia. Better diagnostic methods, such as the use of molecular tools, to detect the viruses in potential vectors, humans, and animals, including the recognition of arboviral risk zones and how the viruses circulate, are important for improved surveillance and design of effective prevention and control measures

First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries

Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 h of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient’s SARS-CoV-2 strain showed that it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa

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

Genomik infektiöser bakterieller Hauterkrankungen bei wilden nichtmenschlichen Primaten: Gieren und Lepra

Yaws-like disease in non-human primates (NHPs) caused by Treponema pallidum subsp. pertenue (TPE) has been largely reported in sub-Saharan Africa with diverse dermatological manifestations. However, it remained unclear how the genomic diversity of TPE lineages that do occur in NHPs is distributed across hosts and space. In Taï National Park (TNP), Côte d’Ivoire, symptomatic Cercocebus atys monkeys were observed to have yaws- and syphilislike lesions. The present study investigated the TPE diversity in wild NHPs in TNP and other sites where the disease occurs in sub-Saharan Africa. Phylogenomic analyses from this study revealed that dermatological pathology observed among sooty mangabeys in TNP were caused by a large diversity of TPE lineages. All TPE genomes determined from these sooty mangabeys were different and exhibited divergence levels not observed in other field sites where the disease seems to be epizootic. The results presented in this dissertation, do not support the epizootic spread of a single TPE clone at TNP, but rather points towards frequent independent introductions of the bacterium, which can cause orofacial and genital-like lesions within a single social group of Cercocebus atys monkeys. Besides, simian TPE isolates determined in this study and those available in the public domain, did not form monophyletic clades based on host species or the type of symptoms caused by an isolate, but rather clustered based on geography. This phylogenetic pattern is compatible with cross-species transmission of TPE within ecosystems where this disease occurs, though it remains unclear how often and by what means this transmission occurs. This study now lays basis for future studies on the potential occurrence of TPE transmission among different NHP species and future studies should aim to reveal transmission pathways of TPE in NHP habitats. This work also demonstrates that informative TPE genomic data can be obtained from old NHPs bones collected from endemic areas; helping to trace the disease back into the past as well as identify new sites that might be affected by the disease where no clinical cases are currently observed. Thus, using bone derived TPE short sequences coupled with phylogenetic read placement algorithm, this study showed that TPE infected NHPs in TNP for at least three decades ago, complementing clinical evidence which only started accumulating from 2014. Additionally, detection of TPE in field sites were no clinical cases are observed indicates that TPE infections in NHPs are underreported, warranting the intensive surveillance of the disease in wild NHPs. In the second part, this study aimed to investigate the causative agent of leprosy-like symptoms observed in NHPs in both Cantanhez National Park and Täi National Park. The investigations involved adapting a suitable non-invasive screening tool to facilitate the determination and characterisation of the causative agent of the observed skin lesions. Using faecal samples, this study determined that M. leprae was the cause of the leprosy- like lesions confirming the first ever observed sylvatic leprosy cases among NHPs in West Africa. This finding shows that faecal samples of NHP that are easily collected, can be used for surveillance of leprosy in wild NHPs and have the potential for scalability in terms of screening huge populations over large areas. Further, this study also presents sequence data highlighting that wild chimpanzees are infected with two genotypes of Mycobacterium leprae that are rare in human populations i.e. 4N/O and 2F and could potentially serve as reservoir hosts of these rare genotypes. For the first time, genotype 2F of M. leprae that circulated mostly in the medieval time in Europe was detected in West Africa. The detection of 2F in a region dominated by genotype 4 M. leprae strains questions the current understanding that the infection in NHPs was a result of a human strains spill overs. Finally, it is now evident that M. leprae is not only a human pathogen since red squirrels, armadillos and NHPs are also naturally infected. Therefore, investigations into the role these animal reservoir hosts play in the ecology of leprosy disease might be useful in informing strategies on the ongoing leprosy eradication campaign by WHO.Es gibt eine vielzahl von Berichten über eine gierartige Krankheit bei nicht-menschlichen Primaten (NHPs), die durch Treponema pallidum subsp. pertenue (TPE) verursacht wird und in ihren verschiedenen dermatologischen Ausprägungen aus weiten Teilen der Subsahararegion Afrikas. Es blieb jedoch bislang unklar wie die genomische Vielfalt der NHPspezifischen TPE-Linien über Wirte und Raum verteilt ist. Im Taï-Nationalpark (TNP), Côte d'Ivoire, wurden symptomatische Rußmangaben (Cercocebus atys atys atys) mit gier- und syphilisähnlichen Läsionen beobachtet. Im Zusammenhang dazu untersucht die vorliegende Studie die Diversität von TPE bei wilden NHPs in TNP und anderen Standorten, an denen die Krankheit in Subsahara-Afrika auch zuvor aufgetreteten is. Phylogenomische Analysen aus dieser Studie zeigten, dass das dermatologische Krankheitsbild von Rußmangaben in TNP, durch eine große Vielfalt von TPE-Linien verursacht wird. Alle TPE-Genome, die aus dieser Mangabenart isoliert werden konnten, waren unterschiedlich und zeigten deutlich andere Divergenzniveaus als bisher für eine einzige Spezies an einem Feldforschungsort, an dem die Krankheit vermutlich epizootisch ist, beobachtet werden konnte. Die in dieser Arbeit vorgestellten Ergebnisse unterstützen nicht die epizootische Ausbreitung eines einzelnen TPE-Klons, sondern weisen stattdessen auf häufige unabhängige Einführungen des Bakteriums hin, die syphilis- und gierähnliche Läsionen innerhalb einer einzigen sozialen Gruppe von Rußmangaben verursachen können. Desweiteren bilden die in dieser Studie bearbeiteten Isolate von simianem TPE keine monophyletischen Kladen mit den bislang veröffentlichten Vergleichsgenomen auf der Grundlage ihrer Wirtsarten oder Art der Symptome, sondern in Bezug auf ihre Geographie. Dieses phylogenetische Muster ist einhergehend mit der artenübergreifenden Übertragung von TPE in denjenigen Ökosystemen, in denen die Krankheit auftritt. Es bleibt allerdings unklar, wie oft und auf welche Weise diese Übertragung stattfindet. Diese Studie bildet nun die Grundlage für zukünftige Studien über das mögliche Auftreten der TPE-Übertragung bei NHPs. Diese Arbeit zeigt auch, dass wertvolle TPE Genomdaten aus alten NHP-Knochen aus endemischen Gebieten gewonnen werden können. Dies kann helfen die Krankheit in die Vergangenheit zurückverfolgen und neue Standorte zu identifizieren, die in der Gegenwart oder Zukunft von der Krankheit betroffen sein könnten, auch wenn zum jetzigen Zeitpunkt keine klinischen Fälle bekannt sind. So zeigte diese Studie unter Verwendung von knochenabgeleiteten TPE-Kurzsequenzen in Verbindung mit einem phylogenetischen Leseplatzierungsalgorithmus , dass TPE in TNP für mindestens drei Jahrzehnte NHPs infiziert hat und ergänzt damit klinische Beweise, die sich erst ab 2014 zu sammeln begannen. Darüber hinaus zeigt der Nachweis von TPE in Freilandanlagen, in denen offiziell keine klinischen Fälle beobachtet werden, dass TPE-Infektionen in NHPs weitgehend unbemerkt bleiben, was eine intensive Überwachung der Krankheit bei wilden NHPs rechtfertigt. Im zweiten Teil zielte diese Studie darauf ab, den Erreger lepraähnlicher Symptome zu untersuchen, die bei NHPs im Cantanhez Nationalpark und im Täi Nationalpark beobachtet wurden. Die Untersuchungen umfassten die Anpassung eines geeigneten nicht-invasiven Screeningtools, um die Bestimmung und Charakterisierung des Erregers der beobachteten Hautläsionen zu erleichtern. Anhand von Stuhlproben konnte in dieser Studie festgestellt werden, dass M. leprae die Ursache für die lepraähnlichen Läsionen war und somit die ersten jemals beobachteten sylvatischen Leprafälle bei NHPs in Westafrika bestätigten. Dieses Ergebnis zeigt, dass Fäkalproben von NHP, die ohne große Schwierigkeiten gesammelt werden können, zur Überwachung der Lepra bei wilden NHPs verwendet werden können und das Potenzial für Skalierbarkeit beim Screening großer Populationen über große Gebiete haben. Darüber hinaus stellt diese Studie auch Sequenzdaten vor, die zeigen, dass wilde Schimpansen mit zwei Genotypen von Mycobacterium leprae infiziert sind, die in menschlichen Populationen selten sind. Dabei handelt es sich um 4O-P und 2F, und somit besteht die Möglichkeit, dass Schimpansen als Reservoirwirte dieser seltenen Genotypen dienen könnten. Zum ersten Mal wurde in Westafrika der Genotyp 2F von M. leprae entdeckt, der hauptsächlich im Mittelalter in Europa zirkulierte. Der Nachweis von 2F in einer Region, die vom Genotype 4 M. leprae dominiert wird, stellt das aktuelle Verständnis in Frage, dass die Infektion in NHPs das Ergebnis einer Übertragung vom Menschen waren. Abschließend ist inzwischen evident, dass M. leprae nicht nur ein menschlicher Erreger ist, da auch rote Eichhörnchen, Gürteltiere und NHPs auf natürlichem Wege infiziert werden können. Somit könnten Untersuchungen über die Rolle dieser Tiere als Reservoirwirte bei der Ökologie der Leprakrankheit nützlich sein, um Strategien für die Leprabekämpfung zu entwickeln