Première nidification réussie du Flamant rose Phoenicopterus roseus dans la vallée de l’Oued Righ (Sahara algérien)

Après une première tentative échouée en 2009, le Flamant rose a réussi sa reproduction en 2010-2011 dans le Chott Merouane, situé dans le nord–est du Sahara algérien. Cette colonie est installée sur un vaste lac saumâtre situé à une altitude de 41m en dessous du niveau de la Méditerranée. Elle présente notamment la caractéristique d’être construite directement dans l’eau et non pas sur un îlot. Cette colonie est l’une des six découvertes en Algérie depuis 2003. Par son importance (2954 nids en 2011), elle est la deuxième d’Algérie et d’Afrique du nord. Les colonies algériennes accueillent actuellement 12.5% (le huitième) de l’effectif de la métapopulation méditerranéenne de l’espèce. Elles sont notamment menacées en premier lieu par des risques d’assèchement accrus en raison du changement climatique et du développement anarchique de l’agriculture (vergers de dattiers et d’oliviers en particulier).Mots clés: Flamant rose - Phoenicopterus roseus - Reproduction - Zone humide - Chott Merouane - Algérie The Greater Flamingo carried out a successful breeding in Chott Merouane in 2010-2011 after its first failure in 2009. Situated in Northeast Algerian Sahara at 41 m below sea level, this colony is set in a vast brackish Lake. It presents an important feature of being set directly on the water without an apparent islet. This colony is among the six Algerian ones that have yet been discovered since 2003. Considering its size (2.954 nests in 2011), it can be ranked as the second largest colony in Algeria as well as North Africa. Algerian colonies currently host approximately 12.5% (1/8) of the Mediterranean metapopulation size of the Greater Flamingo. These colonies are threatened not only by severe dryness risks due to global climate change but also by an uncontrolled agricultural development (date palm and olive orchards).Keyswords: Greater Flamingo, Phoenicopterus roseus - Breeding, Wetland - Chott Merouane - Algeri

Semantic Mutation Testing for Multi-Agent Systems

This paper introduces semantic mutation testing (SMT) into multiagent systems. SMT is a test assessment technique that makes changes to the interpretation of a program and then examines whether a given test set has the ability to detect each change to the original interpretation. These changes represent possible misunderstandings of how the program is interpreted. SMT is also a technique for assessing the robustness of a program to semantic changes. This paper applies SMT to three rule-based agent programming languages, namely Jason, GOAL and 2APL, provides several contexts in which SMT for these languages is useful, and proposes three sets of semantic mutation operators (i.e., rules to make semantic changes) for these languages respectively, and a set of semantic mutation operator classes for rule-based agent languages. This paper then shows, through preliminary evaluation of our semantic mutation operators for Jason, that SMT has some potential to assess tests and program robustness

Multispacer Sequence Typing Relapsing Fever Borreliae in Africa

In Africa, relapsing fevers are caused by four cultured species: Borrelia crocidurae, Borrelia duttonii, Borrelia hispanica and Borrelia recurrentis. These borreliae are transmitted by the bite of Ornithodoros soft ticks except for B. recurrentis which is transmitted by louse Pediculus humanus. They cause potentially undifferentiated fever infection and co-infection with malaria could also occur. The exact prevalence of each Borrelia is unknown and overlaps between B. duttonii and B. crocidurae have been reported. The lack of tools for genotyping these borreliae limits knowledge concerning their epidemiology. We developed multispacer sequence typing (MST) and applied it to blood specimens infected by B. recurrentis (30 specimens), B. duttonii (18 specimens) and B. crocidurae (13 specimens), delineating these 60 strains and the 3 type strains into 13 species-specific spacer types. B. crocidurae strains were classified into 8 spacer types, B. duttonii into 3 spacer types and B. recurrentis into 2 spacer types. These findings provide the proof-of-concept that that MST is a reliable tool for identification and genotyping relapsing fever borreliae in Africa

Variations of Plasmid Content in Rickettsia felis

Background: Since its first detection, characterization of R. felis has been a matter of debate, mostly due to the contamination of an initial R. felis culture by R. typhi. However, the first stable culture of R. felis allowed its precise phenotypic and genotypic characterization, and demonstrated that this species belonged to the spotted fever group rickettsiae. Later, its genome sequence revealed the presence of two forms of the same plasmid, physically confirmed by biological data. In a recent article, Gillespie et al. ( PLoS One. 2007; 2( 3): e266.) used a bioinformatic approach to refute the presence of the second plasmid form, and proposed the creation of a specific phylogenetic group for R. felis. Methodology/ Principal Findings: In the present report, we, and five independent international laboratories confirmed unambiguously by PCR the presence of two plasmid forms in R. felis strain URRWXCal(2)(T), but observed that the plasmid content of this species, from none to 2 plasmid forms, may depend on the culture passage history of the studied strain. We also demonstrated that R. felis does not cultivate in Vero cells at 37 degrees C but generates plaques at 30 degrees C. Finally, using a phylogenetic study based on 667 concatenated core genes, we demonstrated the position of R. felis within the spotted fever group. Significance: We demonstrated that R. felis, which unambiguously belongs to the spotted fever group rickettsiae, may contain up to two plasmid forms but this plasmid content is unstable

Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

BACKGROUND: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). METHODOLOGY/PRINCIPAL FINDINGS: We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (approximately 1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. CONCLUSION/SIGNIFICANCE: Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets

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

Premières données sur la structure et l’écologie des populations de la Foulque macroule Fulica atra (Rallidés) dans les zones humides de la région d’El-Kala (Nord-Est de l’Algérie)

Au niveau des zones humides du Nord-Est de l’Algérie, la Foulque macroule Fulica atra (Rallidés) est une espèce composée de deux populations différentes, une sédentaire nicheuse et une hivernante. La population nicheuse est composée de 510 à 1000 couples et en période hivernale, avec l’arrivée des populations hivernantes, l’effectif total fluctue entre 20.000 et 50.000 individus dans l’ensemble des zones humides. Le bilan des rythmes d’activités diurnes de cette espèce est dominé par une alimentation accrue relatant le rôle de gagnage de ces hydrosystèmes. Cette alimentation peut être observée souvent avec des taux variant entre 65 et 68% en période hivernale et 80-86% pendant la période de reproduction. L’approvisionnement diurne peut être exercé sur les berges ou dans l’eau libre, soit par basculement du corps, ou par immersion du bec ou de la tête de l’oiseau.Mots clés: Fulica atra - El-Kala - Hivernage - Reproduction - Rythmes d’activités. In northeast Algerian wetlands, the Common coot Fulica atra is structured in two different populations, a breeding population and a wintering one. The breeding population counts for 510 to 1000 breeding pairs but it increases up to 20.000 and 50.000 individuals, considering all wetlands, during the winter after the arrival of the migrant wintering population. The diurnal activity rhythms is dominated by an important feeding rate describing the feeding role of these hydrosystems. In winter, feeding activity is often observed with rates varying between 65 and 68% relating to global activity rhythms and between 82 and 86% during the breeding season. This diurnal supply may be displayed on the banks or in the water, either by tilting the body, or by dipping the beak or the head of the bird.Keywords: Fulica atra - El-Kala – Wintering – Breeding – Activity rhythm