Current EOV Report

Merged satellite/in-situ surface current products and impact of AtlantOS observation

Genetic diversity of[i] Rhizoctonia solani[/i] associated with potato tubers in France

Affiche, résuméThe plant pathogenic soil-borne fungus Rhizoctonia solani causes severe damages in crops all around the world. Tubers of potato are frequently affected by R. solani leading to the downgrading of the production. Generally the isolates involved in the sclerotia occurring at the surface of the tuber are assigned to the anastomosis group (AG) 3 but a more precise characterization of the diversity of this deleterious group is needed to set up appropriate control strategies. The diversity of 73 French isolates from the mains potato seed production areas and 31 isolates originating from 9 other countries was assessed according to 3 molecular approaches. Three phylogenetic trees were built up based on the sequences of the internal transcribed spacer (ITS) region and the gene tef-1α as well as the comparison of the total DNA fingerprints of each strain established by amplified fragment length polymorphism (AFLP). The determination of the AGs of R. solani based on the sequencing of the ITS region showed 3 different AGs among our collection (60 AG 3, 8 AG 2-1 and 5 AG 5). Grouping of the isolates belonging to the same AG was confirmed by the sequencing of the gene tef-1α used for the first time to study the genetic diversity of R. solani. About 42 % of the ITS sequences and 73 % of the gene tef-1α sequences contained polymorphic sites where several nucleotides are possible, suggesting that the cells of R. solani strains contain several copies of ITS and gene tef-1α within the same nucleus or between different nuclei. Phylogenetic trees showed a greater genetic diversity within AGs in tef-1α sequences than in ITS sequences. The AFLP analyses showed an even greater diversity among the strains demonstrating that the French strains of R. solani isolated from potatoes were not a clonal population. Moreover, there was no relationship between the geographical origins of the strains or the potato variety from which they were isolated and their genetic diversity. This important and under evaluated genetic diversity as the lack of population structure suggest important genetic mixings leading to a constant evolution within R. solani and could explain the difficulties to control it successfully

Effects of habitat and land use on breeding season density of male Asian Houbara Chlamydotis macqueenii

Landscape-scale habitat and land-use influences on Asian Houbara Chlamydotis macqueenii (IUCN Vulnerable) remain unstudied, while estimating numbers of this cryptic, low-density, over-hunted species is challenging. In spring 2013, male houbara were recorded at 231 point counts, conducted twice, across a gradient of sheep density and shrub assemblages within 14,300 km² of the Kyzylkum Desert, Uzbekistan. Four sets of models related male abundance to: (1) vegetation structure (shrub height and substrate); (2) shrub assemblage; (3) shrub species composition (multidimensional scaling); (4) remote-sensed derived land-cover (GLOBCOVER, 4 variables). Each set also incorporated measures of landscape rugosity and sheep density. For each set, multi-model inference was applied to generalised linear mixed models of visit-specific counts that included important detectability covariates and point ID as a random effect. Vegetation structure received strongest support, followed by shrub species composition and shrub assemblage, with weakest support for the GLOBCOVER model set. Male houbara numbers were greater with lower mean shrub height, more gravel and flatter surfaces, but were unaffected by sheep density. Male density (mean 0.14 km-2, 95% CI, 0.12‒0.15) estimated by distance analysis differed substantially among shrub assemblages, being highest in vegetation dominated by Salsola rigida (0.22 [CI, 0.20‒0.25]), high in areas of S. arbuscula and Astragalus (0.14 [CI, 0.13‒0.16] and 0.15 [CI, 0.14‒0.17] respectively), lower (0.09 [CI, 0.08‒0.10]) in Artemisia and lowest (0.04 [CI, 0.04‒0.05]) in Calligonum. The study area was estimated to hold 1,824 males (CI: 1,645‒2,030). The spatial distribution of relative male houbara abundance, predicted from vegetation structure models, had the strongest correspondence with observed numbers in both model-calibration and the subsequent year’s data. We found no effect of pastoralism on male distribution but potential effects on nesting females are unknown. Density differences among shrub communities suggest extrapolation to estimate country- or range-wide population size must take account of vegetation composition

Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification.

BACKGROUND: The large and constantly evolving HIV-1 pandemic has led to an increasingly complex diversity. Because of some taxonomic difficulties among the most diverse HIV-1 subtypes, and taking advantage of the large amount of sequence data generated in the recent years, we investigated novel lineage patterns among the main HIV-1 subtypes. RESULTS: All HIV full-length genomes available in public databases were analysed (n = 2017). Maximum likelihood phylogenies and pairwise genetic distance were obtained. Clustering patterns and mean distributions of genetic distances were compared within and across the current groups, subtypes and sub-subtypes of HIV-1 to detect and analyse any divergent lineages within previously defined HIV lineages. The level of genetic similarity observed between most HIV clades was deeply consistent with the current classification. However, both subtypes A and D showed evidence of further intra-subtype diversification not fully described by the nomenclature system at the time and could be divided into several distinct sub-subtypes. CONCLUSIONS: With this work, we propose an updated nomenclature of sub-types A and D better reflecting their current genetic diversity and evolutionary patterns. Allowing a more accurate nomenclature and classification system is a necessary step for easier subtyping of HIV strains and a better detection or follow-up of viral epidemiology shifts

HIV-2 diversity displays two clades within group A with distinct geographical distribution and evolution

Genetic diversity of HIV-2 groups A and B has not yet been fully described, especially in a few Western Africa countries such as Ivory-Coast or Mali. We collected 444 pol, 152 vif, 129 env, and 74 LTR sequences from patients of the French ANRS CO5 HIV-2 cohort completed by 221 pol, 18 vif, 377 env, and 63 LTR unique sequences from public databases. We performed phylogenetic reconstructions and revealed two distinct lineages within HIV-2 group A, herein called A1 and A2, presenting non-negligible genetic distances and distinct geographic distributions as A1 is related to coastal Western African countries and A2 to inland Western countries. Estimated early diversification times for groups A and B in human populations were 1940 [95% higher probability densitiy: 1935-53] and 1961 [1952-70]. A1 experienced an early diversification in 1942 [1937-58] with two distinct early epidemics in Guinea-Bissau or Senegal, raising the possibility of group A emergence in those countries from an initial introduction from Ivory-Coast to Senegal, two former French colonies. Changes in effective population sizes over time revealed that A1 exponentially grew concomitantly to Guinea-Bissau independence war, but both A2 and B lineages experienced a latter growth, starting during the 80s economic crisis. This large HIV-2 genetic analysis provides the existence of two distinct subtypes within group A and new data about HIV-2 early spreading patterns and recent epidemiologic evolution for which data are scarce outside Guinea-Bissau

Effects of habitat and livestock on nest productivity of the Asian houbara Chlamydotis macqueenii in Bukhara Province, Uzbekistan

To inform population support measures for the unsustainably hunted Asian houbara Chlamydotis macqueenii (IUCN Vulnerable) we examined potential habitat and land-use effects on nest productivity in the Kyzylkum Desert, Uzbekistan. We monitored 177 nests across different semi-arid shrub assemblages (clay-sand and salinity gradients) and a range of livestock densities (0–80 km-2). Nest success (mean 51.4%, 95% CI 42.4–60.4%) was similar across four years; predation caused 85% of those failures for which the cause was known, and only three nests were trampled by livestock. Nesting begins within a few weeks of arrival when food appears scarce, but later nests were more likely to fail owing to the emergence of a key predator, suggesting foraging conditions on wintering and passage sites may be important for nest productivity. Nest success was similar across three shrub assemblages and was unrelated to landscape rugosity, shrub frequency or livestock density, but was greater with taller mean shrub height (range 13–67 cm) within 50 m. Clutch size (mean = 3.2 eggs) and per-egg hatchability in successful nests (87.5%) did not differ with laying date, shrub assemblage or livestock density. We therefore found no evidence that livestock density reduced nest productivity across the range examined, while differing shrub assemblages appeared to offer similar habitat quality. Asian houbara appear well-adapted to a range of semi-desert habitats and tolerate moderate disturbance by pastoralism. No obvious in situ mitigation measures arise from these findings, leaving regulation and control as the key requirement to render hunting sustainable

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

Interindividual clinical variability in the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is vast. We report that at least 101 of 987 patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia had neutralizing immunoglobulin G (IgG) autoantibodies (auto-Abs) against interferon-w (IFN-w) (13 patients), against the 13 types of IFN-a (36), or against both (52) at the onset of critical disease; a few also had auto-Abs against the other three type I IFNs. The auto-Abs neutralize the ability of the corresponding type I IFNs to block SARS-CoV-2 infection in vitro. These auto-Abs were not found in 663 individuals with asymptomatic or mild SARS-CoV-2 infection and were present in only 4 of 1227 healthy individuals. Patients with auto-Abs were aged 25 to 87 years and 95 of the 101 were men. A B cell autoimmune phenocopy of inborn errors of type I IFN immunity accounts for life-threatening COVID-19 pneumonia in at least 2.6% of women and 12.5% of men

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

Impact of genetic variability within Long Terminal Repeat region and integrase gene on HIV-2 replication

Le VIH-2 est souvent considéré comme un modèle d’infection rétrovirale atténuée, du fait de sa faible réplication virale, des faibles taux de transmission et de la progression plus lente vers le stade SIDA des patients infectés. Les mécanismes causaux de cette moindre physiopathologie sont encore mal connus. Dans ce travail, nous nous sommes intéressés à la diversité du VIH-2, notamment dans deux régions génomiques : l’intégrase et la région Long Terminal Repeat (LTR). Nous avons tout d’abord amélioré la technique classique d’isolement de souches virales afin de disposer de davantage de souches de VIH-2, en purifiant les échantillons de patients avec des billes anti-CD44. Ensuite, nous avons utilisé ces souches pour étudier la sensibilité aux inhibiteurs de transfert de brin de l’intégrase, ou INSTI. Au cours de ce travail, nous avons mis en évidence un nouveau mécanisme de résistance aux INSTI chez le VIH-2, l’insertion de 5 acides aminés après le codon 231 du gène de l’intégrase. Cette insertion est responsable d’une résistance importante au raltegravir (RAL), à l’elvitegravir (EVG), au cabotegravir (CAB), ainsi qu’une résistance modérée au dolutegravir (DTG). La sensibilité au bictegravir (BIC) était conservée pour certains isolats porteurs de cette insertion. Une insertion de deux acides aminés a aussi été observée transitoirement chez un patient. Nous avons confirmé ces observations phénotypiques en construisant des virus porteurs de ces insertions par mutagénèse dirigée. L’insertion, qu’elle soit de 2 ou de 5 acides aminés, n’était pas responsable d’une perte de capacité réplicative, à l’exception du mutant avec l’insertion GIRGK.En revanche, la structure prédite de l’intégrase est fortement modifiée, avec notamment la perte d’un des deux feuillets bêta composant le tonneau bêta du domaine C-terminal.La sensibilité phénotypique des mutants a été déterminée, pour les insertions de 5 acides aminés, les résultats étaient similaires à ceux obtenus avec les isolats cliniques. Nous avons aussi pu déterminer la sensibilité du mutant avec l’insertion GK, qui était sensible au BIC et au DTG, mais déjà pleinement résistant à RAL et au CAB. Dans la dernière partie de notre travail, nous avons étudié la variabilité dans la région LTR des provirus de 66 patients naïfs d’antirétroviraux, inclus dans la cohorte ANRS CO5 VIH-2. La variabilité génétique était plus importante dans les séquences du groupe B, du fait notamment de nombreuses insertions et délétions dans la sous-région «régulatrice» comprenant l’ensemble des sites de fixation de facteurs de transcription cellulaire. Ces virus du groupe B présentaient une délétion de quelques nucléotides dans la région contenant les sites de fixation PuB1 et pets, causant une perte de ce dernier site de fixation. De plus, 4 provirus du groupe B présentaient une délétion du premier site de fixation du facteur de transcription ubiquitaire Sp1. Cette variabilité entraînait des conséquences sur l’activité transcriptionnelle de ces LTR. Les LTR du groupe A et du groupe B présentaient la même activité transcriptionnelle basale mais, dans les cellules Jurkat, après activation cellulaire, l’activité transcriptionnelle des LTR du groupe B et d’un LTR de groupe A dans lequel la zone contenant la délétion de pets a été insérée était 10 fois plus faible que celle du LTR de groupe A. La délétion du premier site de fixation de Sp1 diminuait l’activité transcriptionnelle basale dans les cellules Jurkat et la réponse à la transactivation par la protéine virale Tat dans les cellules HEK293T.HIV-2 is oftenconsidered as an attenuated model of HIV-1 infection. Indeed, HIV-2 is characterized by its lower viral replication, reduced transmission rates and a slower progression towards AIDS of infected-patients. Mechanisms implied in HIV-2 reduced pathogenicity are not entirely understood. In our work, we have focused on HIV-2 diversity, especially in two genomic regions: the integrase and the Long Terminal Repeat (LTR) region.We have improved the culture method, by purifying clinical samples using anti-CD44 paramagnetic beads. This allowed us to increase the number of viral strains in our collection. Then, we used those strains to study phenotypic susceptibility to integrase strand transfer inhibitors (INSTI). During this study, we identified a new molecular mechanism of resistance to INSTI, a 5 amino-acids insertion after codon 231 of HIV-2 integrase. This insertion was responsible for a high level of resistance to raltegravir (RAL), elvitegravir (EVG), cabotegravir (CAB), and a slight increase in the resistance todolutegravir (DTG). Certain isolates harboring this insertion remained susceptible to bictegravir (BIC).A 2 amino-acids insertion was also transiently observed in one patient. We have confirmed those phenotypic data by constructing HIV-2 mutants by site-directed mutagenesis. Whether the insertion was composed of 2 or 5 amino-acids, replicative capacitywas similar to the wild-type virus, except for the mutant with a GIRGK insertion. However, the predicted structure of mutated HIV-2 integrases was modified, notably in the C-terminal domain, due to the loss of one of the two beta sheets composing the beta barrel. Phenotypic susceptibility of mutants was determined and results for HIV-2 mutants witha 5 amino-acids insertion were similar to those obtained with clinical isolates.We also determined the susceptibility of the mutant with a GK insertion. It was susceptible to BIC and DTG, but already resistant to RAL and CAB. In the last part of our work, we have characterized genetic variability within LTR region in 66 antiretroviral-naïve patients, included in the French ANRS CO5 HIV-2 cohort.Genetic variability was higher among group B sequences, due to a high number of insertions and deletions in the «regulatory» sub-region that encompasses all transcription factor binding sites. All group B viruses presented a short deletion in the region encompassing PuB1 andpets binding sites, causing the loss of the pets binding site.Furthermore, 4 group B viruses had also a deletion of the first binding site of Sp1 transcription factor. This variability impacted LTR transcriptional activity. Group A and B LTRs presented asimilar basal transcriptional activity but, in Jurkat cells, after cellular activation, transcriptional activities of group B LTR and a group A LTR in which the deletion of pets binding site has been introduced were 10-fold lower than the transcriptional activity of an intact group A LTR. The deletion of the first Sp1 binding site reduced the basal transcriptional activity in Jurkat cells and the response to transactivation by the viral protein Tat in HEK293T