Random allocation of blastomere descendants to the trophectoderm and ICM of the bovine blastocyst

The first lineage specification during mammalian embryo development can be visually distinguished at the blastocyst stage. Two cell lineages are observed on the embryonic-abembryonic axis of the blastocyst: the inner cell mass and the trophectoderm. The timing and mechanisms driving this process are still not fully understood. In mouse embryos, cells seem prepatterned to become certain cell lineage because the first cleavage plane has been related with further embryonic-abembryonic axis at the blastocyst stage. Nevertheless, this possibility has been very debatable. Our objective was to determine whether this would be the case in another mammalian species, the bovine. To achieve this, cells of in vitro produced bovine embryos were traced from the 2-cell stage to the blastocyst stage. Blastocysts were then classified according to the allocation of the labeled cells in the embryonic and/or abembryonic part of the blastocyst. Surprisingly, we found that there is a significant percentage of the embryos (∼60%) with labeled and nonlabeled cells randomly distributed and intermingled. Using time-lapse microscopy, we have identified the emergence of this random pattern at the third to fourth cell cycle, when cells started to intermingle. Even though no differences were found on morphokinetics among different embryos, these random blastocysts and those with labeled cells separated by the embryonic-abembryonic axis (deviant pattern) are significantly bigger; moreover deviant embryos have a significantly higher number of cells. Interestingly, we observed that daughter cells allocation at the blastocyst stage is not affected by biopsies performed at an earlier stage

Retrospective studies on rabbit haemorrhagic disease outbreaks caused by RHDV GI.2 virus on farms in France from 2013 to 2018

[EN] Rabbit haemorrhagic disease (RHD) is a critical health threat to the rabbit industry in Europe. In 2018, the French rabbit industry adopted a voluntary control plan against this disease. In this context, two epidemiological studies were conducted on RHD outbreaks that occurred between 2013 and 2018 in France. The objectives were to describe the spread of RHD due to the new genotype RHDV GI.2 (rabbit haemorrhagic disease virus GI.2) and to identify rearing factors influencing the occurrence of the disease in order to guide the prevention measures recommended in the control plan. An analysis of cases on 295 farms between 2013 and 2017 showed that 32% of farms were affected at least once; the incidence of the disease increased in 2016-2017 compared to 2013-2015. Farms already affected in 2013-2015 had a higher risk of being infected in 2016-2017 than those that remained unaffected until 2015 (Relative Risk and 95% Confident Interval 1.7 [1.1-2.7]). A case-control study carried out between 2016 and 2018 on 37 outbreaks and 32 control farms revealed variability in biosecurity and decontamination practices between farms. The risk of being infected tends to be linked to these practices, but certain structural factors (e.g. the manure disposal system, transfer of rabbits at weaning) could also influence the risk of virus introduction into farms. In the context of a limited vaccination coverage of the farms (only females are vaccinated), these hypotheses will be studied further, using information from the RHD outbreak monitoring system implemented at the same time as the control plan in 2018.This study was founded by the French Ministry of Agriculture (2017-430 / 170274).Huneau-Salaün, A.; Boucher, S.; Fontaine, J.; Le Normand, B.; Lopez, S.; Maurice, T.; Nouvel, L.... (2021). Retrospective studies on rabbit haemorrhagic disease outbreaks caused by RHDV GI.2 virus on farms in France from 2013 to 2018. World Rabbit Science. 29(2):87-98. https://doi.org/10.4995/wrs.2021.12800OJS8798292Abrantes J., Van der Loo W., Le Pendu J., Esteves P.J. 2012. Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review. Vet. Res., 43: 12.https://doi.org/10.1186/1297-9716-43-12Capucci L., Cavadini P., Schiavitto M., Lombardi G., Lavazza A. 2017. Increased pathogenicity in rabbit haemorrhagic disease virus type 2 (RHDV2). Vet. Record., 180: 426. https://doi.org/10.1136/vr.104132Carvalho C.L., Leclerc Duarte E., Monteiro J.M., Afonso C., Pacheco J., Carvalho P., Mendonça P., Botelho A., Albuquerque T., Themudo P., Fevereiro M., Henriques A.M., Santos Barros S., Dias Duarte M. 2017. Progression of rabbit haemorrhagic disease virus 2 upon vaccination in anindustrial rabbitry: a laboratorial approach. World Rabbit Sci., 25: 73-85. https://doi.org/10.4995/wrs.2017.5708Cooke B.D., Fenner F. 2002. Rabbit haemorrhagic disease and the biological control of wild rabbits, Oryctolagus Cuniculus, in Australia and New Zealand. Wildlife Res., 29: 689-706. https://doi.org/10.1071/WR02010Dalton K.P., Balseiro A., Juste R.A., Podadera A., Nicieza I., del Llano D., González R., Martin Alonso J.M., Prieto J.M., Parra F., Casais R. 2018. Clinical course and pathogenicity of variant rabbit haemorrhagic disease virus in experimentally infected adult and kit rabbits: Significance towards control and spread. Vet. Microbiol., 220: 24-32. https://doi.org/10.1016/j.vetmic.2018.04.033Dohoo I., Martin W., Stryhn H. 2003. Measures of disease frequency. In: Veterinary Epidemiologic Research, First Edition, AVC Inc., Charlottetown, Canada, 65-84.Hall R.N., Huang N., Roberts J., Strive T. 2019. Carrion flies as sentinels for monitoring lagovirus activity in Australia. Transboundary Emerg. Dis., 66: 2025-2032. https://doi.org/10.1111/tbed.13250Henning J., Meers J., Davies R., Morris R.S. 2005. Survival of rabbit haemorrhagic disease virus (RHDV) in the environment. Epidemiol. Infect., 133: 719-730. https://doi.org/10.1017/S0950268805003766Hurand J. 2016. L'élevage de lapins de chair en France, résultats technico-économiques 2015. Tema, 40.ITAVI. 2019. Situation de la filière cunicole. Novembre 2019. 6 p. Available athttps://www.itavi.asso.fr/content/note-deconjoncture-lapins-7Accessed December 2019.Le Gall-Reculé G., Zwingelstein F., Boucher S., Le Normand B., Plassiart G., Portejoie Y., Decors A., Bertagnoli S., Guérin J.L., Marchandeau S. 2011. Detection of a new variant of rabbit haemorrhagic disease virus in France. Vet. Rec., 168: 137- 138. https://doi.org/10.1136/vr.d697Le Gall-Reculé G., Lavazza A., Marchandeau S., Bertagnoli S., Zwingelstein F., Cavadini P., Martinelli N., Lombardi G., Guérin J.L., Lemaitre E., Decors A., Boucher S., Le Normand B., Capucci L. 2013. Emergence of a new lagovirus related to Rabbit haemorrhagic disease virus. Vet. Res., 44:81. https://doi.org/10.1186/1297-9716-44-81Le Gall-Reculé G., Boucher S. 2017. Connaissances et actualités sur la maladie hémorragique du lapin. In Proc.: 17èmes Journées de la Recherche Cunicole, 21-22 November, 2017. Le Mans, France. 97-109.Le Minor O., Joudou L., Le Moullec T., Beilvert F. 2017. Innocuité et efficacité de la vaccination à 2 et 3 semaines d'âge contre le virus RHDV2 de la maladie hémorragique virale du lapin (VHD). In Proc.:17èmes Journées de la Recherche Cunicole, 21-22 November, 2017. Le Mans, France. 127-130.Le Minor O., Boucher S., Joudou L., Mellet R., Sourice M., Le Moullec T., Nicoler A., Beilvert F., Sigognault-Flochlay A. 2019. Rabbit haemorrhagic disease: experimental study of a recent highly pathogenic GI.2/RJDV2/b strain and evaluation of vaccine efficacy. World Rabbit Sci., 27: 143-156.https://doi.org/10.4995/wrs.2019.11082Le Pendu J., Abrantes J., Bertagnoli S., Guitton J.S., Le Gall-Reculé G., Lopes A.M., Marchandeau S., Alda F., Almeida T., Célio A. C., Barcena J., Burmakina G., Blanco E., Calvete C., Cavadini P., Cooke B., Dalton K., Mateos M.D., Deptula W., Eden J.S., Wang F., Ferreira C.C., Ferreira P., Foronda P., Gonçalves D., Gavier-Widén D., Hall R., Hukowska-Szematowicz B., Kerr P., Kovaliski J., Lavazza A., Mahar J., Malogolovkin A., Marques R.M., Marques S., Martin-Alonso A., Monterroso P., MorenoS., Mutze G., Naimanis A., Niedzwiedzka-Rystwej P., Peacock D., Parra F., Rocchi M., Rouco C., Ruvoën-Clouet N., Silva E., Silvério D., Strive T., Thompson G., Tokarz-Deptula B., Esteves P. 2017. Proposal for a unified classification system and nomenclature of lagoviruses. J. Gen. Virol., 98: 1658-1666. https://doi.org/10.1099/jgv.0.000840Matthaei M., Kerr P.J., Read A.J., Hick P., Haboury S., Wright J.D., Strive T. 2014. Comparative quantitative monitoring of rabbit haemorrhagic disease viruses in rabbit kittens. Virol. J., 11: 109. https://doi.org/10.1186/1743-422X-11-109Mc Coll K.A., Merchant J.C., Hardy J., Cooke B.D., Robinson A., Westbury H.A. 2002. Evidence for insect transmission of rabbit haemorrhagic disease virus. Epidemiol. Infect., 129: 655-663. https://doi.org/10.1017/S0950268802007756Neimanis A.S., Larsson Pettersson U., Huang N., Gavier-Widen D., Strive T. 2018. Elucidation of the pathology and tissue distribution of Lagovirus europaeus GI.2/RHDV2 (rabbit haemorrhagic disease virus 2) in young and adult rabbits (Oryctolagus cuniculus). Vet. Res., 49:46. https://doi.org/10.1186/s13567-018-0540-zRosell J.M., de la Fuente L.F., Parra F., Dalton K.P., Badiola Sáiz J.I., Pérez de Rozas A., Badiola Díez J.J., Fernández de Luco D., Casal J., Majó N., Casas J., Garriga R., Fernández Magariños X.M. 2019. Myxomatosis and Rabbit Haemorrhagic Disease: A 30-Year Study of the Occurrence on Commercial Farms in Spain. Animals, 9: 780. https://doi.org/10.3390/ani9100780Rouco C., Aguayo-Adán J.A., Santoro S., Abrantes J., Delibes-Mateos M. 2019. Worldwide rapid spread of the novel rabbit haemorrhagic disease virus (GI.2/RHDV2/b). Transboundary Emerg. Dis., 66: 1762-1764.https://doi.org/10.1111/tbed.1318

Focal non granulomatous orchitis in a patient with Crohn’s disease

Crohn’s disease is a systemic disease and sometimes involves the testicle, usually leading to granulomatous lesions. We report herein a case of focal non-granulomatous orchitis in a 21-year-old patient with active Crohn’s disease treated by an anti-tumor necrosis factor monoclonal antibody. This circumscribed testicular lesion mimicked a tumor, leading to orchiectomy. Pre-operative blood tests (i.e. alpha-fetoprotein, lactate dehydrogenase and human chorionic gonadotrophin) were strictly normal Pathological examination of the testicle revealed a focal inflammatory infiltrate predominantly composed of lymphocytes accompanied by few plasma cells, lacking giant cells or granulomas. Importantly, intratubular germ cell neoplasia, atrophy or lithiasis were not observed. After discussing and excluding other plausible causes (burnt-out /regressed germ cell tumor, infection, vascular or traumatic lesions, iatrogenic effects), we concluded that this particular case of orchitis was most likely an extra-digestive manifestation of inflammatory bowel disease. To our knowledge, this is the first described case of focal non-granulomatous orchitis associated with Crohn’s disease. Virtual Slides: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/211774728416011

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%-43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical "Brownian motion" model and another model ("Ornstein-Uhlenbeck") that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%-43%) is consistent with other studies based on regression of viral load in donor-recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation.Peer reviewe

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 10$^{4}$ and 10$^{5}$ copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 10$^{5}$ copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 104 and 105 copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 105 copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.Peer Reviewe

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between-and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.Peer reviewe

A highly virulent variant of HIV-1 circulating in the Netherlands

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log(10) increase (i.e., a similar to 3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination. with increased transmissibility and an unfamiliar molecular mechanism of virulence