The phylogeography of Indoplanorbis exustus (Gastropoda: Planorbidae) in Asia

<p>Abstract</p> <p>Background</p> <p>The freshwater snail <it>Indoplanorbis exustus </it>is found across India, Southeast Asia, central Asia (Afghanistan), Arabia and Africa. <it>Indoplanorbis </it>is of economic importance in that it is responsible for the transmission of several species of the genus <it>Schistosoma </it>which infect cattle and cause reduced livestock productivity. The snail is also of medical importance as a source of cercarial dermatitis among rural workers, particularly in India. In spite of its long history and wide geographical range, it is thought that <it>Indoplanorbis </it>includes only a single species. The aims of the present study were to date the radiation of <it>Indoplanorbis </it>across Asia so that the factors involved in its dispersal in the region could be tested, to reveal potential historical biogeographical events shaping the phylogeny of the snail, and to look for signs that <it>I. exustus </it>might be polyphyletic.</p> <p>Results</p> <p>The results indicated a radiation beginning in the late Miocene with a divergence of an ancestral bulinine lineage into Assam and peninsular India clades. A Southeast Asian clade diverged from the peninsular India clade late-Pliocene; this clade then radiated at a much more rapid pace to colonize all of the sampled range of <it>Indoplanorbis </it>in the mid-Pleistocene.</p> <p>Conclusions</p> <p>The phylogenetic depth of divergences between the Indian clades and Southeast Asian clades, together with habitat and parasitological differences suggest that <it>I. exustus </it>may comprise more than one species. The timescale estimated for the radiation suggests that the dispersal to Arabia and to Southeast Asia was facilitated by palaeogeographical events and climate change, and did not require human involvement. Further samples from Afghanistan, Africa and western India are required to refine the phylogeographical hypothesis and to include the African Recent dispersal.</p

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control

DNA-Sequence Variation Among Schistosoma mekongi Populations and Related Taxa; Phylogeography and the Current Distribution of Asian Schistosomiasis

Schistosomiasis is a disease caused by parasitic worms of the genus Schistosoma. In the lower Mekong river, schistosomiasis in humans is called Mekong schistosomiasis and is caused by Schistosoma mekongi. In the past, Mekong schistosomiasis was known only from the lower Mekong river. Here DNA-sequence variation is used to study the relationships and history of populations of S. mekongi. Populations from other rivers are compared and shown to be S. mekongi, thus confirming that this species is not restricted to only a small section of one river. The dates of divergence among populations are also estimated. Prior to this study it was assumed that S. mekongi originated in Yunnan, China, migrated southwards across Laos and into Cambodia, later becoming extinct in Laos (due to conditions unsuitable for transmission). In contrast, the dates estimated here indicate that S. mekongi entered Cambodia from Vietnam, 2.5–1 Ma. The pattern of genetic variation fits better with a more recent, and ongoing, northwards migration from Cambodia into Laos. The implications are that Mekong schistosomiasis is more widespread than once thought and that the human population at risk is up to 10 times greater than originally estimated. There is also an increased possibility of the spread of Mekong schistosomiasis across Laos

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.

Funder: Oxford Martin School, University of OxfordThe response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the 'real-time' generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data production has necessitated the development of new analytical methods that can deal with orders of magnitude of more genomes than previously available. Here, we present and describe Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin), a computational tool that has been developed to assign the most likely lineage to a given SARS-CoV-2 genome sequence according to the Pango dynamic lineage nomenclature scheme. To date, nearly two million virus genomes have been submitted to the web-application implementation of pangolin, which has facilitated the SARS-CoV-2 genomic epidemiology and provided researchers with access to actionable information about the pandemic's transmission lineages

Author correction : Divergence across mitochondrial genomes of sympatric members of the 'Schistosoma indicum' group and clues into the evolution of 'Schistosoma spindale'

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Governance and Susceptibility in Conflict Resolution: Possibilities Beyond Control

Governmentality analysis offers a nuanced critique of informal Western conflict resolution by arguing that recently emerged alternatives to adversarial court processes both govern subjects and help to constitute rather than challenge formal regulation. However, this analysis neglects possibilities for transforming governance from within conflict resolution that are suggested by Foucault's contention that there are no relations of power without resistances. To explore this lacuna, I theorise and explore the affective and interpersonal nature of governance in mediation through autoethnographic reflection upon mediation practice, and Levina's insights about the relatedness of selves. The paper argues that two qualitatively different mediator capacities - technical ability and susceptibility - operate in concert to effect liberal governance. Occasionally though, difficulties and failures in mediation practice bring these capacities into tension and reveal the limits of governance. By considering these limits in mediation with Aboriginal Australian people, I argue that the susceptibility of mediator selves contains prospects for mitigating and transforming the very operations of power occurring through conflict resolution. This suggests options for expanded critical thinking about power relations operating through informal processes, and for cultivating a susceptible sensibility to mitigate liberal governance and more ethically respond to difference through conflict resolution

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods - recursive partitioning and regression - to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; Pcombined = 2.01 × 10-19 and 2.35 × 10-13, respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. ©2007 Nature Publishing Group

How to select patients for anti-reflux surgery? The ICARUS guidelines (International Consensus regarding preoperative examinations and clinical characteristics assessment to select adult patients for AntiReflUx Surgery)

Objective: Anti-reflux surgery can be proposed in patients with gastro-esophageal reflux disease, especially when proton pump inhibitor use leads to incomplete symptom improvement. However, to date, international consensus guidelines on the clinical criteria and additional technical examinations used in patient selection for anti-reflux surgery are lacking. We aimed at generating key recommendations in the selection of patients for anti-reflux surgery. Design: We included 35 international experts (gastroenterologists, surgeons and physiologists) in a Delphi process and developed 37 statements that were revised by the Consensus Group, to start the Delphi process. Three voting rounds followed where each statement was presented with the evidence summary. The panel indicated the degree of agreement for the statement. When 80% of the Consensus Group agreed (A+/A) with a statement, this was defined as consensus. All votes were mutually anonymous.Results: Patients with heartburn with a satisfactory response to PPIs, patients with a hiatal hernia (HH), patients with esophagitis LA grade B or higher and patients with Barrett’s esophagus are good candidates for anti-reflux surgery. An endoscopy prior to anti-reflux surgery is mandatory and a barium swallow should be performed in patients with suspicion of a HH or short esophagus. Esophageal manometry is mandatory to rule out major motility disorders. Finally, esophageal pH (+/- impedance) monitoring off PPI is mandatory to select patients for anti-reflux surgery, if endoscopy is negative for unequivocal reflux esophagitis. Conclusion: With the ICARUS guidelines, we generated key recommendations for selection of patients for anti-reflux surgery