Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover, is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, co-circulating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semi-independent epidemiological niches that are not regionally or seasonally defined. Typically, intra-lineage mutational signatures are similar to inter-lineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage-defining. The persistence of virus lineages appears to stem from limited outbreaks within small communities so that only a minor fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.SignificanceNumerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential of causing new pandemics? We show that most human pathogenic RNA viruses form multiple, co-circulating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that a minor fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics.

Challenges and Costs of Asexuality: Variation in Premeiotic Genome Duplication in Gynogenetic Hybrids from Cobitis taenia Complex

The transition from sexual reproduction to asexuality is often triggered by hybridization. The gametogenesis of many hybrid asexuals involves premeiotic genome endoreplication leading to bypass hybrid sterility and forming clonal gametes. However, it is still not clear when endoreplication occurs, how many gonial cells it affects and whether its rate differs among clonal lineages. Here, we investigated meiotic and premeiotic cells of diploid and triploid hybrids of spined loaches (Cypriniformes: Cobitis) that reproduce by gynogenesis. We found that in naturally and experimentally produced F1 hybrids asexuality is achieved by genome endoreplication, which occurs in gonocytes just before entering meiosis or, rarely, one or a few divisions before meiosis. However, genome endoreplication was observed only in a minor fraction of the hybrid’s gonocytes, while the vast majority of gonocytes were unable to duplicate their genomes and consequently could not proceed beyond pachytene due to defects in bivalent formation. We also noted that the rate of endoreplication was significantly higher among gonocytes of hybrids from natural clones than of experimentally produced F1 hybrids. Thus, asexuality and hybrid sterility are intimately related phenomena and the transition from sexual reproduction to asexuality must overcome significant problems with genome incompatibilities with a possible impact on reproductive potential.

The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses

The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.Short abstract (needed in some journals as eLife)The viromes of the mammalian gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing stabled horses, and feral horses that were isolated on an island. The viromes equine fecal viromes feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes were identified. Additionally, many bacteriophage genus-level clusters were found to be present in geographically isolated populations. Only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways.Importance. (needed for mBio)The study presents the first in depth analysis of the composition and variability of the gut dsDNA bacteriophage community in the mammalian species, other than humans. The study demonstrates that the bacteriophage ecology in the gut is substantially different in different animal species. The results also indicate that the genetic diversity of the equine intestinal bacteriophages is immense and almost totally unexplored by the moment.

CD4+ T cells persist for years in the human small intestine and mediate robust TH1 immunity

Studies in mice and humans have shown that CD8+ T cell immunosurveillance in non-lymphoid tissues is dominated by resident populations. Whether CD4+ T cells use the same strategies to survey peripheral tissues is less clear. Here, examining the turnover of CD4+ T cells in transplanted duodenum in humans, we demonstrate that the majority of CD4+ T cells were still donor-derived one year after transplantation. In contrast to memory CD4+ T cells in peripheral blood, intestinal CD4+ TRM cells expressed CD69 and CD161, but only a minor fraction expressed CD103. Functionally, intestinal CD4+ TRM cells were very potent cytokine producers; the vast majority being polyfunctional TH1 cells, whereas a minor fraction produced IL-17. Interestingly, a fraction of intestinal CD4+ T cells produced granzyme-B and perforin after activation. Together, we show that the intestinal CD4+ T-cell compartment is dominated by resident populations that survive for more than 1 year. This finding is of high relevance for the development of oral vaccines and therapies for diseases in the gut.

Towards the Development of a Noninvasive Prenatal Test for Beta-Thalassemia: Utilization of Probe Capture Enrichment and Next Generation Sequencing

β-thalassemia causes significant morbidity and mortality worldwide. Currently, the diagnosis can be made prenatally for couples at risk using invasive procedures such as chorionic villus sampling and amniocentesis. Noninvasive prenatal testing (NIPT) on maternal blood samples would enable earlier fetal diagnosis and eliminate risks associated with these procedures. The discovery of cell-free fetal DNA (cfFDNA) in maternal plasma and advances in next generation sequencing (NGS) have made NIPT a clinical reality for aneuploidies. Diagnosing autosomal recessive (AR) disorders is more challenging as it requires determination of both the paternally and maternally inherited alleles and can be particularly difficult when both parents carry the same mutation. Previous studies used methods to identify the paternally inherited allele in maternal plasma through the detection of a DNA sequence variant present in the father and absent in the mother. Our method expands the target region beyond the β-globin gene into highly polymorphic regions to increase the likelihood of identifying unique paternal sequences. Unlike the detection of the paternal allele, there is no direct qualitative approach for determining the maternally inherited allele. Our solution is an indirect quantitative method that compares the ratio of allelic sequence reads to infer which maternal allele was inherited by the fetus. We have developed a novel NGS assay which utilizes probe capture enrichment, a method employing thousands of short overlapping oligonucleotide probes complementary to a target sequence region. This design makes it uniquely applicable to short, fragmented DNA, such as cell-free DNA (~150 base pairs). Our probe assay targets a contiguous 900 bp region which spans a portion of the β-globin gene (part of exon 2 as well as the entirety of IVS-1 and exon 1) and extends 579 bp into the highly polymorphic 5' UTR region to identify linked sequence variations. Additionally, the assay targets 451 single nucleotide polymorphisms (SNPs) throughout the genome. SNPs that are "informative" (i.e. an allele present in the fetus and absent in the mother) are used to calculate the fraction of cfDNA from the fetus. We have evaluated our assay's performance in a set of experiments designed to simulate the challenging aspects of cfFDNA: very low quantity and short fragment size. The assay's sensitivity was tested by preparing libraries containing amounts of DNA ranging from 50 to 0.05 ngs. At DNA amounts as low as 5 ng (5-fold lower than that expected in plasma), 100% coverage was achieved for the targeted β-globin region and SNPs. The probe/NGS system successfully captured and sequenced DNA fragments as short as 35 bps and as little as 0.5 ng of DNA with >95% coverage. To test the ability of the probe/NGS system to resolve mixtures, DNA samples from patients with known β-globin mutations were combined in ratios ranging from 2.5:97.5 to 20:80 in 25 ng total DNA to mimic the maternal/fetal cfDNA mixture. Our assay was able to detect minority heterozygous mutant alleles at proportions as low as 1.25% and 0.3 ng of DNA. In a mixture designed to simulate a case with a shared parental mutation (CD41/42(-TTCT)), we identified a linked SNP (rs713040) allele, which was within 250 bp of the mutation and unique to the minor fraction. We used this SNP to distinguish the CD41/42 (-TTCT) mutation contributed by the minor fraction. Based on 6 mixtures, we observed 24.3% (110/451) of SNPs to be informative, allowing for a precise estimate of the minor fraction. We estimated the minor fraction to be 11.88% and 5.98% compared to the expected 10% and 5%, respectively. To show proof of concept for inferring the minor ("fetal") genotype when the major ("maternal") genotype was heterozygous mutant (IVS1-5 (G>C)), the estimated minor fraction (10.4% based on 104 informative SNPs) was used to calculate the expected allelic ratios of the 3 different possible minor ("fetal") genotypes. The minor genotype was correctly inferred as wt/wt based on the observed mixture ratio (42.56/57.41 mut/wt) compared to the expected (44.93/55.07). These data show that our probe capture/NGS system can overcome the challenges implicit in the analysis of cfFDNA for NIPT: low DNA amount (<5 ng) and short fragments (<150 bp). We expect that our approach using the fetal fraction estimate will allow us to successfully infer the fetal genotype when applied to maternal plasma. Disclosures Erlich: Allen and Overy, Law Office: Consultancy.

The differential localization of a methyl group confers a different anti-breast cancer activity to two triterpenes present in olives

Uvaol (UV) and erythrodiol (ER) are two triterpenic dialcohols present in the minor fraction of virgin olive oil, in leaves and in the skin and drupe of olives.