Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses

The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized, yet least understood, epidemiological patterns in infectious disease. Central to understanding what drives the seasonal emergence of this important human pathogen is determining what becomes of the virus during the non-epidemic summer months. Herein, we take a step towards elucidating the seasonal emergence of influenza virus by determining the evolutionary relationship between populations of influenza A virus sampled from opposite hemispheres. We conducted a phylogenetic analysis of 487 complete genomes of human influenza A/H3N2 viruses collected between 1999 and 2005 from Australia and New Zealand in the southern hemisphere, and a representative sub-sample of viral genome sequences from 413 isolates collected in New York state, United States, representing the northern hemisphere. We show that even in areas as relatively geographically isolated as New Zealand's South Island and Western Australia, global viral migration contributes significantly to the seasonal emergence of influenza A epidemics, and that this migration has no clear directional pattern. These observations run counter to suggestions that local epidemics are triggered by the climate-driven reactivation of influenza viruses that remain latent within hosts between seasons or transmit at low efficiency between seasons. However, a complete understanding of the seasonal movements of influenza A virus will require greatly expanded global surveillance, particularly of tropical regions where the virus circulates year-round, and during non-epidemic periods in temperate climate areas

Influence of the Fermi Surface Morphology on the Magnetic Field-Driven Vortex Lattice Structure Transitions in YBa2_{2}Cu3_{3}O7−δ:δ=_{7-\delta}:\delta=0, 0.15

We report small-angle neutron scattering measurements of the vortex lattice (VL) structure in single crystals of the lightly underdoped cuprate superconductor YBa2Cu3O6.85. At 2 K, and for fields of up to 16 T applied parallel to the crystal c-axis, we observe a sequence of field-driven and first-order transitions between different VL structures. By rotating the field away from the c-axis, we observe each structure transition to shift to either higher or lower field dependent on whether the field is rotated towards the [100] or [010] direction. We use this latter observation to argue that the Fermi surface morphology must play a key role in the mechanisms that drive the VL structure transitions. Furthermore, we show this interpretation is compatible with analogous results obtained previously on lightly overdoped YBa2Cu3O7. In that material, it has long-been suggested that the high field VL structure transition is driven by the nodal gap anisotropy. In contrast, the results and discussion presented here bring into question the role, if any, of a nodal gap anisotropy on the VL structure transitions in both YBa2Cu3O6.85 and YBa2Cu3O7

Avian oncogenesis induced by lymphoproliferative disease virus: a neglected or emerging retroviral pathogen?

Lymphoproliferative disease virus (LPDV) is an exogenous oncogenic retrovirus that induces lymphoid tumors in some galliform species of birds. Historically, outbreaks of LPDV have been reported from Europe and Israel. Although the virus has previously never been detected in North America, herein we describe the widespread distribution, genetic diversity, pathogenesis, and evolution of LPDV in the United States. Characterization of the provirus genome of the index LPDV case from North America demonstrated an 88% nucleotide identity to the Israeli prototype strain. Although phylogenetic analysis indicated that the majority of viruses fell into a single North American lineage, a small subset of viruses from South Carolina were most closely related to the Israeli prototype. These results suggest that LPDV was transferred between continents to initiate outbreaks of disease. However, the direction (New World to Old World or vice versa), mechanism, and time frame of the transcontinental spread currently remain unknown

Frequent Cross-Species Transmission of Parvoviruses among Diverse Carnivore Hosts

Although parvoviruses are commonly described in domestic carnivores, little is known about their biodiversity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus (“FPV-like”) or canine parvovirus (“CPV-like”). Crossspecies transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species

Limited cross-species virus transmission in a spatially restricted coral reef fish community

The Great Barrier Reef (GBR) - the largest coral reef ecosystem in the world - supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel Santee-Cooper ranavirus (Iridoviridae). We found little evidence for virus transmission between fish species living within a very restricted geographical space - a 100-m2 coral reef ecosystem - suggesting that there might be important host barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition among reef fish families, such that cryptobenthic reef fishes - characterized by small body sizes and short life spans - exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species virus transmission and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species

Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys

We detected 19 complete endogenous retroviruses of the K family in the genome of rhesus monkey (Macaca mulatta; RhERV-K) and 12 full length elements in the genome of the common chimpanzee (Pan troglodytes; CERV-K). These sequences were compared with 55 human HERV-K and 20 CERV-K reported previously, producing a total data set of 106 full-length ERV-K genomes. Overall, 61% of the human elements compared to 21% of the chimpanzee and 47% of rhesus elements had estimated integration times less than 4.5 million years before present (MYBP), with an average integration times of 7.8 MYBP, 13.4 MYBP and 10.3 MYBP for HERV-K, CERV-K and RhERV-K, respectively. By excluding those ERV-K sequences generated by chromosomal duplication, we used 63 of the 106 elements to compare the population dynamics of ERV-K among species. This analysis indicated that both HERV-K and RhERV-K had similar demographic histories, including markedly smaller effective population sizes, compared to CERV-K. We propose that these differing ERV-K dynamics reflect underlying differences in the evolutionary ecology of the host species, such that host ecology and demography represent important determinants of ERV-K dynamics

Antarctic Sea Ice Area in CMIP6

Fully coupled climate models have long shown a wide range of Antarctic sea ice states and evolution over the satellite era. Here, we present a high‐level evaluation of Antarctic sea ice in 40 models from the most recent phase of the Coupled Model Intercomparison Project (CMIP6). Many models capture key characteristics of the mean seasonal cycle of sea ice area (SIA), but some simulate implausible historical mean states compared to satellite observations, leading to large intermodel spread. Summer SIA is consistently biased low across the ensemble. Compared to the previous model generation (CMIP5), the intermodel spread in winter and summer SIA has reduced, and the regional distribution of sea ice concentration has improved. Over 1979–2018, many models simulate strong negative trends in SIA concurrently with stronger‐than‐observed trends in global mean surface temperature (GMST). By the end of the 21st century, models project clear differences in sea ice between forcing scenarios

Effects of inulin propionate ester incorporated into palatable food products on appetite and resting energy expenditure: a randomised crossover study

Supplementation with inulin-propionate ester (IPE), which delivers propionate to the colon, suppresses ad libitum energy intake and stimulates the release of satiety hormones acutely in humans, and prevents weight gain. In order to determine whether IPE remains effective when incorporated into food products (FP), IPE needs to be added to a widely accepted food system. A bread roll and fruit smoothie were produced. Twenty-one healthy overweight and obese humans participated. Participants attended an acclimatisation visit and a control visit where they consumed un-supplemented food products (FP). Participants then consumed supplemented-FP, containing 10 g/d inulin or IPE for six days followed by a post-supplementation visit in a randomised crossover design. On study visits, supplemented-FP were consumed for the seventh time and ad libitum energy intake was assessed 420 min later. Blood samples were collected to assess hormones and metabolites. Resting energy expenditure (REE) was measured using indirect calorimetry. Taste and appearance ratings were similar between FP. Ad libitum energy intake was significantly different between treatments, due to a decreased intake following IPE-FP. These observations were not related to changes in blood hormones and metabolites. There was an increase in REE following IPE-FP. However, this effect was lost after correcting for changes in fat free mass. Our results suggest that IPE suppresses appetite and may alter REE following its incorporation into palatable food products