Geology topics

Arvind Varsani

Publications and source records attributed to Arvind Varsani.

11 recordsLinked to original sources

USGS2026

Novel avian papillomaviruses identified in a south polar skua sampled on Ross Island, Antarctica

Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach to identify viruses from the oral swab taken from a deceased south polar skua ( Stercorarius maccormicki ) found at Cape Royds, Ross Island, Antarctica in late 2024. We identified three papillomaviruses and determined their complete genomes, Stercorarius maccormicki papillomavirus (SmacPV) 1-3. SmacPV1 is the most divergent of the three SmacPVs, sharing 62% genome-wide pairwise identity to SmacPV2 and SmacPV3 and <63.5% to other avian papillomaviruses. The genomes of SmacPV2 and SmacPV3 represent two new papillomavirus types sharing 82.4% genome-wide pairwise identity with each other and <72% to other papillomaviruses. SmacPV2 and SmacPV3 phylogenetically cluster with sequences of the Rissa tridactyla papillomavirus 1 from black-legged kittiwake ( Rissa tridactyla ), Larus smithsonianus papillomavirus 1 from American herring gull ( Larus smithsonianus ) and Fratercula arctica papillomavirus 1 from Atlantic puffin ( Fratercula arctica ), and they collectively represent a new papillomavirus species. These are the first papillomaviruses to be identified in Stercorarius spp . and add to the handful of known papillomaviruses in identified avian species. We also expand the known host range of papillomaviruses in Antarctic animals, which previously included Adélie penguins ( Pygoscelis adeliae ), Weddell seals ( Leptonychotes weddellii ), Antarctic fur seals ( Arctocephalus gazella ), leopard seals ( Hydrurga leptonyx ) and emerald notothen ( Trematomus bernacchii ).

Archives of Virology↗

USGS2025

Diversity of polyomaviruses and papillomaviruses in penguins from eastern and western Antarctica

Polyomaviruses and papillomaviruses are icosahedral viruses with small circular dsDNA genomes. Limited information on their diversity and evolution in avian hosts is available, with even less known regarding Antarctic penguins. Prior to this study, only one polyomavirus and two papillomaviruses had been identified in Adélie penguins ( Pygoscelis adeliae ). To expand our knowledge of these viruses in Antarctic penguins, we collected faecal and cloacal swab samples from 246 Adélie penguins over 3 breeding seasons (2021–2024) and 10 emperor penguins ( Aptenodytes forsteri ) during the 2023–2024 season on Ross Island (Ross Sea). Additionally, we sampled 66 Adélie, 40 chinstrap ( Pygoscelis antarcticus ) and 71 gentoo ( Pygoscelis papua ) penguins during the 2022–2023 season across various sites on the Antarctic Peninsula. All samples were screened for papillomaviruses and polyomaviruses. We identified 31 polyomaviruses in Adélie, gentoo and chinstrap penguins and 4 papillomaviruses in Adélie penguins sampled in both eastern and western Antarctica. The 31 penguin polyomaviruses belong to a single species but form four distinct variants that are host species specific with strong geographic clustering. The four papillomaviruses represent three different types, of which two are new types from Adélie penguins sampled on Yalour Island in the West Antarctic Peninsula. Co-occurrence of two polyomavirus variants was identified in two individual gentoo penguins. Both of these variants appear to be circulating in gentoo penguins at Cierva Cove, Hope Bay in Trinity Peninsula along the Antarctic Peninsula, and at Hannah Point on Livingstone Island and Stranger Point on King George Island in the South Shetland Islands. Here, we expand the known diversity, host and geographical ranges of penguin polyomaviruses and, together with a previously identified polyomavirus on Ross Island from 2012 to 2013, show that they form five distinct lineages. The four papillomaviruses identified in this study, together with two previously identified from Ross Island in 2012 and 2013 breeding seasons, show substantial diversity reflecting four papillomavirus types across three viral species and two distinct genera. Continued surveillance and viral genomic analysis across a larger geographical framework will help understand the evolution, transmission and incidence rates of these viruses.

Microbial Genomics↗

USGS2024

Sex-specific recruitment rates contribute to male-biased sex ratio in Adélie penguins

Sex-related differences in vital rates that drive population change reflect the basic life history of a species. However, for visually monomorphic bird species, determining the effect of sex on demographics can be a challenge. In this study, we investigated the effect of sex on apparent survival, recruitment, and breeding propensity in the Adélie penguin ( Pygoscelis adeliae ), a monochromatic, slightly size dimorphic species with known age, known sex, and known breeding history data collected during 1996–2019 ( n = 2127 birds) from three breeding colonies on Ross Island, Antarctica. Using a multistate capture–mark–recapture maximum-likelihood model, we estimated apparent survival (

Ecology and Evolution↗

USGS2023

DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico

With viruses often having devastating effects on wildlife population fitness and wild mammals serving as pathogen reservoirs for potentially zoonotic diseases, determining the viral diversity present in wild mammals is both a conservation and One Health priority. Additionally, transmission from more abundant hosts could increase the extinction risk of threatened sympatric species. We leveraged an existing circular DNA enriched metagenomic dataset generated from bobcat ( Lynx rufus , n = 9) and puma ( Puma concolor , n = 13) scat samples non-invasively collected from Sonora, Mexico, to characterize fecal DNA viromes of each species and determine the extent that viruses are shared between them. Using the metaWRAP pipeline to co-assemble viral genomes for comparative metagenomic analysis, we observed diverse circular DNA viruses in both species, including circoviruses, genomoviruses, and anelloviruses. We found that differences in DNA virome composition were partly attributed to host species, although there was overlap between viruses in bobcats and pumas. Pumas exhibited greater levels of alpha diversity, possibly due to bioaccumulation of pathogens in apex predators. Shared viral taxa may reflect dietary overlap, shared environmental resources, or transmission through host interactions, although we cannot rule out species-specific host-virus coevolution for the taxa detected through co-assembly. However, our detection of integrated feline foamy virus (FFV) suggests Sonoran pumas may interact with domestic cats. Our results contribute to the growing baseline knowledge of wild felid viral diversity. Future research including samples from additional sources (e.g., prey items, tissues) may help to clarify host associations and determine the pathogenicity of detected viruses.

Sonora↗

USGS2021

Complex evolutionary history of felid anelloviruses

Anellovirus infections are highly prevalent in mammals, however, prior to this study only a handful of anellovirus genomes had been identified in members of the Felidae family. Here we characterise anelloviruses in pumas ( Puma concolor ), bobcats ( Lynx rufus ), Canada lynx ( Lynx canadensis ), caracals ( Caracal caracal ) and domestic cats ( Felis catus ). The complete anellovirus genomes (n = 220) recovered from 149 individuals were diverse. ORF1 protein sequence similarity network analysis coupled with phylogenetic analysis, revealed two distinct clusters that are populated by felid-derived anellovirus sequences, a pattern mirroring that observed for the porcine anelloviruses. Of the two-felid dominant anellovirus groups, one includes sequences from bobcats, pumas, domestic cats and an ocelot, and the other includes sequences from caracals, Canada lynx, domestic cats and pumas. Coinfections of diverse anelloviruses appear to be common among the felids. Evidence of recombination, both within and between felid-specific anellovirus groups, supports a long coevolution history between host and virus.

Virology↗

USGS2020

Novel circoviruses detected in feces of Sonoran felids

Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat ( Lynx rufus ) and puma ( Puma concolor ) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids

Sonoran Desert↗

USGS2019

Identification of a novel Adélie penguin circovirus at Cape Crozier (Ross Island, Antarctica)

Understanding the causes of disease in Antarctic wildlife is crucial as many of these species are already threatened by environmental changes brought about by climate change. In recent years, Antarctic penguins have been showing signs of an unknown pathology: a feather disorder characterised by missing feathers resulting in exposed skin. During the 2018-19 austral summer breeding season at Cape Crozier colony on Ross Island, Antarctica, for the first time we observed an Adlie penguin chick missing down over most of its body. A guano sample was collected from the nest of the featherless chick and, using high throughput sequencing we identified a novel circovirus. Using abutting primers, we amplified the full genome, which we cloned, and Sanger sequenced to determine the complete genome of the circovirus. The Adlie penguin guano-associated circovirus genome shares <67% genome-wide nucleotide identity to other circoviruses, representing a new species of circovirus, therefore we named it penguin circovirus (PenCV). Using the same primer pair, we screened 25 previously collected cloacal swabs taken at Cape Crozier from known-age adult Adlie penguins during the 2014-15 season displaying no clinical signs of feather-loss disorder. Three of the 25 samples (12%) were positive for a PenCV, whose genome shared >99% pairwise identity to the one identified in 2018-19. This is the first report of a circovirus associated with a penguin species and could be a possible etiological agent of the feather-loss disorder in Antarctic penguins.

Viruses↗

USGS2019

Evidence of age-related improvement in the foraging efficiency of Adélie penguins

Age variation in reproductive performance is well-documented but the mechanisms underlying this variation remain unclear. Foraging efficiency is likely to be a key source of demographic variation as it determines the amount of energy that can be invested in fitness-related activities. Evidence of age-related changes in the foraging efficiency of adult seabirds is scarce and inconsistent. We investigated the effects of age on the foraging efficiency of breeding Adélie penguins, a relatively short-lived seabird species, in order to gain a broader perspective on the processes driving variation in ageing rates. We found support for a positive effect of age, either linear or levelling off at old ages, on both our proxies for daily catch rate and catch per unit effort. Across all age classes, males were more performant foragers than females. We found no strong evidence for differing ageing patterns between sexes or individual quality levels, and no evidence for senescence. We infer that continuous individual improvement could be responsible for a larger amount of the variation in foraging efficiency with age at our study site, compared with selective disappearance of underperforming phenotypes. The different results reported by other studies highlight the need to conduct longitudinal studies across a range of species in different environments.

Scientific Reports↗

USGS2017

Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins

The family Papillomaviridae contains more than 320 papillomavirus types, with most having been identified as infecting skin and mucosal epithelium in mammalian hosts. To date, only nine non-mammalian papillomaviruses have been described from birds ( n = 5), a fish ( n = 1), a snake ( n = 1), and turtles ( n = 2). The identification of papillomaviruses in sauropsids and a sparid fish suggests that early ancestors of papillomaviruses were already infecting the earliest Euteleostomi. The Euteleostomi clade includes more than 90 per cent of the living vertebrate species, and progeny virus could have been passed on to all members of this clade, inhabiting virtually every habitat on the planet. As part of this study, we isolated a novel papillomavirus from a 16-year-old female Adélie penguin ( Pygoscelis adeliae ) from Cape Crozier, Ross Island (Antarctica). The new papillomavirus shares ∼64 per cent genome-wide identity to a previously described Adélie penguin papillomavirus. Phylogenetic analyses show that the non-mammalian viruses (expect the python, Morelia spilota , associated papillomavirus) cluster near the base of the papillomavirus evolutionary tree. A papillomavirus isolated from an avian host (Northern fulmar; Fulmarus glacialis ), like the two turtle papillomaviruses, lacks a putative E9 protein that is found in all other avian papillomaviruses. Furthermore, the Northern fulmar papillomavirus has an E7 more similar to the mammalian viruses than the other avian papillomaviruses. Typical E6 proteins of mammalian papillomaviruses have two Zinc finger motifs, whereas the sauropsid papillomaviruses only have one such motif. Furthermore, this motif is absent in the fish papillomavirus. Thus, it is highly likely that the most recent common ancestor of the mammalian and sauropsid papillomaviruses had a single motif E6. It appears that a motif duplication resulted in mammalian papillomaviruses having a double Zinc finger motif in E6. We estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.

Virus Evolution↗

USGS2016

Possibility and challenges of conversion of current virus species names to Linnaean binomials

Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens ). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment.

Systematic Biology↗

USGS2016

Sex-based differences in Adelie penguin (Pygoscelis adeliae) chick growth rates.

Sexually size-dimorphic species must show some difference between the sexes in growth rate and/or length of growing period. Such differences in growth parameters can cause the sexes to be impacted by environmental variability in different ways, and understanding these differences allows a better understanding of patterns in productivity between individuals and populations. We investigated differences in growth rate and diet between male and female Adélie Penguin ( Pygoscelis adeliae ) chicks during two breeding seasons at Cape Crozier, Ross Island, Antarctica. Adélie Penguins are a slightly dimorphic species, with adult males averaging larger than adult females in mass (~11%) as well as bill (~8%) and flipper length (~3%). We measured mass and length of flipper, bill, tibiotarsus, and foot at 5-day intervals for 45 male and 40 female individually-marked chicks. Chick sex was molecularly determined from feathers. We used linear mixed effects models to estimate daily growth rate as a function of chick sex, while controlling for hatching order, brood size, year, and potential variation in breeding quality between pairs of parents. Accounting for season and hatching order, male chicks gained mass an average of 15.6 g d -1 faster than females. Similarly, growth in bill length was faster for males, and the calculated bill size difference at fledging was similar to that observed in adults. There was no evidence for sex-based differences in growth of other morphological features. Adélie diet at Ross Island is composed almost entirely of two species—one krill ( Euphausia crystallorophias ) and one fish ( Pleuragramma antarctica ), with fish having a higher caloric value. Using isotopic analyses of feather samples, we also determined that male chicks were fed a higher proportion of fish than female chicks. The related differences in provisioning and growth rates of male and female offspring provides a greater understanding of the ways in which ecological factors may impact the two sexes differently.

PLoS ONE↗