scholarly journals Poecivirus is present in individuals with beak deformities in seven species of North American birds

2020 ◽  
Author(s):  
Maxine Zylberberg ◽  
Caroline Van Hemert ◽  
Colleen M. Handel ◽  
Rachel M. Liu ◽  
Joseph L. DeRisi
Keyword(s):  
Sanger Sequencing ◽  
Population Level ◽  
Disease Status ◽  
Causal Link ◽  
Avian Species ◽  
Unknown Etiology ◽  
Metagenomic Sequencing ◽  
Coding Region ◽  
Bird Populations ◽  
Northwestern Crow

ABSTRACTAvian keratin disorder (AKD), a disease characterized by debilitating beak overgrowth but with unknown etiology, has increasingly affected wild bird populations since the 1990s. We previously showed that a novel picornavirus, Poecivirus, is closely correlated with disease status in Black-capped Chickadees (Poecile atricapillus) in Alaska. However, our knowledge of the relationship between Poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of Poecivirus: Mew Gull (Larus canus), Hairy Woodpecker (Picoides villosus), Black-billed Magpie (Pica hudsonia), Northwestern Crow (Corvus caurinus), Red-breasted Nuthatch (Sitta canadensis), and Blackpoll Warbler (Setophaga striata); individuals were sampled in Alaska and Maine (1999-2016). We used targeted PCR followed by Sanger sequencing to test for the presence of Poecivirus in each specimen, and to obtain viral genome sequence from virus-positive host individuals. We detected Poecivirus in all individuals tested, but not in negative controls. Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two Northwestern Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequence from several specimens, including the complete coding region of Poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that Poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that Poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.

Assessment of invasive rodent impacts on island avifauna: methods, limitations and the way forward

2015 ◽  
Vol 42 (2) ◽  
pp. 185 ◽  
Author(s):  
Lise Ruffino ◽  
Diane Zarzoso-Lacoste ◽  
Eric Vidal
Keyword(s):  
Population Growth ◽  
Population Level ◽  
Bird Conservation ◽  
Bird Population ◽  
Breeding Parameters ◽  
Population Growth Rates ◽  
Bird Populations ◽  
Field Evidence ◽  
Bird Breeding

Bird conservation is nowadays a strong driving force for prioritising rodent eradications, but robust quantitative estimates of impacts are needed to ensure cost-effectiveness of management operations. Here, we review the published literature to investigate on what methodological basis rodent effects on island bird communities have been evaluated for the past six decades. We then discuss the advantages and limitations of each category of methods for the detection and quantification of impacts, and end with some recommendations on how to strengthen current approaches and extend our knowledge on the mechanisms of impacts. Impact studies (152 studies considered) emphasised seabirds (67%), black rats (63%) and the Pacific Ocean (57%). Among the most commonly used methods to study rodent impacts on birds were the observation of dead eggs or empty nests while monitoring bird breeding success, and the analyses of rodent diets, which can both lead to misleading conclusions if the data are not supported by direct field evidence of rodent predation. Direct observations of rodent–bird interactions (19% of studies) are still poorly considered despite their potential to reveal cryptic behaviours and shed light on the mechanisms of impacts. Rodent effects on birds were most often measured as a change or difference in bird breeding parameters (74% of studies), while estimates of bird population growth rates (4%) are lacking. Based on the outcomes of this literature review, we highlight the need for collecting unbiased population-level estimates of rodent impacts, which are essential prerequisites for predicting bird population growth scenarios and prioritising their conservation needs. This could be achieved by a more systematic integration of long-term monitoring of bird populations into rodent management operations and modelling bird population dynamics. We also strongly recommend including various complementary methods in impact assessment strategies to unravel complex interactions between rodents and birds and avoid faulty evidence. Finally, more research should be devoted to a better understanding of the cases of non-impacts (i.e. long-term coexistence) and those impacts mediated by mechanisms other than predation and ecosystem-level processes.

Pathogens from Wild Birds at the Wildlife–Agriculture Interface

2021 ◽  
pp. 207-228
Author(s):  
Alan B. Franklin ◽  
Sarah N. Bevins ◽  
Susan A. Shriner
Keyword(s):  
Disease Ecology ◽  
Influenza A ◽  
Wild Birds ◽  
Avian Species ◽  
Influenza A Viruses ◽  
Agricultural Health ◽  
Bird Populations ◽  
Food Borne ◽  
Global Movement ◽  
Agricultural Operations

Birds are known to carry pathogens affecting human and agricultural health. Conversely, agricultural operations can serve as sources of pathogens that affect wild bird populations. This chapter provides guidelines to identify focal avian species that frequently use agricultural operations. These guidelines are coupled with identifying host types, such as maintenance and bridge hosts, and potential direct and indirect pathways for pathogen contamination from wild birds to agricultural operations, including patterns of spillover and spillback. The chapter also identifies major bacterial and viral pathogens of concern that are prevalent in birds and that affect human and agricultural health. These pathogens are then used to illustrate disease ecology concepts important at the wildlife–agriculture interface. These microorganisms include food-borne bacteria, influenza A viruses, and Newcastle disease virus. The chapter introduces the concept of contamination potential for categorizing avian species in terms of the risk they pose to contamination of agricultural operations with pathogens of concern. Finally, the chapter examines long-distance movements of wild birds in relation to pathogen introduction and illustrates this with global movement of influenza A viruses by wild birds.

Snag Densities in Managed Stands of the South Carolina Coastal Plain

1983 ◽  
Vol 7 (4) ◽  
pp. 224-229 ◽  
Author(s):  
Richard F. Harlow ◽  
David C. Guynn
Keyword(s):  
South Carolina ◽  
Coastal Plain ◽  
Avian Species ◽  
National Forest ◽  
Population Densities ◽  
Bird Populations ◽  
Cavity Nesters ◽  
Minimum Number ◽  
Pine Stands ◽  
Avian Populations

Abstract The availability of pine and hardwood snags was determined in managed pine and nonpine stands on the Francis Marion National Forest in the Coastal Plain of South Carolina. An estimate was made of snags required for nesting by avian cavity nesters indigenous to the region and of the density of cavity nesters currently provided for on the forest. Avian species that use snags 5 to 9 in. d.b.h. were apparently provided with more than 100 percent of the minimum number of suitable-size snags for average bird populations in the nonpine stands, which encompassed about 30 percent of the area. In pine stands, by contrast, there were enough snags of this size for only 20 percent of the average avian populations. For species using larger snags (≥10 in. d.b.h.), nonpine stands provided enough for approximately 27 percent of average bird populations, while pine stands provided snags for only about 6 percent of average population densities.

scholarly journals Prioritizing Avian Species for Their Risk of Population-Level Consequences from Wind Energy Development

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0150813 ◽  
Author(s):  
Julie A. Beston ◽  
Jay E. Diffendorfer ◽  
Scott R. Loss ◽  
Douglas H. Johnson
Keyword(s):  
Wind Energy ◽  
Population Level ◽  
Energy Development ◽  
Avian Species ◽  
Wind Energy Development

scholarly journals Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates

2015 ◽  
Vol 53 (12) ◽  
pp. 3779-3783 ◽  
Author(s):  
Nontuthuko E. Maningi ◽  
Luke T. Daum ◽  
John D. Rodriguez ◽  
Matsie Mphahlele ◽  
Remco P. H. Peters ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Detection Sensitivity ◽  
Next Generation ◽  
Resistance Mutations ◽  
Coding Region ◽  
Content Type ◽  
Mdr Tb ◽  
Generation Sequencing

The technical limitations of common tests used for detecting pyrazinamide (PZA) resistance inMycobacterium tuberculosisisolates pose challenges for comprehensive and accurate descriptions of drug resistance in patients with multidrug-resistant tuberculosis (MDR-TB). In this study, a 606-bp fragment (comprising thepncAcoding region plus the promoter) was sequenced using Ion Torrent next-generation sequencing (NGS) to detect associated PZA resistance mutations in 88 recultured MDR-TB isolates from an archived series collected in 2001. These 88 isolates were previously Sanger sequenced, with 55 (61%) designated as carrying the wild-typepncAgene and 33 (37%) showing mutations. PZA susceptibility of the isolates was also determined using the Bactec 460 TB system and the Wayne test. In this study, isolates were recultured and susceptibility testing was performed in Bactec 960 MGIT. Concordance between NGS and MGIT results was 93% (n= 88), and concordance values between the Bactec 460, the Wayne test, orpncAgene Sanger sequencing and NGS results were 82% (n= 88), 83% (n= 88), and 89% (n= 88), respectively. NGS confirmed the majority ofpncAmutations detected by Sanger sequencing but revealed several new and mixed-strain mutations that resolved discordancy in other phenotypic results. Importantly, in 53% (18/34) of these isolates,pncAmutations were located in the 151 to 360 region and warrant further exploration. In these isolates, with their known resistance to rifampin, NGS ofpncAimproved PZA resistance detection sensitivity to 97% and specificity to 94% using NGS as the gold standard and helped to resolve discordant results from conventional methodologies.

Platypus (Ornithorhynchus anatinus) body size, condition and population structure in Tasmanian river catchments: variability and potential mucormycosis impacts

2011 ◽  
Vol 38 (4) ◽  
pp. 271 ◽  
Author(s):  
Nick Gust ◽  
Josh Griffiths
Keyword(s):  
Population Structure ◽  
Body Size ◽  
Spatial Scales ◽  
Population Level ◽  
Disease Status ◽  
Volume Index ◽  
Adult Males ◽  
Ornithorhynchus Anatinus ◽  
Size Condition ◽  
River Catchments

Context Despite widespread interest in platypus (Ornithorhynchus anatinus) conservation, it is unclear how their fundamental morphometric and demographic characteristics differ over a range of scales. This hampers impact assessments and understanding of platypus ecology. Although the ulcerative fungal disease mucormycosis has infected platypuses in Tasmania for three decades, its population level impacts and conservation significance remain unknown. Aims This study examined morphometric and demographic patterns in Tasmanian platypuses to provide a basis for investigating impacts of mucormycosis or other anthropogenic disturbances. It also sought to identify important spatial scales of natural variability and the magnitude of seasonal variation in platypus body size, condition and population structure. The hypothesis of higher mucormycosis prevalence and mortality in adult males was also investigated. Methods Extensive live-trapping surveys were conducted from January 2008 to July 2009 in 75 streams and 18 river catchments across Tasmania including King Island. The sex, age, body size, tail volume index, health and moult condition of 195 individuals were assessed, and population age and sex structures characterised. Sampling focussed on assessing variability within and between river catchments and compared populations in river catchments with contrasting disease status. Key results Differences in platypus morphometrics within and between catchments and seasonal moulting patterns were detected. Adult males had higher fat stores than adult females, especially during winter. This study also provided the first evidence of population level consequences of disease in platypuses. The demographic group most commonly affected by mucormycosis was confirmed to be adult males. Differences in male age structure among catchments of varying disease status were consistent with the hypothesis of higher adult male mortality rates and turnover in currently affected catchments. Conclusions More than 25 years after mucormycosis was first detected in Tasmanian platypuses, the disease continues to play a low-level, ongoing role in affected populations. Implications The present study provides the first systematic multi-scale spatial investigation of platypus mucormycosis, which contributes to unravelling the epidemiology of the disease and detecting its impacts. By identifying the magnitude and important scales of morphometric and demographic differences in Tasmanian platypuses the study also assists researchers choose comparable demographic groups and spatial scales for meaningful comparisons in future impact studies.

scholarly journals SARS-CoV-2 variants in Paraguay: Detection and surveillance with a readily modifiable, multiplex real-time RT-PCR

2021 ◽  
Author(s):  
Magaly Martinez ◽  
Phuong-Vi Nguyen ◽  
Maxwell Su ◽  
Fatima Cardozo ◽  
Adriana Valenzuela ◽  
...  
Keyword(s):  
Real Time ◽  
Sanger Sequencing ◽  
Lower Cost ◽  
Population Level ◽  
Nanopore Sequencing ◽  
Receptor Binding Domain ◽  
Rt Pcr ◽  
High Quality ◽  
Rna Detection ◽  
Detection Of Mutations

Objectives The objective of the current study was to develop a lower-cost and scalable protocol to identify and monitor SARS-CoV-2 variants in Paraguay by pairing real-time RT-PCR detection of spike mutations with amplicon Sanger sequencing and whole-genome Nanopore sequencing. Methods 201 acute-phase nasopharyngeal samples from SARS-CoV-2-positive individuals were tested with two rRT-PCRs: 1) N2RP assay to confirm SARS-CoV-2 RNA detection (CDC N2 target), and 2) the Spike SNP assay to detect mutations in the spike receptor binding domain. The assay was performed with probes to identify mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S). Results All samples were positive for SARS-CoV-2 in the N2RP assay (mean Ct, 20.8; SD 5.6); 198/201 (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%) and most consistent with P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%); and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). Results were confirmed by Sanger sequencing in 181/181 samples (100%) with high-quality amplicon sequences, and variant calls were consistent with Nanopore sequencing in 29/29 samples. Conclusions The Spike SNP assay provides accurate detection of mutations associated with SARS-CoV-2 variants. This can be implemented in laboratories performing rRT-PCR to improve population-level surveillance for these mutations and inform the judicious use of scarce sequencing resources.

scholarly journals Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease

2021 ◽  
Vol 9 ◽  
Author(s):  
Qiaoxing Liang ◽  
Jing Li ◽  
Yanli Zou ◽  
Xiao Hu ◽  
Xiuli Deng ◽  
...  
Keyword(s):  
Dry Eye ◽  
Disease Status ◽  
Meibomian Gland ◽  
Dry Eye Disease ◽  
Species Level ◽  
Eye Disease ◽  
Significant Heterogeneity ◽  
Metagenomic Sequencing ◽  
Female Patients ◽  
Α Diversity

Background: Dry eye disease (DED) is a multifactorial inflammatory disease of the ocular surface. It is hypothesized that dysbiosis of the conjunctival microbiota contributes to the development of DED. However, species-level compositions of the conjunctival microbiota in DED and the potential dysbiosis involving microorganisms other than bacteria remain largely uncharacterized.Methods: We collected conjunctival impression samples from a cohort of 95 individuals, including 47 patients with DED and 48 healthy subjects. We examined the conjunctival microbiota of these samples using shotgun metagenomic sequencing and analyzed microbial dysbiosis in DED at the species level.Results: The conjunctival microbiota in DED exhibited a decreased α-diversity and an increased inter-individual variation. The α-diversity of female patients with DED was higher than that of male patients. Despite a decreased prevalence in DED, 23 microbial species were identified to show abnormally high abundance in DED samples positive for the species. Among these species, a fungal species Malassezia globosa was enriched female patients. In addition, distinct patterns of associations with disease status were observed for different species of the same genus. For DED subtypes, Staphylococcus aureus and S. capitis were associated with meibomian gland dysfunction (MGD), whereas S. hominis was enriched in patients solely with aqueous tear deficiency (ATD). The microbiota of patients with a mixed type of diagnosis was more similar to MGD patients than ATD patients.Conclusion: We demonstrated that the conjunctival microbiota dysbiosis in DED is characterized by significant heterogeneity. Microbial signatures may offer novel insights into the complicated etiology of DED and potentially promote the development of personalized treatment for DED in the future.

scholarly journals Genomic associations with poxvirus across divergent island populations in Berthelot's pipit

2021 ◽  
Author(s):  
Eleanor Sheppard ◽  
Claudia Martin ◽  
Claire Armstrong ◽  
Catalina González-Quevedo ◽  
Juan Carlos Illera ◽  
...  
Keyword(s):  
Viral Infection ◽  
Population Level ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Individual Level ◽  
Island Populations ◽  
Bird Populations ◽  
Animal Populations ◽  
Infection Pressure ◽  
Avian Pox

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot’s pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses provide evidence that pathogen-mediated selection has shaped genomic variation among relatively recently colonised island bird populations, and highlights the utility of genotype-environment associations for identifying candidate genes involved in adaption to local pathogen pressures.

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