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Wight J, Byrne AS, Tahlan K, Lang AS. Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Appl Environ Microbiol 2024; 90:e0180923. [PMID: 38349150 PMCID: PMC10952509 DOI: 10.1128/aem.01809-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024] Open
Abstract
Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.
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Affiliation(s)
- Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Alexander S. Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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Alkie TN, Byrne AMP, Jones MEB, Mollett BC, Bourque L, Lung O, James J, Yason C, Banyard AC, Sullivan D, Signore AV, Lang AS, Baker M, Dawe B, Brown IH, Berhane Y. Recurring Trans-Atlantic Incursion of Clade 2.3.4.4b H5N1 Viruses by Long Distance Migratory Birds from Northern Europe to Canada in 2022/2023. Viruses 2023; 15:1836. [PMID: 37766243 PMCID: PMC10536465 DOI: 10.3390/v15091836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
In December 2022 and January 2023, we isolated clade 2.3.4.4b H5N1 high-pathogenicity avian influenza (HPAI) viruses from six American crows (Corvus brachyrhynchos) from Prince Edward Island and a red fox (Vulpes vulpes) from Newfoundland, Canada. Using full-genome sequencing and phylogenetic analysis, these viruses were found to fall into two distinct phylogenetic clusters: one group containing H5N1 viruses that had been circulating in North and South America since late 2021, and the other one containing European H5N1 viruses reported in late 2022. The transatlantic re-introduction for the second time by pelagic/Icelandic bird migration via the same route used during the 2021 incursion of Eurasian origin H5N1 viruses into North America demonstrates that migratory birds continue to be the driving force for transcontinental dissemination of the virus. This new detection further demonstrates the continual long-term threat of H5N1 viruses for poultry and mammals and the subsequent impact on various wild bird populations wherever these viruses emerge. The continual emergence of clade 2.3.4.4b H5Nx viruses requires vigilant surveillance in wild birds, particularly in areas of the Americas, which lie within the migratory corridors for long-distance migratory birds originating from Europe and Asia. Although H5Nx viruses have been detected at higher rates in North America since 2021, a bidirectional flow of H5Nx genes of American origin viruses to Europe has never been reported. In the future, coordinated and systematic surveillance programs for HPAI viruses need to be launched between European and North American agencies.
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Affiliation(s)
- Tamiru N. Alkie
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Alexander M. P. Byrne
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
| | - Megan E. B. Jones
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PE C1A 4P3, Canada; (M.E.B.J.); (L.B.)
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Benjamin C. Mollett
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
| | - Laura Bourque
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PE C1A 4P3, Canada; (M.E.B.J.); (L.B.)
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Joe James
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Carmencita Yason
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Ashley C. Banyard
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Daniel Sullivan
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Anthony V. Signore
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada;
| | - Meghan Baker
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, Provincial Agriculture Building, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada; (M.B.); (B.D.)
| | - Beverly Dawe
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, Provincial Agriculture Building, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada; (M.B.); (B.D.)
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Alim NTB, Koppenhöfer S, Lang AS, Beatty JT. Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA. Genes (Basel) 2023; 14:genes14051124. [PMID: 37239483 DOI: 10.3390/genes14051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.
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Affiliation(s)
- Nawshin T B Alim
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - J Thomas Beatty
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Koppenhöfer S, Lang AS. Patterns of abundance, chromosomal localization, and domain organization among c-di-GMP-metabolizing genes revealed by comparative genomics of five alphaproteobacterial orders. BMC Genomics 2022; 23:834. [PMID: 36522693 PMCID: PMC9756655 DOI: 10.1186/s12864-022-09072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/17/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a bacterial second messenger that affects diverse processes in different bacteria, including the cell cycle, motility, and biofilm formation. Its cellular levels are controlled by the opposing activities of two types of enzymes, with synthesis by diguanylate cyclases containing a GGDEF domain and degradation by phosphodiesterases containing either an HD-GYP or an EAL domain. These enzymes are ubiquitous in bacteria with up to 50 encoded in some genomes, the specific functions of which are mostly unknown. RESULTS We used comparative analyses to identify genomic patterns among genes encoding proteins with GGDEF, EAL, and HD-GYP domains in five orders of the class Alphaproteobacteria. GGDEF-containing sequences and GGDEF-EAL hybrids were the most abundant and had the highest diversity of co-occurring auxiliary domains while EAL and HD-GYP containing sequences were less abundant and less diverse with respect to auxiliary domains. There were striking patterns in the chromosomal localizations of the genes found in two of the orders. The Rhodobacterales' EAL-encoding genes and Rhizobiales' GGDEF-EAL-encoding genes showed opposing patterns of distribution compared to the GGDEF-encoding genes. In the Rhodobacterales, the GGDEF-encoding genes showed a tri-modal distribution with peaks mid-way between the origin (ori) and terminus (ter) of replication and at ter while the EAL-encoding genes peaked near ori. The patterns were more complex in the Rhizobiales, but the GGDEF-encoding genes were biased for localization near ter. CONCLUSIONS The observed patterns in the chromosomal localizations of these genes suggest a coupling of synthesis and hydrolysis of c-di-GMP with the cell cycle. Moreover, the higher proportions and diversities of auxiliary domains associated with GGDEF domains and GGDEF-EAL hybrids compared to EAL or HD-GYP domains could indicate that more stimuli affect synthesis compared to hydrolysis of c-di-GMP.
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Affiliation(s)
- Sonja Koppenhöfer
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
| | - Andrew S. Lang
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
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Langille E, Bottaro CS, Lang AS. Purification of Functional Gene Transfer Agents Using Two-Step Preparative Monolithic Chromatography. Phage (New Rochelle) 2022; 3:194-203. [PMID: 36793882 PMCID: PMC9917305 DOI: 10.1089/phage.2022.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background Gene transfer agents (GTAs) are phage-like particles that transfer cellular genomic DNA between cells. A hurdle faced in studying GTA function and interactions with cells is the difficulty in obtaining pure and functional GTAs from cultures. Materials and Methods We used a novel two-step method for purification of GTAs from R. capsulatus by monolithic chromatography. Results Our efficient and simple process had advantages compared to previous approaches. The purified GTAs retained gene transfer activity and the packaged DNA could be used for further studies. Conclusions This method is applicable to GTAs produced by other species and small phages, and could be useful for therapeutic applications.
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Affiliation(s)
- Evan Langille
- Department of Chemistry and Memorial University of Newfoundland, St. John's, Canada
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| | - Christina S. Bottaro
- Department of Chemistry and Memorial University of Newfoundland, St. John's, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
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Koppenhöfer S, Tomasch J, Lang AS. Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria. Microb Genom 2022; 8:mgen000890. [PMID: 36350115 PMCID: PMC9836097 DOI: 10.1099/mgen.0.000890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Gene transfer agents (GTAs) are phage-like particles that transfer pieces of cellular genomic DNA to other cells. Homologues of the Rhodobacter capsulatus GTA (RcGTA) structural genes are widely distributed in the Alphaproteobacteria and particularly well conserved in the order Rhodobacterales. Possible reasons for their widespread conservation are still being discussed. It has been suggested that these alphaproteobacterial elements originate from a prophage that was present in an ancestral bacterium and subsequently evolved into a GTA that is now widely maintained in extant descendant lineages. Here, we analysed genomic properties that might relate to the conservation of these alphaproteobacterial GTAs. This revealed that the chromosomal locations of the GTA gene clusters are biased. They primarily occur on the leading strand of DNA replication, at large distances from long repetitive elements, and thus are in regions of lower plasticity, and in areas of extreme GC skew, which also accumulate core genes. These extreme GC skew regions arise from the preferential use of codons with an excess of G over C, a distinct phenomenon from the elevated GC content that has previously been found to be associated with GTA genes. The observed properties, along with their high level of conservation, show that GTA genes share multiple features with core genes in the examined lineages of the Alphaproteobacteria.
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Affiliation(s)
- Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St John’s, Newfoundland and Labrador, Canada
| | - Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Science – Centre Algatech, Třeboň, Czech Republic
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St John’s, Newfoundland and Labrador, Canada,*Correspondence: Andrew S. Lang,
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Lang AS. Virus-derived gene transfer agents benefit host cells by providing templates for DNA repair. PLoS Biol 2022; 20:e3001874. [PMID: 36346786 PMCID: PMC9642860 DOI: 10.1371/journal.pbio.3001874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The potential benefits of producing gene transfer agents (GTAs) have long been speculated. A new study in PLOS Biology shows that DNA transfer by these phage-like elements allows cells with DNA damage to perform DNA repair and survive.
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Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
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Kogay R, Koppenhöfer S, Beatty JT, Kuhn JH, Lang AS, Zhaxybayeva O. Formal recognition and classification of gene transfer agents as viriforms. Virus Evol 2022; 8:veac100. [DOI: 10.1093/ve/veac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/10/2022] [Accepted: 10/14/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Morphological and genetic features strongly suggest that gene transfer agents (GTAs) are caudoviricete-derived entities that have evolved in concert with cellular genomes to such a degree that they should not be considered viruses. Indeed, GTA particles resemble caudoviricete virions but, in contrast to caudoviricetes (or any viruses), GTAs can encapsidate at best only part of their own genomes, are induced solely in small subpopulations of prokaryotic host cells and are transmitted vertically as part of cellular genomes during replication and division. Therefore, the lifecycles of GTAs are analogous to virus-derived entities found in parasitoid wasps, which have recently been recognized as non-virus entities and therefore reclassified as viriforms We evaluated three distinct, independently exapted GTA groups for which the genetic basis for GTA particle production has been established. Based on the evidence, we outline a classification scheme for these viriforms
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Affiliation(s)
- Roman Kogay
- Department of Biological Sciences, Dartmouth College , Hanover, NH, USA
| | - Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland , St. John’s, NL, Canada
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia , Vancouver, BC, Canada
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Frederick, MD, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland , St. John’s, NL, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College , Hanover, NH, USA
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Canuti M, Pénzes JJ, Lang AS. A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics. Virus Evol 2022; 8:veac056. [PMID: 35783582 PMCID: PMC9242002 DOI: 10.1093/ve/veac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/13/2022] [Accepted: 06/13/2022] [Indexed: 12/11/2022] Open
Abstract
Amdoparvoviruses (genus Amdoparvovirus, family Parvoviridae) are primarily viruses of carnivorans, but recent studies have indicated that their host range might also extend to rodents and chiropterans. While their classification is based on the full sequence of the major nonstructural protein (NS1), several studies investigating amdoparvoviral diversity have been focused on partial sequences, leading to difficulties in accurately determining species demarcations and leaving several viruses unclassified. In this study, while reporting the complete genomic sequence of a novel amdoparvovirus identified in an American mink (British Columbia amdoparvovirus, BCAV), we studied the phylogenetic relationships of all amdoparvovirus-related sequences and provide a comprehensive reevaluation of their diversity and evolution. After excluding recombinant sequences, phylogenetic and pairwise sequence identity analyses allowed us to define fourteen different viruses, including the five currently classified species, BCAV, and four additional viruses that fulfill the International Committee on Taxonomy of Viruses criteria to be classified as species. We show that the group of viruses historically known as Aleutian mink disease virus (species Carnivore amdoparvovirus 1) should be considered as a cluster of at least four separate viral species that have been co-circulating in mink farms, facilitating the occurrence of inter-species recombination. Genome organization, splicing donor and acceptor sites, and protein sequence motifs were surprisingly conserved within the genus. The sequence of the major capsid protein virus protein 2 (VP2) was significantly more conserved between and within species compared to NS1, a phenomenon possibly linked to antibody-dependent enhancement (ADE). Homology models suggest a remarkably high degree of conservation of the spikes located near the icosahedral threefold axis of the capsid, comprising the surface region associated with ADE. A surprisingly high number of divergent amino acid positions were found in the luminal threefold and twofold axes of the capsid, regions of hitherto unknown function. We emphasize the importance of complete genome analyses and, given the marked phylogenetic inconsistencies across the genome, advise to obtain the complete coding sequences of divergent strains. Further studies on amdoparvovirus biology and structure as well as epidemiological and virus discovery investigations are required to better characterize the ecology and evolution of this important group of viruses.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland , 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
| | - Judit J Pénzes
- Institute for Quantitative Biomedicine, Rutgers the State University of New Jersey , 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland , 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
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Canuti M, Mira F, Sorensen RG, Rodrigues B, Bouchard É, Walzthoni N, Hopson M, Gilroy C, Whitney HG, Lang AS. Distribution and diversity of dog parvoviruses in wild, free-roaming and domestic canids of Newfoundland and Labrador, Canada. Transbound Emerg Dis 2022; 69:e2694-e2705. [PMID: 35689408 DOI: 10.1111/tbed.14620] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/21/2022] [Accepted: 05/28/2022] [Indexed: 01/02/2023]
Abstract
Some parvoviruses of carnivorans can infect multiple host species. Since many canine parvoviruses were only discovered recently, their host-range is still unexplored. We examined the host distribution and diversity of five dog parvoviruses in four canine populations from Newfoundland and Labrador, Canada, and investigated the potential for these viruses to cross the species barriers. Canine bocavirus 2 (CBoV-2) and the minute virus of canines were detected in stool from free-roaming dogs from Labrador (5/48 [10.4%] and 3/48 [6.3%], respectively) and two different CBoV-2 variants were identified. Canine bufavirus was identified in stool from free-roaming dogs (1/48, 2.1%) and foxes (3/80, 3.8%) from Labrador, but two different variants were observed in the two host species. The variant found in foxes was highly divergent from previously identified strains. Two cachavirus 1 variants, genetically similar to those circulating in other Canadian wildlife, were found in spleens from Newfoundland coyotes (3/87, 3.5%). Canine parvovirus type 2 (CPV-2) was found in stool from free-roaming dogs from Labrador (2/48, 4.2%) and in spleens from Newfoundland coyotes (3/87, 3.5%). Comparing CPV-2 sequences from these hosts to those retrieved from local symptomatic domestic dogs revealed the presence of a highly heterogeneous viral population as detected strains belonged to five different clades. The close relationship between CPV-2a strains from a dog and a coyote suggests the occurrence of viral transfer between wild and domestic canids. The identification of highly related strains with a similar molecular signature characteristic of older CPV-2 strains in free-roaming and domestic dogs suggests a probable common ancestry and that older CPV-2 strains, which have not been identified in dogs since the 1990s, persist in this part of Canada. Follow-up studies should evaluate samples from a larger number of animals and host species to extensively investigate the possible occurrence of cross-species transmission for recently discovered parvoviruses.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Francesco Mira
- Istituto Zooprofilattico Sperimentale della Sicilia 'A. Mirri', Palermo, Italy
| | - Rachel G Sorensen
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Bruce Rodrigues
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, Corner Brook, Newfoundland and Labrador, Canada
| | - Émilie Bouchard
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Natasha Walzthoni
- Veterinary Specialty Centre of Newfoundland and Labrador, Mount Pearl, Newfoundland and Labrador, Canada
| | - Marti Hopson
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Cornelia Gilroy
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
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11
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Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Rep Med 2022; 3:100583. [PMID: 35480627 PMCID: PMC8913280 DOI: 10.1016/j.xcrm.2022.100583] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/30/2021] [Accepted: 03/01/2022] [Indexed: 12/11/2022]
Abstract
The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
| | - Rockib Uddin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas Matluk
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Sarah E Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA; Departments of Neurosurgery and Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
| | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Marie L Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Heather Grieser
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - Sim Meak
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | - John Martha
- Maine Center for Disease Control and Prevention, Augusta, ME 04333, USA; Health and Environmental Testing Laboratory, Augusta, ME 04333, USA
| | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Ewa King
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Richard C Huard
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Vlad Novitsky
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Mark Howison
- Research Improving People's Lives, Providence, RI 02903, USA
| | - Josephine Darpolor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Akarsh Manne
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02906, USA
| | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | | | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Andrew S Lang
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Glen R Gallagher
- Massachusetts Department of Public Health, Boston, MA 02130, USA
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Ryan Tewhey
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey; Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob E Lemieux
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA.
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12
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Alex CE, Canuti M, Schlesinger MS, Jackson KA, Needle D, Jardine C, Nituch L, Bourque L, Lang AS, Pesavento PA. Natural disease and evolution of an amdoparvovirus endemic in striped skunks (
Mephitis mephitis
). Transbound Emerg Dis 2022; 69:e1758-e1767. [DOI: 10.1111/tbed.14511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Charles E. Alex
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine University of California‐Davis Davis CA USA
| | - Marta Canuti
- Department of Biology Memorial University of Newfoundland St. John's NL Canada
| | - Maya S. Schlesinger
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine University of California‐Davis Davis CA USA
| | - Kenneth A. Jackson
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine University of California‐Davis Davis CA USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture University of New Hampshire Durham NH USA
| | - Claire Jardine
- Department of Pathobiology, Canadian Wildlife Health Cooperative University of Guelph Guelph ON Canada
| | - Larissa Nituch
- Ontario Ministry of Northern Development Mines, Natural Resources and Forestry Peterborough ON Canada
| | - Laura Bourque
- Canadian Wildlife Health Cooperative – Atlantic Region University of Prince Edward Island 550 University Ave Charlottetown PE C1A4P3 Canada
| | - Andrew S. Lang
- Department of Biology Memorial University of Newfoundland St. John's NL Canada
| | - Patricia A. Pesavento
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine University of California‐Davis Davis CA USA
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13
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Canuti M, Fry K, Dean Cluff H, Mira F, Fenton H, Lang AS. Co‐circulation of five species of dog parvoviruses and canine adenovirus type 1 among gray wolves (
Canis lupus
) in northern Canada. Transbound Emerg Dis 2022; 69:e1417-e1433. [DOI: 10.1111/tbed.14474] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Marta Canuti
- Department of Biology Memorial University of Newfoundland St. John's NL Canada
| | - Kelsi Fry
- Department of Biology Memorial University of Newfoundland St. John's NL Canada
| | - H. Dean Cluff
- Environment and Natural Resources ‐ North Slave Region Government of the Northwest Territories Yellowknife Canada
| | - Francesco Mira
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri” Palermo Italy
| | - Heather Fenton
- Environment and Natural Resources ‐ North Slave Region Government of the Northwest Territories Yellowknife Canada
| | - Andrew S. Lang
- Department of Biology Memorial University of Newfoundland St. John's NL Canada
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14
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Siddle KJ, Krasilnikova LA, Moreno GK, Schaffner SF, Vostok J, Fitzgerald NA, Lemieux JE, Barkas N, Loreth C, Specht I, Tomkins-Tinch CH, Paull JS, Schaeffer B, Taylor BP, Loftness B, Johnson H, Schubert PL, Shephard HM, Doucette M, Fink T, Lang AS, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet GL, DeRuff KC, Vodzak ME, Adams GC, Dobbins ST, Slack SD, Reilly SK, Anderson LM, Cipicchio MC, DeFelice MT, Grimsby JL, Anderson SE, Blumenstiel BS, Meldrim JC, Rooke HM, Vicente G, Smith NL, Messer KS, Reagan FL, Mandese ZM, Lee MD, Ray MC, Fisher ME, Ulcena MA, Nolet CM, English SE, Larkin KL, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage WP, Bernard C, Philippakis A, Lennon NJ, Gabriel SB, Gallagher GR, Smole S, Madoff LC, Brown CM, Park DJ, MacInnis BL, Sabeti PC. Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak. Cell 2022; 185:485-492.e10. [PMID: 35051367 PMCID: PMC8695126 DOI: 10.1016/j.cell.2021.12.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 12/17/2021] [Indexed: 02/08/2023]
Abstract
An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.
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Affiliation(s)
| | - Lydia A Krasilnikova
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gage K Moreno
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Johanna Vostok
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | | | - Jacob E Lemieux
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nikolaos Barkas
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Ivan Specht
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Christopher H Tomkins-Tinch
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Jillian S Paull
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Beau Schaeffer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Bradford P Taylor
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Bryn Loftness
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hillary Johnson
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Petra L Schubert
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Hanna M Shephard
- Massachusetts Department of Public Health, Boston, MA 02199, USA; Applied Epidemiology Fellowship, Council of State and Territorial Epidemiologists, Atlanta, GA 30345, USA
| | - Matthew Doucette
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Andrew S Lang
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Stephanie Baez
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - John Beauchamp
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Scott Hennigan
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Erika Buzby
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Stephanie Ash
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Jessica Brown
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Selina Clancy
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Seana Cofsky
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Luc Gagne
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Joshua Hall
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | | | | | | | - Megan E Vodzak
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gordon C Adams
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Sarah D Slack
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Steven K Reilly
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lisa M Anderson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | | | - Jonna L Grimsby
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | | | - James C Meldrim
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Heather M Rooke
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gina Vicente
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Natasha L Smith
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Faye L Reagan
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zoe M Mandese
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew D Lee
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Marianne C Ray
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Maesha A Ulcena
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Corey M Nolet
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sean E English
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Katie L Larkin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kyle Vernest
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Deirdre Arvidson
- Barnstable County Department of Health and the Environment, Barnstable, MA 02630, USA
| | - Maurice Melchiono
- Barnstable County Department of Health and the Environment, Barnstable, MA 02630, USA
| | - Theresa Covell
- Barnstable County Department of Health and the Environment, Barnstable, MA 02630, USA
| | - Vaira Harik
- Barnstable County Department of Human Services, Barnstable, MA 02630, USA
| | - Taylor Brock-Fisher
- Community Tracing Collaborative, Commonwealth of Massachusetts, Boston, MA 02199, USA
| | - Molly Dunn
- Community Tracing Collaborative, Commonwealth of Massachusetts, Boston, MA 02199, USA
| | - Amanda Kearns
- Community Tracing Collaborative, Commonwealth of Massachusetts, Boston, MA 02199, USA
| | - William P Hanage
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Clare Bernard
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Niall J Lennon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Glen R Gallagher
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA 02199, USA
| | | | | | - Daniel J Park
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Bronwyn L MacInnis
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Massachusetts Consortium for Pathogen Readiness, Boston, MA 02115, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Massachusetts Consortium for Pathogen Readiness, Boston, MA 02115, USA
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15
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Ramey AM, Hill NJ, DeLiberto TJ, Gibbs SEJ, Camille Hopkins M, Lang AS, Poulson RL, Prosser DJ, Sleeman JM, Stallknecht DE, Wan X. Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrew M. Ramey
- U.S. Geological Survey Alaska Science Center 4210 University Drive Anchorage AK 99508 USA
| | - Nichola J. Hill
- Department of Infectious Disease & Global Health, Cummings School of Veterinary Medicine Tufts University 200 Westboro Road North Grafton MA 01536 USA
| | - Thomas J. DeLiberto
- National Wildlife Disease Program, Wildlife Services, Animal and Plant Health Inspection Service U.S. Department of Agriculture 4101 LaPorte Avenue Fort Collins CO 80521 USA
| | - Samantha E. J. Gibbs
- Wildlife Health Office Natural Resource Program Center, National Wildlife Refuge System, U.S. Fish and Wildlife Service 16450 NW 31st Place Chiefland FL 32626 USA
| | - M. Camille Hopkins
- U.S. Geological Survey Ecosystems Mission Area 12201 Sunrise Valley Drive, MS 300 (Room 4A100F) Reston VA 20192 USA
| | - Andrew S. Lang
- Department of Biology Memorial University of Newfoundland 232 Elizabeth Avenue St. John's Newfoundland A1B 3X9 Canada
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia 589 D.W. Brooks Drive Athens GA 30602 USA
| | - Diann J. Prosser
- U.S. Geological Survey Eastern Ecological Science Center at the Patuxent Research Refuge 12100 Beech Forest Road Laurel MD 20708 USA
| | - Jonathan M. Sleeman
- U.S. Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison WI 53711 USA
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia 589 D.W. Brooks Drive Athens GA 30602 USA
| | - Xiu‐Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, Department of Electronic Engineering and Computer Science University of Missouri Columbia MO 65211 USA
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16
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Farrar VS, Harris RM, Austin SH, Nava Ultreras BM, Booth AM, Angelier F, Lang AS, Feustel T, Lee C, Bond A, MacManes MD, Calisi RM. Prolactin and prolactin receptor expression in the HPG axis and crop during parental care in both sexes of a biparental bird (Columba livia). Gen Comp Endocrinol 2022; 315:113940. [PMID: 34756919 DOI: 10.1016/j.ygcen.2021.113940] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/11/2021] [Accepted: 10/22/2021] [Indexed: 12/31/2022]
Abstract
During breeding, multiple circulating hormones, including prolactin, facilitate reproductive transitions in species that exhibit parental care. Prolactin underlies parental behaviors and related physiological changes across many vertebrates, including birds and mammals. While circulating prolactin levels often fluctuate across breeding, less is known about how relevant target tissues vary in their prolactin responsiveness via prolactin receptor (PRLR) expression. Recent studies have also investigated prolactin (PRL) gene expression outside of the pituitary (i.e., extra-pituitary PRL), but how PRL gene expression varies during parental care in non-pituitary tissue (e.g., hypothalamus, gonads) remains largely unknown. Further, it is unclear if and how tissue-specific PRL and PRLR vary between the sexes during biparental care. To address this, we measured PRL and PRLR gene expression in tissues relevant to parental care, the endocrine reproductive hypothalamic-pituitary- gonadal (HPG) axis and the crop (a tissue with a similar function as the mammalian mammary gland), across various reproductive stages in both sexes of a biparental bird, the rock dove (Columba livia). We also assessed how these genes responded to changes in offspring presence by adding chicks mid-incubation, simulating an early hatch when prolactin levels were still moderately low. We found that pituitary PRL expression showed similar increases as plasma prolactin levels, and detected extra-pituitary PRL in the hypothalamus, gonads and crop. Hypothalamic and gonadal PRLR expression also changed as birds began incubation. Crop PRLR expression correlated with plasma prolactin, peaking when chicks hatched. In response to replacing eggs with a novel chick mid-incubation, hypothalamic and gonadal PRL and PRLR gene expression differed significantly compared to mid-incubation controls, even when plasma prolactin levels did not differ. We also found sex differences in PRL and PRLR that suggest gene expression may allow males to compensate for lower levels in prolactin by upregulating PRLR in all tissues. Overall, this study advances our understanding of how tissue-specific changes in responsiveness to parental hormones may differ across key reproductive transitions, in response to offspring cues, and between the sexes.
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Affiliation(s)
- Victoria S Farrar
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States.
| | - Rayna M Harris
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
| | - Suzanne H Austin
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
| | - Brandon M Nava Ultreras
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
| | - April M Booth
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
| | - Frédéric Angelier
- Centre d'Etudes Biologiques de Chizé, CNRS, UMR 7372, 79360 Villiers en Bois, France
| | - Andrew S Lang
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Tanner Feustel
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
| | - Candice Lee
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
| | - Annie Bond
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
| | - Matthew D MacManes
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Rebecca M Calisi
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, United States
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17
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Canuti M, Rodrigues B, Bouchard É, Whitney HG, Lang AS, Dufour SC, Verhoeven JT. Distinct epidemiological profiles of porcine circovirus 3 and fox circovirus in Canadian foxes (Vulpes spp.). Current Research in Microbial Sciences 2022; 3:100161. [DOI: 10.1016/j.crmicr.2022.100161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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18
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Siddle KJ, Krasilnikova LA, Moreno GK, Schaffner SF, Vostok J, Fitzgerald NA, Lemieux JE, Barkas N, Loreth C, Specht I, Tomkins-Tinch CH, Silbert J, Schaeffer B, Taylor BP, Loftness B, Johnson H, Schubert PL, Shephard HM, Doucette M, Fink T, Lang AS, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet GL, DeRuff KC, Vodzak ME, Adams GC, Dobbins ST, Slack SD, Reilly SK, Anderson LM, Cipicchio MC, DeFelice MT, Grimsby JL, Anderson SE, Blumenstiel BS, Meldrim JC, Rooke HM, Vicente G, Smith NL, Messer KS, Reagan FL, Mandese ZM, Lee MD, Ray MC, Fisher ME, Ulcena MA, Nolet CM, English SE, Larkin KL, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage WP, Bernard C, Philippakis A, Lennon NJ, Gabriel SB, Gallagher GR, Smole S, Madoff LC, Brown CM, Park DJ, MacInnis BL, Sabeti PC. Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts. medRxiv 2021. [PMID: 34704102 PMCID: PMC8547534 DOI: 10.1101/2021.10.20.21265137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most cases were fully vaccinated, many of whom were also symptomatic, prompting a comprehensive public health response, motivating changes to national masking recommendations, and raising questions about infection and transmission among vaccinated individuals. To characterize the outbreak and the viral population underlying it, we combined genomic and epidemiological data from 467 individuals, including 40% of known outbreak-associated cases. The Delta variant accounted for 99% of sequenced outbreak-associated cases. Phylogenetic analysis suggests over 40 sources of Delta in the dataset, with one responsible for a single cluster containing 83% of outbreak-associated genomes. This cluster was likely not the result of extensive spread at a single site, but rather transmission from a common source across multiple settings over a short time. Genomic and epidemiological data combined provide strong support for 25 transmission events from, including many between, fully vaccinated individuals; genomic data alone provides evidence for an additional 64. Together, genomic epidemiology provides a high-resolution picture of the Provincetown outbreak, revealing multiple cases of transmission of Delta from fully vaccinated individuals. However, despite its magnitude, the outbreak was restricted in its onward impact in MA and the US, likely due to high vaccination rates and a robust public health response.
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Earnest R, Uddin R, Matluk N, Renzette N, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CB, Turbett S, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HH, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. medRxiv 2021:2021.10.06.21264641. [PMID: 34642698 PMCID: PMC8509091 DOI: 10.1101/2021.10.06.21264641] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.
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Affiliation(s)
- Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Rockib Uddin
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicholas Matluk
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Nicholas Renzette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | | | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Robert Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Kendall Billig
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sarah Turbett
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
- Departments of Neurosurgery and Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
| | - Bony De Kumar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David R. Peaper
- Departments of Laboratory Medicine and Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Heather Grieser
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - Sim Meak
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | - John Martha
- Maine Center for Disease Control and Prevention, Augusta, ME 04333
- Health and Environmental Testing Laboratory, Augusta, ME 04333
| | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | | | - Ewa King
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Richard C. Huard
- Rhode Island Department of Health, State Health Laboratories, Providence, RI 02904, USA
| | - Sandra C. Smole
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | - Timelia Fink
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | - Andrew S. Lang
- Massachusetts Department of Public Health, Boston MA 02130, USA
| | | | | | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Ryan Tewhey
- Department of Medical Genetics, Acibadem University School of Medicine, Istanbul, Turkey
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Mark D. Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Daniel J. Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacob E. Lemieux
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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20
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Canuti M, Bouchard É, Rodrigues B, Whitney HG, Hopson M, Gilroy C, Stenson G, Dufour SC, Lang AS, Verhoeven JTP. Newlavirus, a Novel, Highly Prevalent, and Highly Diverse Protoparvovirus of Foxes ( Vulpes spp.). Viruses 2021; 13:1969. [PMID: 34696399 PMCID: PMC8537079 DOI: 10.3390/v13101969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
The genus Protoparvovirus (family Parvoviridae) includes several viruses of carnivores. We describe a novel fox protoparvovirus, which we named Newlavirus as it was discovered in samples from Newfoundland and Labrador, Canada. Analysis of the full non-structural protein (NS1) sequence indicates that this virus is a previously uncharacterized species. Newlavirus showed high prevalence in foxes from both the mainland (Labrador, 54/137, 39.4%) and the island of Newfoundland (22/50, 44%) but was not detected in samples from other carnivores, including coyotes (n = 92), lynx (n = 58), martens (n = 146), mink (n = 47), ermines (n = 17), dogs (n = 48), and ringed (n = 4), harp (n = 6), bearded (n = 6), and harbor (n = 2) seals. Newlavirus was found at similar rates in stool and spleen (24/80, 30% vs. 59/152, 38.8%, p = 0.2) but at lower rates in lymph nodes (2/37, 5.4%, p < 0.01). Sequencing a fragment of approximately 750 nt of the capsid protein gene from 53 samples showed a high frequency of co-infection by more than one strain (33.9%), high genetic diversity with 13 genotypes with low sequence identities (70.5-87.8%), and no geographic segregation of strains. Given the high prevalence, high diversity, and the lack of identification in other species, foxes are likely the natural reservoir of Newlavirus, and further studies should investigate its distribution.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Émilie Bouchard
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada;
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, 3200 rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Bruce Rodrigues
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook, NL A2H 7S1, Canada;
| | - Hugh G. Whitney
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Marti Hopson
- Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PE C1A 4P3, Canada;
| | - Cornelia Gilroy
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PE C1A 4P3, Canada;
| | - Garry Stenson
- Fisheries and Oceans Canada, Government of Canada, P.O. Box 5667, St. John’s, NL A1C 5X1, Canada;
| | - Suzanne C. Dufour
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Andrew S. Lang
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Joost T. P. Verhoeven
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
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21
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Abstract
The family Marnaviridae comprises small non-enveloped viruses with positive-sense RNA genomes of 8.6-9.6 kb. Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets derived from marine and freshwater environments. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Marnaviridae, which is available at ictv.global/report/marnaviridae.
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Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alexander I Culley
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Curtis A Suttle
- Departments of Botany, Earth, Ocean and Atmospheric Sciences and Microbiology and Immunology, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Yoshitake Takao
- Department of Marine Bioscience, Fukui Prefectural University, Fukui, Japan
| | - Yuji Tomaru
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, Hiroshima, Japan
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22
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Klompas M, Baker MA, Rhee C, Tucker R, Fiumara K, Griesbach D, Bennett-Rizzo C, Salmasian H, Wang R, Wheeler N, Gallagher GR, Lang AS, Fink T, Baez S, Smole S, Madoff L, Goralnick E, Resnick A, Pearson M, Britton K, Sinclair J, Morris CA. A SARS-CoV-2 Cluster in an Acute Care Hospital. Ann Intern Med 2021; 174:794-802. [PMID: 33556277 PMCID: PMC7924623 DOI: 10.7326/m20-7567] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Little is known about clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in acute care hospitals. OBJECTIVE To describe the detection, mitigation, and analysis of a large cluster of SARS-CoV-2 infections in an acute care hospital with mature infection control policies. DESIGN Descriptive study. SETTING Brigham and Women's Hospital, Boston, Massachusetts. PARTICIPANTS Patients and staff with cluster-related SARS-CoV-2 infections. INTERVENTION Close contacts of infected patients and staff were identified and tested every 3 days, patients on affected units were preemptively isolated and repeatedly tested, affected units were cleaned, room ventilation was measured, and specimens were sent for whole-genome sequencing. A case-control study was done to compare clinical interactions, personal protective equipment use, and breakroom and workroom practices in SARS-CoV-2-positive versus negative staff. MEASUREMENTS Description of the cluster, mitigation activities, and risk factor analysis. RESULTS Fourteen patients and 38 staff members were included in the cluster per whole-genome sequencing and epidemiologic associations. The index case was a symptomatic patient in whom isolation was discontinued after 2 negative results on nasopharyngeal polymerase chain reaction testing. The patient subsequently infected multiple roommates and staff, who then infected others. Seven of 52 (13%) secondary infections were detected only on second or subsequent tests. Eight of 9 (89%) patients who shared rooms with potentially contagious patients became infected. Potential contributing factors included high viral loads, nebulization, and positive pressure in the index patient's room. Risk factors for transmission to staff included presence during nebulization, caring for patients with dyspnea or cough, lack of eye protection, at least 15 minutes of exposure to case patients, and interactions with SARS-CoV-2-positive staff in clinical areas. Whole-genome sequencing confirmed that 2 staff members were infected despite wearing surgical masks and eye protection. LIMITATION Findings may not be generalizable. CONCLUSION SARS-CoV-2 clusters can occur in hospitals despite robust infection control policies. Insights from this cluster may inform additional measures to protect patients and staff. PRIMARY FUNDING SOURCE None.
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Affiliation(s)
- Michael Klompas
- Harvard Medical School, Harvard Pilgrim Health Care Institute, and Brigham and Women's Hospital, Boston, Massachusetts (M.K., M.A.B., C.R.)
| | - Meghan A Baker
- Harvard Medical School, Harvard Pilgrim Health Care Institute, and Brigham and Women's Hospital, Boston, Massachusetts (M.K., M.A.B., C.R.)
| | - Chanu Rhee
- Harvard Medical School, Harvard Pilgrim Health Care Institute, and Brigham and Women's Hospital, Boston, Massachusetts (M.K., M.A.B., C.R.)
| | - Robert Tucker
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Karen Fiumara
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Diane Griesbach
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Carin Bennett-Rizzo
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Hojjat Salmasian
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Rui Wang
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts (R.W.)
| | - Noah Wheeler
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Glen R Gallagher
- Massachusetts Department of Public Health, Boston, Massachusetts (G.R.G., A.S.L., T.F., S.B., S.S., L.M.)
| | - Andrew S Lang
- Massachusetts Department of Public Health, Boston, Massachusetts (G.R.G., A.S.L., T.F., S.B., S.S., L.M.)
| | - Timelia Fink
- Massachusetts Department of Public Health, Boston, Massachusetts (G.R.G., A.S.L., T.F., S.B., S.S., L.M.)
| | - Stephanie Baez
- Massachusetts Department of Public Health, Boston, Massachusetts (G.R.G., A.S.L., T.F., S.B., S.S., L.M.)
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, Massachusetts (G.R.G., A.S.L., T.F., S.B., S.S., L.M.)
| | - Larry Madoff
- Massachusetts Department of Public Health, Boston, Massachusetts (G.R.G., A.S.L., T.F., S.B., S.S., L.M.)
| | - Eric Goralnick
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Andrew Resnick
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Madelyn Pearson
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Kathryn Britton
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Julia Sinclair
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
| | - Charles A Morris
- Brigham and Women's Hospital, Boston, Massachusetts (R.T., K.F., D.G., C.B., H.S., N.W., E.G., A.R., M.P., K.B., J.S., C.A.M.)
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23
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Tomasch J, Koppenhöfer S, Lang AS. Connection Between Chromosomal Location and Function of CtrA Phosphorelay Genes in Alphaproteobacteria. Front Microbiol 2021; 12:662907. [PMID: 33995326 PMCID: PMC8116508 DOI: 10.3389/fmicb.2021.662907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022] Open
Abstract
Most bacterial chromosomes are circular, with replication starting at one origin (ori) and proceeding on both replichores toward the terminus (ter). Several studies have shown that the location of genes relative to ori and ter can have profound effects on regulatory networks and physiological processes. The CtrA phosphorelay is a gene regulatory system conserved in most alphaproteobacteria. It was first discovered in Caulobacter crescentus where it controls replication and division into a stalked and a motile cell in coordination with other factors. The locations of the ctrA gene and targets of this response regulator on the chromosome affect their expression through replication-induced DNA hemi-methylation and specific positioning along a CtrA activity gradient in the dividing cell, respectively. Here we asked to what extent the location of CtrA regulatory network genes might be conserved in the alphaproteobacteria. We determined the locations of the CtrA phosphorelay and associated genes in closed genomes with unambiguously identifiable ori from members of five alphaproteobacterial orders. The location of the phosphorelay genes was the least conserved in the Rhodospirillales followed by the Sphingomonadales. In the Rhizobiales a trend toward certain chromosomal positions could be observed. Compared to the other orders, the CtrA phosphorelay genes were conserved closer to ori in the Caulobacterales. In contrast, the genes were highly conserved closer to ter in the Rhodobacterales. Our data suggest selection pressure results in differential positioning of CtrA phosphorelay and associated genes in alphaproteobacteria, particularly in the orders Rhodobacterales, Caulobacterales and Rhizobiales that is worth deeper investigation.
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Affiliation(s)
- Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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24
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Klompas M, Baker MA, Griesbach D, Tucker R, Gallagher GR, Lang AS, Fink T, Cumming M, Smole S, Madoff LC, Rhee C. Transmission of SARS-CoV-2 from asymptomatic and presymptomatic individuals in healthcare settings despite medical masks and eye protection. Clin Infect Dis 2021; 73:1693-1695. [PMID: 33704451 PMCID: PMC7989527 DOI: 10.1093/cid/ciab218] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 01/14/2023] Open
Abstract
We describe 3 instances of SARS-CoV-2 transmission despite medical masks and eye protection, including transmission despite the source person being masked, transmission despite the exposed person being masked, and transmission despite both parties being masked. Whole genome sequencing confirmed perfect homology between source and exposed persons’ viruses in all cases.
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Affiliation(s)
- Michael Klompas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA.,Brigham and Women's Hospital, Boston, MA
| | - Meghan A Baker
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA.,Brigham and Women's Hospital, Boston, MA
| | | | | | | | - Andrew S Lang
- Massachusetts Department of Public Health, Boston, MA
| | - Timelia Fink
- Massachusetts Department of Public Health, Boston, MA
| | - Melissa Cumming
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
| | - Sandra Smole
- Massachusetts Department of Public Health, Boston, MA
| | | | - Chanu Rhee
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA.,Brigham and Women's Hospital, Boston, MA
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25
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Austin SH, Harris RM, Booth AM, Lang AS, Farrar VS, Krause JS, Hallman TA, MacManes M, Calisi RM. Isolating the Role of Corticosterone in the Hypothalamic-Pituitary-Gonadal Transcriptomic Stress Response. Front Endocrinol (Lausanne) 2021; 12:632060. [PMID: 34149609 PMCID: PMC8207517 DOI: 10.3389/fendo.2021.632060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
Investigation of the negative impacts of stress on reproduction has largely centered around the effects of the adrenal steroid hormone, corticosterone (CORT), and its influence on a system of tissues vital for reproduction-the hypothalamus of the brain, the pituitary gland, and the gonads (the HPG axis). Research on the action of CORT on the HPG axis has predominated the stress and reproductive biology literature, potentially overshadowing other influential mediators. To gain a more complete understanding of how elevated CORT affects transcriptomic activity of the HPG axis, we experimentally examined its role in male and female rock doves (Columba livia). We exogenously administrated CORT to mimic circulating levels during the stress response, specifically 30 min of restraint stress, an experimental paradigm known to increase circulating CORT in vertebrates. We examined all changes in transcription within each level of the HPG axis as compared to both restraint-stressed birds and vehicle-injected controls. We also investigated the differential transcriptomic response to CORT and restraint-stress in each sex. We report causal and sex-specific effects of CORT on the HPG transcriptomic stress response. Restraint stress caused 1567 genes to uniquely differentially express while elevated circulating CORT was responsible for the differential expression of 304 genes. Only 108 genes in females and 8 in males differentially expressed in subjects that underwent restraint stress and those who were given exogenous CORT. In response to elevated CORT and restraint-stress, both sexes shared the differential expression of 5 genes, KCNJ5, CISH, PTGER3, CEBPD, and ZBTB16, all located in the pituitary. The known functions of these genes suggest potential influence of elevated CORT on immune function and prolactin synthesis. Gene expression unique to each sex indicated that elevated CORT affected more gene transcription in females than males (78 genes versus 3 genes, respectively). To our knowledge, this is the first study to isolate the role of CORT in HPG genomic transcription during a stress response. We present an extensive and openly accessible view of the role corticosterone in the HPG transcriptomic stress response. Because the HPG system is well conserved across vertebrates, these data have the potential to inspire new therapeutic strategies for reproductive dysregulation in multiple vertebrate systems, including our own.
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Affiliation(s)
- Suzanne H. Austin
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, United States
- *Correspondence: Suzanne H. Austin,
| | - Rayna M. Harris
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, United States
| | - April M. Booth
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, United States
| | - Andrew S. Lang
- Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH, United States
| | - Victoria S. Farrar
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, United States
| | - Jesse S. Krause
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, United States
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Tyler A. Hallman
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States
| | - Matthew MacManes
- Department of Molecular, Cellular and Biomedical Sciences, The University of New Hampshire, Durham, NH, United States
| | - Rebecca M. Calisi
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, United States
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Wight J, Varin MP, Robertson GJ, Huot Y, Lang AS. Microbiology in the Field: Construction and Validation of a Portable Incubator for Real-Time Quantification of Coliforms and Other Bacteria. Front Public Health 2020; 8:607997. [PMID: 33324604 PMCID: PMC7723852 DOI: 10.3389/fpubh.2020.607997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022] Open
Abstract
Performing microbiological assays on environmental samples in field settings poses logistical challenges with respect to the availability of suitable equipment or the ability to get samples to the laboratory in a timely fashion. For example, the viability of some bacteria can decrease greatly between sampling and arrival to the laboratory for processing. We developed and constructed rugged, reliable, and cost-effective portable incubators that were used by 10 independent field teams to perform microbiological assays on surface water samples from lakes across Canada. Rigorous testing and validation of our incubators ensured that incubation conditions were consistent within and across all 10 field teams and 2 sampling years. Samples from all sites were processed in duplicate and bacterial counts were highly repeatable within and across sampling teams. Bacterial counts were also found to be statistically equivalent to counts obtained with standard laboratory techniques using a conventional incubator. Using this method, thermotolerant coliforms (TTCs) and Escherichia coli were quantified from 432 lakes, allowing comparison to both historical datasets that relied on TTCs and those following current guidelines that use E. coli counts. We found higher loads at the shoreline than the middle of lakes and different patterns between ecozones. E. coli was not frequently detected, but many lakes exceeded Canadian guideline values for activities such as swimming and some even exceeded the guideline value for secondary recreational activities such as boating. To the best of our knowledge, this is the largest bacteriological water quality assessment of freshwater lakes to date in terms of both spatial scale and the number of lakes sampled. Our incubator design can be easily adapted for a wide variety of researcher goals and represents a robust platform for field studies and other applications, including those in remote or low-resources settings.
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Affiliation(s)
- Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Marie-Pierre Varin
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, Mount Pearl, NL, Canada
| | - Yannick Huot
- Département de Géomatique Appliquée, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Canuti M, McDonald E, Graham SM, Rodrigues B, Bouchard É, Neville R, Pitcher M, Whitney HG, Marshall HD, Lang AS. Multi-host dispersal of known and novel carnivore amdoparvoviruses. Virus Evol 2020; 6:veaa072. [PMID: 36158990 PMCID: PMC9492287 DOI: 10.1093/ve/veaa072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Amdoparvoviruses (family Parvoviridae) are ssDNA viruses that cause an immune complex-mediated wasting syndrome in carnivores. They are multi-host pathogens and cross-species infection is facilitated by the fact that viral entry is mediated by cellular Fc receptors recognizing antibody-coated viruses. We developed a pan-amdoparvovirus PCR and screened tissue samples from 666 wild carnivores (families Felidae, Canidae, and Mustelidae) from Newfoundland or Labrador (Canada) and molecularly characterized the identified strains. Fifty-four out of 666 (8.1%) animals were amdoparvovirus-positive. Infection rate was the highest in American mink (34/47, 72.3%), followed by foxes (Arctic and red foxes, 13/311, 4.2%), lynx (2/58, 3.5%), and American martens (5/156, 3.4%). No virus was detected in samples from 87 coyotes and 17 ermines. Viruses from Newfoundland were classified as Aleutian mink disease virus (AMDV). Mink harvested near AMDV-affected fur farms had higher prevalence (24/24, 100%) than other mink (10/23, 43.5%; P < 0.001) and their viruses were phylogenetically closely related to those from farms, while most viruses from other mink were in other clades. Strains from three foxes and two lynx were highly related to mink strains. This proves that farms disperse AMDV that subsequently spreads among wild mink (maintenance host) and transmits to other spillover carnivore hosts. In Labrador two novel viruses were identified, Labrador amdoparvovirus 1 (LaAV-1) found in foxes (9/261, 3.5%) and martens (5/156, 3.4%), and LaAV-2 found in one fox (0.4%). LaAV-1 fulfills all requirements to be classified as a novel species. LaAV-1 was most similar to viruses of mink and skunks (AMDV and skunk amdoparvovirus (SKAV)) while LaAV-2 was more closely related to other viruses infecting canids. LaAV-1 capsid proteins were almost indistinguishable from those of AMDV in some regions, suggesting that LaAV-1 could be a virus of mustelids that can infect foxes. While intensive farming practices provide occasions for inter-species transmission in farms, niche overlap or predation could explain cross-species transmission in the wild, but competition among sympatric species reduces the chances of direct contacts, making this an infrequent event. Pan-amdoparvovirus detection methods in wide epidemiological investigations can play a crucial role in defining amdoparvoviral ecology and evolution and discovering novel viruses.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Emily McDonald
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Stephanie M Graham
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Bruce Rodrigues
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook, Newfoundland and Labrador A2H 7S1 Canada
| | - Émilie Bouchard
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Richard Neville
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 3014, Stn. B, Happy Valley-Goose Bay, Newfoundland and Labrador A0P 1E0, Canada
| | - Mac Pitcher
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook, Newfoundland and Labrador A2H 7S1 Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - H Dawn Marshall
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
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Ramey AM, Reeves AB, Drexler JZ, Ackerman JT, De La Cruz S, Lang AS, Leyson C, Link P, Prosser DJ, Robertson GJ, Wight J, Youk S, Spackman E, Pantin-Jackwood M, Poulson RL, Stallknecht DE. Influenza A viruses remain infectious for more than seven months in northern wetlands of North America. Proc Biol Sci 2020; 287:20201680. [PMID: 32901574 DOI: 10.1098/rspb.2020.1680] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In this investigation, we used a combination of field- and laboratory-based approaches to assess if influenza A viruses (IAVs) shed by ducks could remain viable for extended periods in surface water within three wetland complexes of North America. In a field experiment, replicate filtered surface water samples inoculated with duck swabs were tested for IAVs upon collection and again after an overwintering period of approximately 6-7 months. Numerous IAVs were molecularly detected and isolated from these samples, including replicates maintained at wetland field sites in Alaska and Minnesota for 181-229 days. In a parallel laboratory experiment, we attempted to culture IAVs from filtered surface water samples inoculated with duck swabs from Minnesota each month during September 2018-April 2019 and found monthly declines in viral viability. In an experimental challenge study, we found that IAVs maintained in filtered surface water within wetlands of Alaska and Minnesota for 214 and 226 days, respectively, were infectious in a mallard model. Collectively, our results support surface waters of northern wetlands as a biologically important medium in which IAVs may be both transmitted and maintained, potentially serving as an environmental reservoir for infectious IAVs during the overwintering period of migratory birds.
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Affiliation(s)
- Andrew M Ramey
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA
| | - Andrew B Reeves
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA
| | - Judith Z Drexler
- US Geological Survey, California Water Science Center, 6000 J Street, Placer Hall, Sacramento, CA 95819, USA
| | - Joshua T Ackerman
- US Geological Survey, Western Ecological Research Center, Dixon Field Station, 800 Business Park Drive, Suite D, Dixon, CA 95620, USA
| | - Susan De La Cruz
- US Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, 350 N Akron Road, Building 19, Moffett Field, CA 94035, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St John's, Newfoundland, A1B 3X9, Canada
| | - Christina Leyson
- Exotic and Emerging Avian Viral Diseases Research Unit, US National Poultry Research Center, US Department of Agriculture, Agricultural Research Service, Athens, Georgia, USA
| | - Paul Link
- Louisiana Department of Wildlife and Fisheries, 2000 Quail Drive, Room 436, Baton Rouge, LA 70808, USA
| | - Diann J Prosser
- US Geological Survey Patuxent Wildlife Research Center, 12100 Beech Forest Road, Laurel, MD 20708, USA
| | - Gregory J Robertson
- Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, Newfoundland, A1N 4T3, Canada
| | - Jordan Wight
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St John's, Newfoundland, A1B 3X9, Canada
| | - Sungsu Youk
- Exotic and Emerging Avian Viral Diseases Research Unit, US National Poultry Research Center, US Department of Agriculture, Agricultural Research Service, Athens, Georgia, USA
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Research Unit, US National Poultry Research Center, US Department of Agriculture, Agricultural Research Service, Athens, Georgia, USA
| | - Mary Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, US National Poultry Research Center, US Department of Agriculture, Agricultural Research Service, Athens, Georgia, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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Pallegar P, Canuti M, Langille E, Peña-Castillo L, Lang AS. A Two-Component System Acquired by Horizontal Gene Transfer Modulates Gene Transfer and Motility via Cyclic Dimeric GMP. J Mol Biol 2020; 432:4840-4855. [PMID: 32634380 DOI: 10.1016/j.jmb.2020.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/08/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important intracellular signaling molecule that affects diverse physiological processes in bacteria. The intracellular levels of c-di-GMP are controlled by proteins acting as diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that synthesize and degrade c-di-GMP, respectively. In the alphaproteobacterium Rhodobacter capsulatus, flagellar motility and gene exchange via production of the gene transfer agent RcGTA are regulated by c-di-GMP. One of the R. capsulatus proteins involved in this regulation is Rcc00620, which contains an N-terminal two-component system response regulator receiver (REC) domain and C-terminal DGC and PDE domains. We demonstrate that the enzymatic activity of Rcc00620 is regulated through the phosphorylation status of its REC domain, which is controlled by a cognate histidine kinase protein, Rcc00621. In this system, the phosphorylated form of Rcc00620 is active as a PDE enzyme and stimulates gene transfer and motility. In addition, we discovered that the rcc00620 and rcc00621 genes are present in only one lineage within the genus Rhodobacter and were acquired via horizontal gene transfer from a distantly related alphaproteobacterium in the order Sphingomonadales. Therefore, a horizontally acquired regulatory system regulates gene transfer in the recipient organism.
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Affiliation(s)
- Purvikalyan Pallegar
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Evan Langille
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X7, Canada.
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada; Department of Computer Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada.
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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Sawangproh W, Hedenäs L, Lang AS, Hansson B, Cronberg N. Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum. Ann Bot 2020; 125:565-579. [PMID: 31872857 PMCID: PMC7102947 DOI: 10.1093/aob/mcz209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/20/2019] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS The mosses Homalothecium lutescens and H. sericeum are genetically, morphologically and ecologically differentiated; mixed populations sometimes occur. In sympatric populations, intermediate character states among gametophytes and sporophytes have been observed, suggesting hybridization and introgression in such populations. METHODS We determined genotypes using bi-allelic co-dominant single nucleotide polymorphism (SNP) markers, specific to either H. lutescens or H. sericeum, to estimate the degree of genetic mixing in 449 moss samples collected from seven sympatric and five allopatric populations on the island of Öland, south Sweden. The samples represented three generations: haploid maternal gametophytes; diploid sporophytes; and haploid sporelings. KEY RESULTS Admixture analyses of SNP genotypes identified a majority as pure H. lutescens or H. sericeum, but 76 samples were identified as mildly admixed (17 %) and 17 samples (3.8 %) as strongly admixed. Admixed samples were represented in all three generations in several populations. Hybridization and introgression were bidirectional. CONCLUSIONS Our results demonstrate that admixed genomes are transferred between the generations, so that the populations behave as true hybrid zones. Earlier studies of sympatric bryophyte populations with admixed individuals have not been able to show that admixed alleles are transferred beyond the first generation. The presence of true hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly exposed to selection in the long-lived haploid generation of the bryophyte life cycle, and contribute to local adaptation, long-term survival and speciation.
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Affiliation(s)
- W Sawangproh
- Biodiversity, Department of Biology, Lund University, Lund, Sweden
- Division of Conservation Biology, School of Interdisciplinary Studies, Mahidol University (Kanchanaburi Campus), Kanchanaburi Province, Thailand
| | - L Hedenäs
- Department of Botany, Swedish Museum of Natural History, Stockholm, Sweden
| | - A S Lang
- Biodiversity, Department of Biology, Lund University, Lund, Sweden
| | - B Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - N Cronberg
- Biodiversity, Department of Biology, Lund University, Lund, Sweden
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Lang AS, Austin SH, Harris RM, Calisi RM, MacManes MD. Stress-mediated convergence of splicing landscapes in male and female rock doves. BMC Genomics 2020; 21:251. [PMID: 32293250 PMCID: PMC7092514 DOI: 10.1186/s12864-020-6600-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/20/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus contributing to more refined traits on which natural and sexual selection can act. While it has been long known that various forms of environmental stress can negatively affect sexual behavior and reproduction, we know little of how stress can affect the alternative splicing associated with these events, and less still about how splicing may differ between sexes. Using the model of the rock dove (Columba livia), our team previously uncovered sexual dimorphism in the basal and stress-responsive gene transcription of a biological system necessary for facilitating sexual behavior and reproduction, the hypothalamic-pituitary-gonadal (HPG) axis. In this study, we delve further into understanding the mechanistic underpinnings of how changes in the environment can affect reproduction by testing the alternative splicing response of the HPG axis to an external stressor in both sexes. RESULTS This study reveals dramatic baseline differences in HPG alternative splicing between males and females. However, after subjecting subjects to a restraint stress paradigm, we found a significant reduction in these differences between the sexes. In both stress and control treatments, we identified a higher incidence of splicing activity in the pituitary in both sexes as compared to other tissues. Of these splicing events, the core exon event is the most abundant form of splicing and more frequently occurs in the coding regions of the gene. Overall, we observed less splicing activity in the 3'UTR (untranslated region) end of transcripts than the 5'UTR or coding regions. CONCLUSIONS Our results provide vital new insight into sex-specific aspects of the stress response on the HPG axis at an unprecedented proximate level. Males and females uniquely respond to stress, yet exhibit splicing patterns suggesting a convergent, optimal splicing landscape for stress response. This information has the potential to inform evolutionary theory as well as the development of highly-specific drug targets for stress-induced reproductive dysfunction.
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Affiliation(s)
- Andrew S Lang
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, USA.
| | - Suzanne H Austin
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, USA
| | - Rayna M Harris
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, USA
| | - Rebecca M Calisi
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, USA
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, USA
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Canuti M, Todd M, Monteiro P, Van Osch K, Weir R, Schwantje H, Britton AP, Lang AS. Ecology and Infection Dynamics of Multi-Host Amdoparvoviral and Protoparvoviral Carnivore Pathogens. Pathogens 2020; 9:pathogens9020124. [PMID: 32075256 PMCID: PMC7168296 DOI: 10.3390/pathogens9020124] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Amdoparvovirus and Protoparvovirus are monophyletic viral genera that infect carnivores. We performed surveillance for and sequence analyses of parvoviruses in mustelids in insular British Columbia to investigate parvoviral maintenance and cross-species transmission among wildlife. Overall, 19.1% (49/256) of the tested animals were parvovirus-positive. Aleutian mink disease virus (AMDV) was more prevalent in mink (41.6%, 32/77) than martens (3.1%, 4/130), feline panleukopenia virus (FPV) was more prevalent in otters (27.3%, 6/22) than mink (5.2%, 4/77) or martens (2.3%, 3/130), and canine parvovirus 2 (CPV-2) was found in one mink, one otter, and zero ermines (N = 27). Viruses were endemic and bottleneck events, founder effects, and genetic drift generated regional lineages. We identified two local closely related AMDV lineages, one CPV-2 lineage, and five FPV lineages. Highly similar viruses were identified in different hosts, demonstrating cross-species transmission. The likelihood for cross-species transmission differed among viruses and some species likely represented dead-end spillover hosts. We suggest that there are principal maintenance hosts (otters for FPV, raccoons for CPV-2/FPV, mink for AMDV) that enable viral persistence and serve as sources for other susceptible species. In this multi-host system, viral and host factors affect viral persistence and distribution, shaping parvoviral ecology and evolution, with implications for insular carnivore conservation.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada
- Correspondence: (M.C.); (A.S.L.); Tel.: +1-709-864-8761 (M.C.); +1-709-864-7517 (A.S.L.)
| | - Melissa Todd
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Paige Monteiro
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Kalia Van Osch
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Richard Weir
- British Columbia Ministry of Environment and Climate Change Strategy, PO Box 9338 STN Prov Govt, Victoria, BC V8W 9M2, Canada;
| | - Helen Schwantje
- British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Wildlife Health Program, Wildlife and Habitat Branch, 2080 Labieux Rd., Nanaimo, BC V9T 6J9, Canada;
| | - Ann P. Britton
- Animal Health Center, British Columbia Ministry of Agriculture, 1767 Angus Campbell Rd., Abbotsford, BC V3G 2M3, Canada;
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada
- Correspondence: (M.C.); (A.S.L.); Tel.: +1-709-864-8761 (M.C.); +1-709-864-7517 (A.S.L.)
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Pallegar P, Peña-Castillo L, Langille E, Gomelsky M, Lang AS. Cyclic di-GMP-Mediated Regulation of Gene Transfer and Motility in Rhodobacter capsulatus. J Bacteriol 2020; 202:e00554-19. [PMID: 31659012 PMCID: PMC6941535 DOI: 10.1128/jb.00554-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/19/2019] [Indexed: 02/08/2023] Open
Abstract
Gene transfer agents (GTAs) are bacteriophage-like particles produced by several bacterial and archaeal lineages that contain small pieces of the producing cells' genomes that can be transferred to other cells in a process similar to transduction. One well-studied GTA is RcGTA, produced by the alphaproteobacterium Rhodobacter capsulatus RcGTA gene expression is regulated by several cellular regulatory systems, including the CckA-ChpT-CtrA phosphorelay. The transcription of multiple other regulator-encoding genes is affected by the response regulator CtrA, including genes encoding putative enzymes involved in the synthesis and hydrolysis of the second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). To investigate whether c-di-GMP signaling plays a role in RcGTA production, we disrupted the CtrA-affected genes potentially involved in this process. We found that disruption of four of these genes affected RcGTA gene expression and production. We performed site-directed mutagenesis of key catalytic residues in the GGDEF and EAL domains responsible for diguanylate cyclase (DGC) and c-di-GMP phosphodiesterase (PDE) activities and analyzed the functions of the wild-type and mutant proteins. We also measured RcGTA production in R. capsulatus strains where intracellular levels of c-di-GMP were altered by the expression of either a heterologous DGC or a heterologous PDE. This adds c-di-GMP signaling to the collection of cellular regulatory systems controlling gene transfer in this bacterium. Furthermore, the heterologous gene expression and the four gene disruptions had similar effects on R. capsulatus flagellar motility as found for gene transfer, and we conclude that c-di-GMP inhibits both RcGTA production and flagellar motility in R. capsulatusIMPORTANCE Gene transfer agents (GTAs) are virus-like particles that move cellular DNA between cells. In the alphaproteobacterium Rhodobacter capsulatus, GTA production is affected by the activities of multiple cellular regulatory systems, to which we have now added signaling via the second messenger dinucleotide molecule bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). Similar to the CtrA phosphorelay, c-di-GMP also affects R. capsulatus flagellar motility in addition to GTA production, with lower levels of intracellular c-di-GMP favoring increased flagellar motility and gene transfer. These findings further illustrate the interconnection of GTA production with global systems of regulation in R. capsulatus, providing additional support for the notion that the production of GTAs has been maintained in this and related bacteria because it provides a benefit to the producing organisms.
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Affiliation(s)
- Purvikalyan Pallegar
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Evan Langille
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Mark Gomelsky
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
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Vlok M, Lang AS, Suttle CA. Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales. Virus Evol 2019; 5:vez056. [PMID: 31908848 PMCID: PMC6938265 DOI: 10.1093/ve/vez056] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metagenomics has altered our understanding of microbial diversity and ecology. This includes its applications to viruses in marine environments that have demonstrated their enormous diversity. Within these are RNA viruses, many of which share genetic features with members of the order Picornavirales; yet, very few of these have been taxonomically classified. The only recognized family of marine RNA viruses is the Marnaviridae, which was founded based on discovery and characterization of the species Heterosigma akashiwo RNA virus. Two additional genera of marine RNA viruses, Labyrnavirus (one species) and Bacillarnavirus (three species), were subsequently defined within the order Picornavirales but not assigned to a family. We have defined a sequence-based framework for taxonomic classification of twenty marine RNA viruses into the family Marnaviridae. Using RNA-dependent RNA polymerase (RdRp) phylogeny and distance-based analyses, we assigned the genera Labyrnavirus and Bacillarnavirus to the family Marnaviridae and created four additional genera in the family: Locarnavirus (four species), Kusarnavirus (one species), Salisharnavirus (four species) and Sogarnavirus (six species). We used pairwise capsid protein comparisons to delineate species within families, with 75 per cent identity as the species demarcation threshold. The family displays high sequence diversities and Jukes-Cantor distances for both the RdRp and capsid genes, suggesting that the classified viruses are not representative of all of the virus diversity within the family and that there are many more extant taxa. Our proposed taxonomic framework provides a sound classification system for this group of viruses that will have broadly applicable principles for other viral groups. It is based on sequence data alone and provides a robust taxonomic framework to include viruses discovered via metagenomic studies, thereby greatly expanding the realm of viruses subject to taxonomic classification.
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Affiliation(s)
- Marli Vlok
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.,Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Curtis A Suttle
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.,Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada.,Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, 2207 Main Mall, Vancouver, BC V6T 1Z4, Canada.,Department of Microbiology and Immunology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z4, Canada
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Huot Y, Brown CA, Potvin G, Antoniades D, Baulch HM, Beisner BE, Bélanger S, Brazeau S, Cabana H, Cardille JA, Del Giorgio PA, Gregory-Eaves I, Fortin MJ, Lang AS, Laurion I, Maranger R, Prairie YT, Rusak JA, Segura PA, Siron R, Smol JP, Vinebrooke RD, Walsh DA. The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate. Sci Total Environ 2019; 695:133668. [PMID: 31419692 DOI: 10.1016/j.scitotenv.2019.133668] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
The distribution and quality of water resources vary dramatically across Canada, and human impacts such as land-use and climate changes are exacerbating uncertainties in water supply and security. At the national level, Canada has no enforceable standards for safe drinking water and no comprehensive water-monitoring program to provide detailed, timely reporting on the state of water resources. To provide Canada's first national assessment of lake health, the NSERC Canadian Lake Pulse Network was launched in 2016 as an academic-government research partnership. LakePulse uses traditional approaches for limnological monitoring as well as state-of-the-art methods in the fields of genomics, emerging contaminants, greenhouse gases, invasive pathogens, paleolimnology, spatial modelling, statistical analysis, and remote sensing. A coordinated sampling program of about 680 lakes together with historical archives and a geomatics analysis of over 80,000 lake watersheds are used to examine the extent to which lakes are being altered now and in the future, and how this impacts aquatic ecosystem services of societal importance. Herein we review the network context, objectives and methods.
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Affiliation(s)
- Yannick Huot
- Département de géomatique appliquée, Université de Sherbrooke, QC J1K 2R1, Canada; Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada.
| | - Catherine A Brown
- Département de géomatique appliquée, Université de Sherbrooke, QC J1K 2R1, Canada
| | - Geneviève Potvin
- Département de géomatique appliquée, Université de Sherbrooke, QC J1K 2R1, Canada; Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada
| | - Dermot Antoniades
- Département de géographie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Helen M Baulch
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon S7N 3H5, SK, Canada
| | - Beatrix E Beisner
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Department of Biological Sciences, Université du Québec à Montréal, Montréal H3C 3P8, QC, Canada
| | - Simon Bélanger
- Département de biologie, chimie et géographie, Groupe BORÉAS, Université du Québec à Rimouski, QC G5L 3A1, Canada
| | - Stéphanie Brazeau
- National Microbiology Laboratory, Public Health Agency of Canada, St-Hyacinthe J2S 7C6, QC, Canada
| | - Hubert Cabana
- Département de génie civil et de génie du bâtiment, Université de Sherbrooke, QC J1K 2R1, Canada
| | - Jeffrey A Cardille
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Department of Natural Resource Sciences and McGill School of Environment, McGill University, Montreal H9X 3V9, QC, Canada
| | - Paul A Del Giorgio
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Department of Biological Sciences, Université du Québec à Montréal, Montréal H3C 3P8, QC, Canada
| | - Irene Gregory-Eaves
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Department of Biology, McGill University, Montreal H3A 1B1, QC, Canada
| | - Marie-Josée Fortin
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto M5S 3B2, ON, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's A1M 2A9, NL, Canada
| | - Isabelle Laurion
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Centre Eau Terre Environnement, Institut national de la recherche scientifique, Québec G1K 9A9, QC, Canada
| | - Roxane Maranger
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Département des sciences biologiques, Université de Montréal, C.P. 6128 succ. Centre-ville, Montréal, QC, Canada
| | - Yves T Prairie
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Department of Biological Sciences, Université du Québec à Montréal, Montréal H3C 3P8, QC, Canada
| | - James A Rusak
- Dorset Environmental Science Centre, Ontario Ministry of the Environment, Conservation and Parks, Dorset P0A 1E0, ON, Canada
| | - Pedro A Segura
- Département de chimie, Université de Sherbrooke, QC J1K 2R1, Canada
| | | | - John P Smol
- Paleoecological Assessment and Research Laboratory (PEARL), Department of Biology, Queen's University, Kingston K7L 3N6, ON, Canada
| | - Rolf D Vinebrooke
- Department of Biological Sciences, Centennial Centre of Interdisciplinary Science, University of Alberta, Edmonton T6G 2E9, AB, Canada
| | - David A Walsh
- Groupe de recherche interuniversitaire en limnologie et en environnement aquatique (GRIL), Canada; Department of Biology, Concordia University, Montreal H4B 1R6, QC, Canada
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Ding H, Grüll MP, Mulligan ME, Lang AS, Beatty JT. Induction of Rhodobacter capsulatus Gene Transfer Agent Gene Expression Is a Bistable Stochastic Process Repressed by an Extracellular Calcium-Binding RTX Protein Homologue. J Bacteriol 2019; 201:e00430-19. [PMID: 31501287 PMCID: PMC6832060 DOI: 10.1128/jb.00430-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/06/2019] [Indexed: 01/28/2023] Open
Abstract
Bacteriophage-like gene transfer agents (GTAs) have been discovered in both of the prokaryotic branches of the three-domain phylogenetic tree of life. The production of a GTA (RcGTA) by the phototrophic alphaproteobacterium Rhodobacter capsulatus is regulated by quorum sensing and a phosphorelay homologous to systems in other species that control essential functions such as the initiation of chromosome replication and cell division. In wild-type strains, RcGTA is produced in <3% of cells in laboratory cultures. Mutants of R. capsulatus that exhibit greatly elevated production of RcGTA were created decades ago by chemical mutagenesis, but the nature and molecular consequences of the mutation were unknown. We show that the number of cells in a population that go on to express RcGTA genes is controlled by a stochastic process, in contrast to a genetic process. We used transposon mutagenesis along with a fluorescent protein reporter system and genome sequence data to identify a gene, rcc00280, that encodes an RTX family calcium-binding protein homologue. The Rc280 protein acts as an extracellular repressor of RcGTA gene expression by decreasing the percentage of cells that induce the production of RcGTA.IMPORTANCE GTAs catalyze horizontal gene transfer (HGT), which is important for genomic evolution because the majority of genes found in bacterial genomes have undergone HGT at some point in their evolution. Therefore, it is important to determine how the production of GTAs is regulated to understand the factors that modulate the frequency of gene transfer and thereby specify the tempo of evolution. This work describes a new type of genetic regulation in which an extracellular calcium-binding protein homologue represses the induction of the Rhodobacter capsulatus GTA, RcGTA.
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Affiliation(s)
- Hao Ding
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc P Grüll
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Martin E Mulligan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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Grüll MP, Mulligan ME, Lang AS. Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents. FEMS Microbiol Lett 2019; 365:5067299. [PMID: 30085064 DOI: 10.1093/femsle/fny192] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/04/2018] [Indexed: 12/18/2022] Open
Abstract
Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.
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Affiliation(s)
| | - M E Mulligan
- Biochemistry, Memorial University of Newfoundland, St John's, NL, Canada
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Canuti M, Kroyer ANK, Ojkic D, Whitney HG, Robertson GJ, Lang AS. Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds. Viruses 2019; 11:E768. [PMID: 31438486 PMCID: PMC6784231 DOI: 10.3390/v11090768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/25/2022] Open
Abstract
Wild birds are recognized viral reservoirs but our understanding about avian viral diversity is limited. We describe here three novel RNA viruses that we identified in oropharyngeal/cloacal swabs collected from wild birds. The complete genome of a novel gull metapneumovirus (GuMPV B29) was determined. Phylogenetic analyses indicated that this virus could represent a novel avian metapneumovirus (AMPV) sub-group, intermediate between AMPV-C and the subgroup of the other AMPVs. This virus was detected in an American herring (1/24, 4.2%) and great black-backed (4/26, 15.4%) gulls. A novel gull coronavirus (GuCoV B29) was detected in great black-backed (3/26, 11.5%) and American herring (2/24, 8.3%) gulls. Phylogenetic analyses of GuCoV B29 suggested that this virus could represent a novel species within the genus Gammacoronavirus, close to other recently identified potential novel avian coronaviral species. One GuMPV-GuCoV co-infection was detected. A novel duck calicivirus (DuCV-2 B6) was identified in mallards (2/5, 40%) and American black ducks (7/26, 26.9%). This virus, of which we identified two different types, was fully sequenced and was genetically closest to other caliciviruses identified in Anatidae, but more distant to other caliciviruses from birds in the genus Anas. These discoveries increase our knowledge about avian virus diversity and host distributions.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
| | - Ashley N K Kroyer
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Davor Ojkic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, 419 Gordon St., Guelph, ON N1H 6R8, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL A1N 4T3, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
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Munro HJ, Ogden NH, Mechai S, Lindsay LR, Robertson GJ, Whitney H, Lang AS. Genetic diversity of Borrelia garinii from Ixodes uriae collected in seabird colonies of the northwestern Atlantic Ocean. Ticks Tick Borne Dis 2019; 10:101255. [PMID: 31280947 DOI: 10.1016/j.ttbdis.2019.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
The occurrence of Borrelia garinii in seabird ticks, Ixodes uriae, associated with different species of colonial seabirds has been studied since the early 1990s. Research on the population structure of this bacterium in ticks from seabird colonies in the northeastern Atlantic Ocean has revealed admixture between marine and terrestrial tick populations. We studied B. garinii genetic diversity and population structure in I. uriae collected from seabird colonies in the northwestern Atlantic Ocean, in Newfoundland and Labrador, Canada. We applied a multi-locus sequence typing (MLST) scheme to B. garinii found in ticks from four species of seabirds. The B. garinii strains found in this seabird colony ecosystem were diverse. Some were very similar to strains from Asia and Europe, including some obtained from human clinical samples, while others formed a divergent group specific to this region of the Atlantic Ocean. Our findings highlight the genetic complexity of B. garinii circulating in seabird ticks and their avian hosts but also demonstrate surprisingly close connections between B. garinii in this ecosystem and terrestrial sources in Eurasia. Genetic similarities among B. garinii from seabird ticks and humans indicate the possibility that B. garinii circulating within seabird tick-avian host transmission cycles could directly, or indirectly via connectivity with terrestrial transmission cycles, have consequences for human health.
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Affiliation(s)
- Hannah J Munro
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, A1B 3X9, Canada.
| | - Nicholas H Ogden
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Saint-Hyacinthe, Québec, J2S 2M2, Canada; Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, J2S 2M2, Canada.
| | - Samir Mechai
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Saint-Hyacinthe, Québec, J2S 2M2, Canada; Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, J2S 2M2, Canada.
| | - L Robbin Lindsay
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada.
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, Mount Pearl, Newfoundland and Labrador, A1N 4T3, Canada.
| | - Hugh Whitney
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, A1B 3X9, Canada.
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, A1B 3X9, Canada.
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Hendrikse LD, Kambli A, Kayko C, Canuti M, Rodrigues B, Stevens B, Vashon J, Lang AS, Needle DB, Troyer RM. Identification of a Novel Gammaherpesvirus in Canada lynx ( Lynx canadensis). Viruses 2019; 11:v11040363. [PMID: 31010021 PMCID: PMC6520957 DOI: 10.3390/v11040363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/25/2022] Open
Abstract
Gammaherpesviruses (GHVs) infect many animal species and are associated with lymphoproliferative disorders in some. Previously, we identified several novel GHVs in North American felids; however, a GHV had never been identified in Canada lynx (Lynx canadensis). We, therefore, hypothesized the existence of an unidentified GHV in lynx. Using degenerate nested and subsequently virus-specific PCR, we amplified and sequenced 3.4 kb of DNA from a novel GHV in lynx, which we named Lynx canadensis gammaherpesvirus 1 (LcaGHV1). Phylogenetic analysis determined that LcaGHV1 is a distinct GHV species belonging to the genus Percavirus. We then estimated the prevalence of LcaGHV1 in lynx by developing a PCR-based assay and detected LcaGHV1 DNA in 36% (95% CI: 22-53%) of lynx spleen DNA samples from Maine, USA and 17% (95% CI: 8-31%) from Newfoundland, Canada. The LcaGHV1 DNA sequences from Maine and Newfoundland lynx were nearly identical to each other (two nucleotide substitutions in 3.4 kb), suggesting that the unique lynx subspecies present on the island of Newfoundland (Lynx canadensis subsolanus) is infected with virus that very closely resembles virus found in mainland lynx. The potential ecologic and pathologic consequences of this novel virus for Canada lynx populations warrant further study.
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Affiliation(s)
- Liam D Hendrikse
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., London, ON N6A 5C1, Canada.
| | - Ankita Kambli
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., London, ON N6A 5C1, Canada.
| | - Caroline Kayko
- Map and Data Centre, Western Libraries, University of Western Ontario, 1151 Richmond St., London, ON N6A 5C1, Canada.
| | - Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NF A1B 3X9, Canada.
| | - Bruce Rodrigues
- Wildlife Division, Newfoundland and Labrador Department of Fisheries and Land Resources, P.O. Box 2007, Corner Brook, NF A2H 7S1, Canada.
| | - Brian Stevens
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire, 21 Botanical Lane, Durham, NH 03824, USA.
- Canadian Wildlife Health Cooperative⁻Ontario/Nunavut, Guelph, ON N1G 2W1, Canada.
| | - Jennifer Vashon
- Maine Department of Inland Fisheries and Wildlife, 650 State St., Bangor, ME 04401, USA.
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NF A1B 3X9, Canada.
| | - David B Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire, 21 Botanical Lane, Durham, NH 03824, USA.
| | - Ryan M Troyer
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., London, ON N6A 5C1, Canada.
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Canuti M, Munro HJ, Robertson GJ, Kroyer ANK, Roul S, Ojkic D, Whitney HG, Lang AS. New Insight Into Avian Papillomavirus Ecology and Evolution From Characterization of Novel Wild Bird Papillomaviruses. Front Microbiol 2019; 10:701. [PMID: 31031718 PMCID: PMC6473165 DOI: 10.3389/fmicb.2019.00701] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 11/24/2022] Open
Abstract
Viruses in the family Papillomaviridae have circular dsDNA genomes of approximately 5.7–8.6 kb that are packaged within non-enveloped, icosahedral capsids. The known papillomavirus (PV) representatives infect vertebrates, and there are currently more than 130 recognized PV species in more than 50 genera. We identified 12 novel avian papillomavirus (APV) types in wild birds that could represent five distinct species and two genera. Viruses were detected in paired oropharyngeal/cloacal swabs collected from six bird species, increasing the number of avian species known to harbor PVs by 40%. A new duck PV (DuPV-3) was found in mallard and American black duck (27.6% estimated prevalence) that was monophyletic with other known DuPVs. A single viral type was identified in Atlantic puffin (PuPV-1, 9.8% estimated prevalence), while a higher genetic diversity was found in other Charadriiformes. Specifically, three types [gull PV-1 (GuPV-1), -2, and -3] were identified in two gull species (estimated prevalence of 17% and 2.6% in American herring and great black-backed gull, respectively), and seven types [kittiwake PV-1 (KiPV-1) through -7] were found in black-legged kittiwake (81.3% estimated prevalence). Significantly higher DuPV-3 circulation was observed in spring compared to fall and in adults compared to juveniles. The studied host species’ tendencies to be in crowded environments likely affect infection rates and their migratory behaviors could explain the high viral diversity, illustrating how host behavior can influence viral ecology and distribution. For DuPV-3, GuPV-1, PuPV-1, and KiPV-2, we obtained the complete genomic sequences, which showed the same organization as other known APVs. Phylogenetic analyses showed evidence for virus–host co-divergence at the host taxonomic levels of family, order, and inter-order, but we also observed that host-specificity constraints are relaxed among highly related hosts as we found cross-species transmission within ducks and within gulls. Furthermore, the phylogeny of viruses infecting the Charadriiformes did not match the host phylogeny and gull viruses formed distinct monophyletic clades with kittiwake viruses, possibly reflecting past host-switching events. Considering the vast PV genotype diversity in other hosts and the large number of bird species, many more APVs likely remain to be discovered.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hannah J Munro
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, Mount Pearl, NL, Canada
| | - Ashley N K Kroyer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sheena Roul
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Tomasch J, Wang H, Hall ATK, Patzelt D, Preusse M, Petersen J, Brinkmann H, Bunk B, Bhuju S, Jarek M, Geffers R, Lang AS, Wagner-Döbler I. Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random. Genome Biol Evol 2018; 10:359-369. [PMID: 29325123 PMCID: PMC5786225 DOI: 10.1093/gbe/evy005] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 02/07/2023] Open
Abstract
Gene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world’s oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a “headful” type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated.
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Affiliation(s)
- Jürgen Tomasch
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany.,Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Hui Wang
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - April T K Hall
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Diana Patzelt
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Matthias Preusse
- Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, Braunschweig, Germany
| | - Jörn Petersen
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Henner Brinkmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabin Bhuju
- Group Genome Analytics, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Michael Jarek
- Group Genome Analytics, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Robert Geffers
- Group Genome Analytics, Helmholtz-Center for Infection Research, Braunschweig, Germany
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Irene Wagner-Döbler
- Group Microbial Communication, Helmholtz-Centre for Infection Research, Braunschweig, Germany
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Verhoeven JT, Canuti M, Munro HJ, Dufour SC, Lang AS. ViDiT–CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications. Can J Microbiol 2018; 64:761-773. [DOI: 10.1139/cjm-2018-0097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (less than US$5 per sample), and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing, and microbiome profiling. ViDiT–CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal–cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT–CACTUS demonstrated its validity in a wide range of microbiology applications, and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.
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Affiliation(s)
- Joost T.P. Verhoeven
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Hannah J. Munro
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Suzanne C. Dufour
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John’s, NL A1B 3X9, Canada
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Calisi RM, Austin SH, Lang AS, MacManes MD. Sex-biased transcriptomic response of the reproductive axis to stress. Horm Behav 2018; 100:56-68. [PMID: 29378207 DOI: 10.1016/j.yhbeh.2017.11.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 02/07/2023]
Abstract
Stress is a well-known cause of reproductive dysfunction in many species, including birds, rodents, and humans, though males and females may respond differently. A powerful way to investigate how stress affects reproduction is by examining its effects on a biological system essential for regulating reproduction, the hypothalamic-pituitary-gonadal (HPG) axis. Often this is done by observing how a stressor affects the amount of glucocorticoids, such as cortisol or corticosterone, circulating in the blood and their relationship with a handful of known HPG-producing reproductive hormones, like testosterone and estradiol. Until now, we have lacked a full understanding of how stress affects all genomic activity of the HPG axis and how this might differ between the sexes. We leveraged a highly replicated and sex-balanced experimental approach to test how male and female rock doves (Columba livia) respond to restraint stress at the level of their transcriptome. Females exhibit increased genomic responsiveness to stress at all levels of their HPG axis as compared to males, and these responsive genes are mostly unique to females. Reasons for this may be due to fluctuations in the female endocrine environment over the reproductive cycle and/or their evolutionary history, including parental investment and the potential for maternal effects. Direct links between genome to phenome cause and effect cannot be ascertained at this stage; however, the data we report provide a vital genomic foundation on which sex-specific reproductive dysfunction and adaptation in the face of stress can be further experimentally studied, as well as novel gene targets for genetic intervention and therapy investigations.
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Affiliation(s)
- Rebecca M Calisi
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States.
| | - Suzanne H Austin
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, United States
| | - Andrew S Lang
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, United States
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, United States
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Zheng Q, Wang Y, Xie R, Lang AS, Liu Y, Lu J, Zhang X, Sun J, Suttle CA, Jiao N. Dynamics of Heterotrophic Bacterial Assemblages within Synechococcus Cultures. Appl Environ Microbiol 2018; 84:e01517-17. [PMID: 29150500 PMCID: PMC5772231 DOI: 10.1128/aem.01517-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/02/2017] [Indexed: 02/01/2023] Open
Abstract
Interactions between photoautotrophic and heterotrophic microorganisms are central to the marine microbial ecosystem. Lab cultures of one of the dominant marine photoautotrophs, Synechococcus, have historically been difficult to render axenic, presumably because these bacteria depend upon other organisms to grow under these conditions. These tight associations between Synechococcus and heterotrophic bacteria represent a good relevant system to study interspecies interactions. Ten individual Synechococcus strains, isolated from eutrophic and oligotrophic waters, were chosen for investigation. Four to six dominant associated heterotrophic bacteria were detected in the liquid cultures of each Synechococcus isolate, comprising members of the Cytophaga-Flavobacteria-Bacteroides (CFB) group (mainly from Flavobacteriales and Cytophagales), Alphaproteobacteria (mainly from the Roseobacter clade), Gammaproteobacteria (mainly from the Alteromonadales and Pseudomonadales), and Actinobacteria The presence of the CFB group, Gammaproteobacteria, and Actinobacteria showed clear geographic patterns related to the isolation environments of the Synechococcus bacteria. An investigation of the population dynamics within a growing culture (XM-24) of one of the isolates, including an evaluation of the proportions of cells that were free-living versus aggregated/attached, revealed interesting patterns for different bacterial groups. In Synechococcus sp. strain XM-24 culture, flavobacteria, which was the most abundant group throughout the culture period, tended to be aggregated or attached to the Synechococcus cells, whereas the actinobacteria demonstrated a free-living lifestyle, and roseobacters displayed different patterns depending on the culture growth phase. Factors contributing to these succession patterns for the heterotrophs likely include interactions among the culture community members, their relative abilities to utilize different compounds produced by Synechococcus cells and changes in the compounds released as culture growth proceeds, and their responses to other changes in the environmental conditions throughout the culture period.IMPORTANCE Marine microbes exist within an interactive ecological network, and studying their interactions is an important part of understanding their roles in global biogeochemical cycling and the determinants of microbial diversity. In this study, the dynamic relationships between Synechococcus spp. and their associated heterotrophic bacteria were investigated. Synechococcus-associated heterotrophic bacteria had similar geographic distribution patterns as their "host" and displayed different lifestyles (free-living versus attached/aggregated) according to the Synechococcus culture growth phases. Combined organic carbon composition and bacterial lifestyle data indicated a potential for succession in carbon utilization patterns by the dominant associated heterotrophic bacteria. Comprehending the interactions between photoautotrophs and heterotrophs and the patterns of organic carbon excretion and utilization is critical to understanding their roles in oceanic biogeochemical cycling.
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Affiliation(s)
- Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Rui Xie
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Yanting Liu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Jiayao Lu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
| | - Xiaodong Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Jun Sun
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany and Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China
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Canuti M, Rodrigues B, Whitney HG, Lang AS. Introduction of canine parvovirus 2 into wildlife on the Island of Newfoundland, Canada. Infection, Genetics and Evolution 2017; 55:205-208. [DOI: 10.1016/j.meegid.2017.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
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Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, A1B 3X9, Canada
| | - Alexander B. Westbye
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL. CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo. Sci Rep 2017; 7:8642. [PMID: 28819186 PMCID: PMC5561059 DOI: 10.1038/s41598-017-08094-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 07/07/2017] [Indexed: 12/20/2022] Open
Abstract
The CD24 cell surface receptor promotes apoptosis in developing B cells, and we recently found that it induces B cells to release plasma membrane-derived, CD24-bearing microvesicles (MVs). Here we have performed a systematic characterization of B cell MVs released from WEHI-231 B lymphoma cells in response to CD24 stimulation. We found that B cells constitutively release MVs of approximately 120 nm, and that CD24 induces an increase in phosphatidylserine-positive MV release. RNA cargo is predominantly comprised of 5S rRNA, regardless of stimulation; however, CD24 causes a decrease in the incorporation of protein coding transcripts. The MV proteome is enriched with mitochondrial and metabolism-related proteins after CD24 stimulation; however, these changes were variable and could not be fully validated by Western blotting. CD24-bearing MVs carry Siglec-2, CD63, IgM, and, unexpectedly, Ter119, but not Siglec-G or MHC-II despite their presence on the cell surface. CD24 stimulation also induces changes in CD63 and IgM expression on MVs that is not mirrored by the changes in cell surface expression. Overall, the composition of these MVs suggests that they may be involved in releasing mitochondrial components in response to pro-apoptotic stress with changes to the surface receptors potentially altering the cell type(s) that interact with the MVs.
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Affiliation(s)
- D Craig Ayre
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Ian C Chute
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Andrew P Joy
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - David A Barnett
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Andrew M Hogan
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Marc P Grüll
- Departments of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Lourdes Peña-Castillo
- Departments of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.,Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Andrew S Lang
- Departments of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada.,Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada.,Department of Chemistry & Biochemistry, Université de Moncton, Moncton, New Brunswick, Canada
| | - Sherri L Christian
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.
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Westbye AB, Beatty JT, Lang AS. Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA) production and recipient capability by cellular regulators. Curr Opin Microbiol 2017; 38:122-129. [DOI: 10.1016/j.mib.2017.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/24/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
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Canuti M, Doyle HE, P Britton A, Lang AS. Full genetic characterization and epidemiology of a novel amdoparvovirus in striped skunk (Mephitis mephitis). Emerg Microbes Infect 2017; 6:e30. [PMID: 28487558 PMCID: PMC5520478 DOI: 10.1038/emi.2017.13] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 11/09/2022]
Abstract
Amdoparvovirus is a newly defined parvoviral genus that contains four species (Carnivore amdoparvovirus 1-4), including the well-known Aleutian mink disease virus (AMDV). Amdoparvoviruses cause an immune-associated and often lethal wasting syndrome in Mustelidae and Caninae hosts. In this study, we molecularly investigated amdoparvoviruses detected in 44 striped skunks (Mephitis mephitis) found dead in and around Vancouver, British Columbia, Canada. Some of the animals exhibited pathological changes compatible with amdoparvovirus-associated disease. The nearly complete genomic sequence was obtained for seven different strains and our analyses show how this virus, which we named skunk amdoparvovirus (SKAV), should be classified as a separate species within the genus (proposed Carnivore amdoparvovirus 5). We detected co-infections, recombinant genomes, at least three separate viral lineages, and preliminary evidence for geographic segregation of lineages. Furthermore, we proved that similar viruses, only partially characterized in previous studies and labeled as AMDV, circulate in skunks from other distant areas of North America (Ontario and California) and found evidence for spillover events in mink (Neovison vison). Although SKAVs are capable of causing disease in infected animals, a high proportion of sub-clinical infections has been observed, suggesting these animals might act as asymptomatic carriers and pose a threat to wild and captive carnivores. Finally, we highlight the need for more specific diagnostic tests and further molecular investigations to clarify the epidemiology and host- and geographical distributions of amdoparvoviruses in terrestrial carnivores, especially because the whole spectrum of viral diversity in this group is likely still unknown.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B3X9, Canada
| | - Hillary E Doyle
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B3X9, Canada
| | - Ann P Britton
- Animal Health Centre, BC Ministry of Agriculture, Abbotsford, BC V3G2M3, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B3X9, Canada
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