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      Novel Rickettsia Species Infecting Dogs, United States

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          Abstract

          In 2018 and 2019, spotted fever was suspected in 3 dogs in 3 US states. The dogs had fever and hematological abnormalities; blood samples were Rickettsia seroreactive. Identical Rickettsia DNA sequences were amplified from the samples. Multilocus phylogenetic analysis showed the dogs were infected with a novel Rickettsia species related to human Rickettsia pathogens.

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          New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

          Stéphane Guindon, Jean-François Dufayard, Vincent Lefort … (2010)
          PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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            Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

            K Tamura, M Nei (1993)
            Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition/transversion ratio for the entire control region was approximately 15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.
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              Potential Spatial Distribution of the Newly Introduced Long-horned Tick, Haemaphysalis longicornis in North America

              R. K. Raghavan, S C Barker, M. Cobos … (2019)
              The North American distributional potential of the recently invaded tick, Haemaphysalis longicornis, was estimated using occurrence data from its geographic range in other parts of the world and relevant climatic data sets. Several hundred candidate models were built using a correlative maximum entropy approach, and best-fitting models were selected based on statistical significance, predictive ability, and complexity. The median of the best-fitting models indicates a broad potential distribution for this species, but restricted to three sectors—the southeastern United States, the Pacific Northwest, and central and southern Mexico.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Emerg Infect Dis
                Journal ID (iso-abbrev): Emerg Infect Dis
                Journal ID (publisher-id): EID
                Title: Emerging Infectious Diseases
                Publisher: Centers for Disease Control and Prevention
                ISSN (Print): 1080-6040
                ISSN (Electronic): 1080-6059
                Publication date (Print): December 2020
                Volume: 26
                Issue: 12
                Pages: 3011-3015
                Affiliations
                [1]North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA (J.M. Wilson, E.B. Breitschwerdt, N.B. Juhasz, H.S. Marr, B.A. Qurollo);
                [2]VCA Arboretum View Animal Hospital, Downers Grove, Illinois, USA (J.F. de Brito Galvão);
                [3]Oklahoma Veterinary Specialists, Tulsa Oklahoma, USA (C.L. Pratt)
                Author notes
                Address for correspondence: Barbara A. Qurollo, Department of Clinical Sciences College of Veterinary Medicine, North Carolina State University, Research Bldg, Office 464, 1060 William Moore Dr, Raleigh, NC 27606, USA; email: baquroll@ 123456ncsu.edu
                Article
                Publisher ID: 20-0272
                DOI: 10.3201/eid2612.200272
                PMC ID: 7706976
                PubMed ID: 33219793
                SO-VID: 061f4d11-d423-4a55-8c64-d90bedec70a2
                History
                Categories
                Subject: Dispatch
                Subject: Dispatch
                Subject: Novel Rickettsia Species Infecting Dogs, United States

                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: spotted-fever group rickettsia,tickborne diseases,vector-borne diseases,parasites,bacteria,rickettsia,zoonoses,united states,dogs
                Data availability:
                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: spotted-fever group rickettsia, tickborne diseases, vector-borne diseases, parasites, bacteria, rickettsia, zoonoses, united states, dogs

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