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      Molecular prevalence, characterization and associated risk factors of Anaplasma spp. and Theileria spp. in small ruminants in Northern Pakistan Translated title: Prévalence moléculaire, caractérisation et facteurs de risque associés d’ Anaplasma spp. et Theileria spp. chez les petits ruminants du nord du Pakistan

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          This study was conducted in four districts (Malakand, Swat, Bajaur and Shangla) of Northern Pakistan to investigate the prevalence, associated risk factors and phylogenetic analyses of Theileria and Anaplasma species in small ruminants. A total of 800 blood samples, 200 from each district, were collected from apparently healthy animals. PCR assays were performed using generic primers for Anaplasma spp. and Theileria spp. as well as species specific primers for A. ovis and T. ovis. Overall infection prevalence was 361/800 (45.1%). Theileria spp. infection prevalence (187/800, 23.3%) was higher than Anaplasma spp. (174/800, 21.7%). Amplified partial 18S rRNA genes were sequenced and enrolled animals were found to be infected by T. ovis (115/800, 14.3%), and at least two more Theileria species (72/800, 9%) were present ( T. lestoquardi and T. annulata). All blood samples that were found to be positive for Anaplasma spp. were also positive for A. ovis. Infection prevalence was higher in sheep (227/361, 28.3%) compared to goats (134/361, 16.6%) ( p < 0.005). Univariable analysis of risk factors showed that host, age, grazing system and acaricide treatment were significant determinants ( p < 0.05) for both Theileria and Anaplasma infections. Multivariable analysis revealed that host, sex, age, tick infestation and grazing system were significant risk factors ( p < 0.005) for both pathogens. Phylogenetic analysis revealed variants among the A. ovis and T. annulata samples analysed, indicating that different genotypes are circulating in the field while T. ovis presented the same genotype for the samples analysed.

          Translated abstract

          Cette étude a été menée dans quatre districts (Malakand, Swat, Bajaur et Shangla) du nord du Pakistan pour étudier la prévalence, les facteurs de risque associés et les analyses phylogénétiques des espèces de Theileria et Anaplasma chez les petits ruminants. Au total, 800 échantillons de sang, 200 de chaque district, ont été prélevés sur des animaux apparemment sains. Les tests PCR ont été réalisés en utilisant des amorces génériques pour Anaplasma spp. et Theileria spp. ainsi que des amorces spécifiques à l’espèce pour A. ovis et T. ovis. La prévalence globale de l’infection était de 361/800 (45,1 %). La prévalence de l’infection à Theileria spp. (187/800, 23,3 %) était plus élevée que celle d’ Anaplasma spp. (174/800, 21,7 %). Le gène de l’ARNr partiel 18S amplifié a été séquencé et les animaux concernés se sont révélés infectés par T. ovis (115/800, 14,3 %) et au moins deux autres espèces de Theileria (72/800, 9 %) étaient présentes ( T. lestoquardi et T. annulata). Tous les échantillons de sang trouvés positifs pour Anaplasma spp. ont également été trouvés positifs pour A. ovis. La prévalence de l’infection était plus élevée chez les moutons (227/361, 28,3 %) que chez les chèvres (134/361, 16,6 %) ( p < 0,005). Une analyse univariée des facteurs de risque a montré que l’hôte, l’âge, le système de pâturage et le traitement acaricide étaient des déterminants significatifs ( p < 0,05) pour les infections à Theileria et Anaplasma. L’analyse multivariée des facteurs de risque a révélé que l’hôte, le sexe, l’âge, l’infestation par les tiques et le système de pâturage étaient des éléments de facteurs de risque importants ( p < 0,005) pour les deux agents pathogènes. L’analyse phylogénétique a révélé des variantes parmi les échantillons d’ A. ovis et de T. annulata analysés indiquant que différents génotypes circulent sur le terrain tandis que T. ovis présentait le même génotype pour tous les échantillons analysés.

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          Most cited references 75

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

             Robert Edgar (2004)
            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

               Motoo Kimura (1980)
              Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.

                Author and article information

                EDP Sciences
                08 January 2021
                : 28
                : ( publisher-idID: parasite/2021/01 )
                [1 ] Department of Zoology, Abdul Wali Khan University Mardan Toru Road, Sheikh Maltoon Town 23200 Mardan Pakistan
                [2 ] Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias INIFAP, Carr. Fed. Cuernavaca-Cuautla No. 8534 Jiutepec 62550 Morelos México
                [3 ] Department of Biological Sciences, Faculty of Science and Humanities, Shaqra University P.O. Box 1040 11911 Ad-Dawadimi Saudi Arabia
                Author notes
                [* ]Corresponding author: zoologyawkum@ 123456gmail.com
                parasite200137 10.1051/parasite/2020075
                © S. Niaz et al., published by EDP Sciences, 2021

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 4, Tables: 3, Equations: 0, References: 66, Pages: 13
                Research Article


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