Phylogenetic analysis involves the study of the evolutionary relationships among horse species and their ancestors. This scientific approach uses genetic data to construct phylogenetic trees that illustrate the evolutionary pathways and divergence of different equine lineages. By analyzing DNA sequences, researchers can infer the genetic similarities and differences among horse breeds and their relatives, providing insights into their evolutionary history and adaptation processes. Phylogenetic analysis can also help identify genetic markers associated with specific traits or health conditions. This page compiles peer-reviewed research studies and scholarly articles that explore the methodologies, findings, and implications of phylogenetic analysis in understanding horse evolution and diversity.
Goodchild OA, Rosen SN, Mennecart B, Meng J, Tissier J.Perissodactyla, or odd-toed ungulates, are represented today by 16 species of rhinoceroses, tapirs, and horses. Perissodactyls were much more diverse in the past, having a rich fossil record spanning from the earliest Eocene (~56 Ma) to recent, including a myriad of extinct lineages. Despite over a century of study, the inter-relationships of some extinct perissodactyl families remain poorly resolved. New morphological characters are needed to help solve this issue. Recent studies suggest that the ear region, ., the petrosal and the bony labyrinth of the inner ear, is a valuable source of morp...
Pourmahdi Borujeni M, Ghobadian Diali H, Mashhadi AG, Aliabad MJ.The recent identification of novel viruses associated with hepatitis in horses has prompted equine veterinarians to investigate the viral factors contributing to equine hepatitis. Hepacivirus equi (EqHV), a member of the Flaviviridae family within the Hepacivirus genus, has been detected in horses affected by hepatitis. Globally, EqHV is highly conserved, existing as a single genotype with three distinct subtypes (Subtypes 1-3). Numerous studies have detected the virus by PCR and identified EqHV-specific antibodies through serological tests in different regions worldwide. However, to the best ...
In 2017, Spain reported its first equine infectious anemia virus (EIAV) outbreak in 34 years, affecting three horses in two unrelated holdings in Candeleda (Ávila) and Serradilla (Cáceres), with no apparent epidemiological link between premises. Phylogenetic analysis of whole genome and the gene revealed that the Spanish EIAV strains form a distinct monophyletic clade, sharing more than 99% nucleotide identity, suggesting a common contamination event. Interestingly, these three viral strains seem to cluster with North American strains, sharing up to 80.12% nucleotide identity, notably with ...
Bhat S, Karunakaran S, Frossard JP, Choudhury B, Steinbach F.Equine arteritis virus (EAV) is the causative agent of equine viral arteritis, a notifiable respiratory and reproductive disease of equids that causes significant losses to the equine industry. This study presents a comprehensive analysis of two EAV outbreaks in the UK in 2019, combining virus isolation, sequencing and phylogenetic analysis to provide a holistic understanding of EAV dynamics in these outbreaks. Genetic characterization revealed that all outbreak strains were similar to viruses detected in the UK and Europe from 2004 to 2011, belonging to phylogroup D and clustering in two grou...
Nemoto M, Kawanishi N, Kamei R, Furusho K, Kawauchi K, Yabuuchi Y, Oue Y, Uchida Y, Nishiura H, Reedy SE, Chambers TM, Li F, Bannai H, Yamanaka T....In April and May 2025, outbreaks of equine influenza occurred for the first time in 17 years in Japan. Equine influenza virus (EIV) of the H3N8 subtype was mainly detected in heavy draft horse populations in Kumamoto Prefecture and the Tokachi area of Hokkaido. In total, 10 EIVs were isolated from infected horses and then were used for genetic and serological analyses. Phylogenetic analysis of all eight genes revealed that all Japanese isolates were clustered with the Florida sublineage clade 1 (Fc1) viruses and were closely related to North American Fc1 viruses detected in 2024-2025. The resu...
Celik F, Karabulut B, Uslug M, Cankaya E, Eroksuz Y, Simsek S. is a parasitic cestode primarily maintained within an equine-canine life cycle, with horses, donkeys, mules, and other ungulates serving as intermediate hosts. Although has historically been considered non-zoonotic, recent molecular studies suggest that this assumption may need to be reevaluated. This study aimed to investigate the presence and molecular characterization of in equids from Türkiye. A retrospective analysis of 52 equine necropsies performed between 2020 and 2025 identified hydatid cysts in one Arabian horse and two donkeys. Gross and histopathological examination confirmed t...
Aziz KJ, Issa NA, Mikaeel FB, Ismael SS.This study investigated the prevalence, intensity, and associated risk factors of Parascaris equorum (P. equorum) infection in equids using both parasitological and molecular methods. Data on age, sex, body condition, and housing conditions were systematically collected to evaluate their influence on infection risk. Fecal samples from 294 equines (148 horses, 47 mules, 63 donkeys, and 36 ponies) were examined microscopically using direct wet-mount and flotation techniques, with infection intensity quantified using the McMaster technique to determine eggs per gram (EPG). Molecular confirmation ...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D, Zhao Y.Speed and endurance are the primary goals in racehorse breeding. The Grassland-Thoroughbred is a newly developed breed in northern China that combines speed, endurance, and environmental adaptability. However, current research on the genetic background of this breed and the genes associated with athletic performance remains limited. We conducted whole-genome resequencing on Mongolian (MG), Thoroughbred (TB), Xilingol (XL), and Grassland-Thoroughbred (CY) horses, generating 3813.74 Gb of clean data after quality control. The number of transitions was significantly higher than that of transversi...
Abdul-Latif SAK, Yousif AA.Strangles is a highly contagious equine respiratory disease caused by . It is a globally significant pathogen and one of the most common infectious agents in horses. In Iraq, no sequencing data on this pathogen are available, and only two molecular studies have been published to date. This study provides preliminary insights into strain diversity and provides a foundation for future large-scale investigations. Unassigned: This study aimed to investigate the molecular characteristics, identify gene alleles, and perform a phylogenetic analysis of isolates from horses in Baghdad, Iraq. Unassign...
Fernandes TA, Paulino PG, Dos Santos Juliano D, Rabello CA, de Oliveira NVB, de Souza Santana M, Peckle M, Massard CL, da Costa Angelo I, Jacob JCF....Equine piroplasmosis (EP) is a reportable disease according to the World Organization for Animal Health (WOAH), caused by Babesia caballi, Theileria equi and T. haneyi. This syndrome is prevalent in tropical and subtropical regions, including various areas in Brazilian. This study examines EP in the Distrito Federal, Brazil, focusing on prevalence, epidemiological characteristics, and circulating genotypes. Epidemiological data and whole blood samples were collected from horses in the Distrito Federal. DNA was analyzed using qPCR for Theileria sp. and B. caballi, followed by cPCR for 18S rDNA ...
Montini M, Torrents J, Nava S, Sebastian PS. ticks collected on horses from the North-West of Argentina were analyzed for the presence of the Piroplasm agents and . A total of 97 adult ticks from four different provinces (Jujuy, Santiago del Estero, Salta, Tucumán) were included in this study. Genomic DNA was isolated, and conventional PCR assays were applied for the detection of the 18S rDNA gene of and species. One sample corresponding to a male of collected in Tapia, Tucumán Province, resulted positive. Phylogenetic analyses carried out with the obtained 18S rDNA partial gene sequences resulted in the identification of . Althou...
Akbari H, Basaki M, Imani Baran A, Akbarzadeh Z.Anaplasmosis, a tick-borne disease with worldwide distribution, impacts ruminants, equines, carnivores, and humans. This study aimed to investigate Anaplasma phagocytophilum in horses from Ardabil province and Anaplasma ovis in small ruminants from East Azerbaijan province using the Nested Polymerase Chain Reaction (PCR) method. Blood samples were taken from the jugular vein of 100 healthy horses in the Ardabil province and 156 healthy sheep and goats (116 sheep and 40 goats) in the East Azerbaijan province during the spring and summer seasons of 2016 in northwest Iran. The collected blood sam...
Maharana BR, Ganguly A, Potliya S, Kumar B, Singh H, Dash A, Khanna S.Equine piroplasmosis caused by Theileria equi is a febrile, tick-borne disease of equids. However, there is limited literature about the genotyping of T. equi in India. Blood samples were collected from 202 horses and subjected to microscopy and PCR to detect T. equi. Initially, a universal screening primer pair targeting 18S ribosomal RNA genes common for Babesia caballi and T. equi was employed to amplify the DNA of both parasites. Thereafter additional primers were employed for species-specific detection resulting in amplification of approximately 435 bp specific for T. equi. T.equi was de...
Otgonsuren D, Amgalanbaatar T, Narantsatsral S, Enkhtaivan B, Munkhgerel D, Zoljargal M, Davkharbayar B, Myagmarsuren P, Battur B, Battsetseg B....Equine piroplasmosis is a tick-borne disease caused by Theileria equi and Babesia caballi in horses. Because of its impact on horse industry, control of this disease is crucial for endemic countries. The control of equine piroplasmosis may be influenced by the genotypic diversity of T. equi and B. caballi. Mongolia, a country with a thriving livestock industry, is endemic for T. equi and B. caballi. However, nationwide epidemiological surveys have not been conducted to determine the current status of infections and genetic diversity of these two parasite species. Therefore, the objective of th...
El-Zayat M, Shemies OA, Mosad SM, El Rahman SA.Equine herpes viruses (EHVs) are considered one of the most important respiratory pathogens in equids, resulting in serious outcomes for equine health worldwide. The objectives of the current research were the detection, molecular characterization, and isolation of EHV-1 and EHV-4 circulating within different equine populations in Egypt, either clinically or in apparently healthy horses. Unassigned: A total of 120 field samples were collected, and DNA was extracted. Screening and typing of extracted DNA were done by consensus and conventional PCR assays for detection of EHV-1 and EHV-4, follow...
Olofsson KM, van de Velde N, Peletto S, Iulini B, Pratley L, Modabberzadeh B, Małek E, Grandi G.Halicephalobus gingivalis is a nematode with zoonotic potential which can cause fatal opportunistic infections in various mammals. The parasite has never been diagnosed in Sweden, in any species, prior to the presented case. Methods: An imported 21-year-old Icelandic mare developed severe neurological signs. The horse was eventually euthanized and submitted for post-mortem examination where severe lesions in the kidneys were noted. Histopathology revealed the presence of H. gingivalis in both kidneys and the brain. Phylogenetic analysis of the parasite determined it to belong to Lineage 1. Con...
Chien RC, Mingqun L, Yan Q, Randolph N, Huang W, Wellman M, Toribio R, Rikihisa Y.The tick-borne obligatory intracellular bacterium Anaplasma phagocytophilum infects humans as well as domesticated and wild animals, causing a febrile disease collectively called granulocytic anaplasmosis. The epidemiology and the host species specificity and zoonotic potential of A. phagocytophilum strains remain unclear. In this study, ankA (encoding ankyrin A) and p44 gene sequences of A. phagocytophilum were determined in clinical specimens from horses in Ohio and compared with those found in A. phagocytophilum strains from various hosts and geographic regions. With increasing numbers of s...
Phetkarl T, Fungwithaya P, Udompornprasith S, Amendt J, Sontigun N. and tabanid flies are of medical and veterinary importance because they play crucial roles in disease transmission as mechanical vectors of various hemopathogens. However, its role as a hemoprotozoan parasite vector in horse farms has not been studied. Therefore, we investigated the occurrence of hemoprotozoan parasites belonging to the genera , , and in and tabanid flies using conventional polymerase chain reaction (PCR) and DNA sequencing. Unassigned: All samples ( and tabanid flies) were collected using an Nzi trap for three consecutive days each month from November 2022 to March 2023. T...
Li S, Guo K, Wang X, Lin Y, Wang J, Wang Y, Du C, Hu Z, Wang X.Equine infectious anemia (EIA) has a worldwide distribution and causes severe economic losses to the equine industry. The EIA virus (EIAV) genome sequences from different countries are highly diverse, which poses a great challenge for pathogen identification with PCR. Phylogenetic analysis showed that although gag is the most conserved structural gene, it still has great genome variability. Currently, most existing PCR methods are designed based on the gag gene sequence and therefore do not cover all the viral strains, especially Asian EIAV strains. In this study, we developed a tat-gag-based ...
Jung HS, Yun JU, Jung MJ, Song HS, Kim YB, Kim Y, Kim JG, Jeon CO, Roh SW, Whon TW, Lee SH.A novel, anaerobic, Gram-stain-positive coccoid strain, CBA3646, was isolated from the faeces of a thoroughbred racehorse. Phylogenetic analysis based on 16S rRNA gene sequencing yielded results indicative of CBA3646 representing a member of the genus , with the species most closely related to it being DSM 20463, with a similarity of 94.79 %. DNA-DNA relatedness and average nucleotide identity values between CBA3646 and DSM 20463 were 21.4 and 67.6 %, respectively. CBA3646 has a circular chromosomal genome of 1 709 189 bp (45.5 mol% DNA G+C content), containing 1652 genes in tota...
Sohail Ashraf M, Basheer A, Iqbal F, Zahoor I.The current study aimed to evaluate the genetic diversity, level of admixture, and phylogenetic relationship, of the Pakistani horse breeds, along with their morphological characterization. Data for the body measurements showed that Morna horses had the highest values of body height, body length, chest girth, leg length, and head length, whereas the Baluchi horses had the lowest values for these traits. For the genetic diversity 64 animals, 15/breed except for Baluchi(14) and Topras(05), were genotyped by using the 17-plex equine genotyping kit. The AMOVA results showed that 13% of genetic div...
Virtanen J, Hautaniemi M, Dutra L, Plyusnin I, Hautala K, Smura T, Vapalahti O, Sironen T, Kant R, Kinnunen PM.We report a sequencing protocol and 121-kb poxvirus sequence from a clinical sample from a horse in Finland with dermatitis. Based on phylogenetic analyses, the virus is a novel parapoxvirus associated with a recent epidemic; previous data suggest zoonotic potential. Increased awareness of this virus and specific diagnostic protocols are needed.
Sheikh A.The Arabian horse breed is well known for its purity and played a key role in the genetic improvement of other horses worldwide. The mitochondrial genome plays a vital role in maternal inheritance and it's helpful to evaluate its genetic diversity and conservation. It has higher mutation rates than nuclear DNA in vertebrates and therefore reveals phylogenetic relationships and haplotypes. In this study, the mitochondrial genome mutations in two Saudi horse strains, Kehilan and Hamdani demonstrated various changes in the gene and amino acid levels and included two other Saudi horses (Hadban and...
Machmoum M, Badaoui B, Petit D, Germot A, El Alaoui MA, Boujenane I, Piro M.Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
Zhou M, Lu Y, Han L, Lu M, Guan C, Yu J, Liu H, Chen D, Li H, Yang Y, Zhang L, Tian L, Liu Q, Hou Z.The roundworms, Parascaris spp., are important nematode parasites of foals and were historically model organisms in the field of cell biology, leading to many important discoveries. According to karyotype, ascarids in Equus are commonly divided into Parascaris univalens (2n = 2) and Parascaris equorum (2n = 4). Methods: Here, we performed morphological identification, karyotyping and sequencing of roundworms from three different hosts (horses, zebras and donkeys). Phylogenetic analysis was performed to study the divergence of these ascarids based on cytochrome c oxidase subunit I (COI)...
Spotin A, Dalir F, Hazratian T, Shekarchi AA, Mahami-Oskouei M, Farmani M, Dolatkhah A, Ahmadpour E.The genetic variability of apicomplexan parasite Babesia species is a principal strategy used by piroplasma to evade their hosts' immune responses. The purpose of this review was to evaluate our current knowledge on global haplotype distribution and phylogeography of Babesia ovis derived from sheep, goat, horse and ixodid (hard) ticks. Bibliographic English databases were searched from 2017 to 2023, identifying a total of 11 publications. The 18S ribosomal RNA (18S rRNA) sequences of B. ovis from Asia, Europe, and Africa were retrieved and subjected to estimate the genetic diversity and phylog...
Huang J, Chen M, He Y, Chen H, Huang M, Li N, Ryan U, Kváč M, Feng Y, Xiao L, Guo Y.The horse genotype is one of three common Cryptosporidium spp. in equine animals and has been identified in some human cases. The species status of Cryptosporidium horse genotype remains unclear due to the lack of extensive morphological, biological, and genetic data. In the present study, we have conducted biological and whole genome sequence analyses of an isolate of the genotype from hedgehogs and proposed to name it Cryptosporidium equi n. sp. to reflect its common occurrence in equine animals. Oocysts of C. equi measured 5.12 ± 0.36 μm × 4.46 ± 0.21 μm with a shape index of 1...
Zhang Y, Shi Q, Laven R, Li C, He W, Zheng H, Liu S, Lu M, Yang DA, Guo Q, Chahan B.Theileria equi is a tick-borne intracellular apicomplexan protozoan parasite that causes equine theileriosis (ET). ET is an economically important disease with a worldwide distribution that significantly impacts international horse movement. Horses are an essential part of the economy in Xinjiang which is home to ∼10% of all the horses in China. However, there is very limited information on the prevalence and genetic complexity of T. equi in this region. Blood samples from 302 horses were collected from May to September 2021 in Ili, Xinjiang, and subjected to PCR examination for the presence...
Pellegrini F, Buonavoglia A, Omar AH, Diakoudi G, Lucente MS, Odigie AE, Sposato A, Augelli R, Camero M, Decaro N, Elia G, Bányai K, Martella V....Massive sequencing techniques have allowed us to develop straightforward approaches for the whole genome sequencing of viruses, including influenza viruses, generating information that is useful for improving the levels and dimensions of data analysis, even for archival samples. Using the Nanopore platform, we determined the whole genome sequence of an H3N8 equine influenza virus, identified from a 2005 outbreak in Apulia, Italy, whose origin had remained epidemiologically unexplained. The virus was tightly related (>99% at the nucleotide level) in all the genome segments to viruses identif...
Kawamura Y, Fujimoto Y, Kutsuna R, Tomida J, Yamamoto KI, Miyoshi-Akiyama T, Okuno M, Ogura Y, Matsuoka M, Kawaguchi T, Tsutsuki H, Sawa T.A Gram-stain-negative, spiral bacterium (PAGU 1991T) was isolated from the blood of a patient with diffuse large B-cell lymphoma. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was very closely related to Helicobacter equorum LMG 23362T (99.1 % similarity), originally isolated from a faecal sample from a healthy horse. PAGU 1991T was also very closely related to PAGU 1750 in our strain library (=CCUG 41437) with 99.7 % similarity. Additional phylogenetic analyses based on the 23S rRNA gene sequence and GyrA amino acid sequence further supported the close rel...
Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C, Weber J, Olek K.The place and date of the domestication of the horse has long been a matter for debate among archaeologists. To determine whether horses were domesticated from one or several ancestral horse populations, we sequenced the mitochondrial D-loop for 318 horses from 25 oriental and European breeds, including American mustangs. Adding these sequences to previously published data, the total comes to 652, the largest currently available database. From these sequences, a phylogenetic network was constructed that showed that most of the 93 different mitochondrial (mt)DNA types grouped into 17 distinct p...
de la Fuente J, Massung RF, Wong SJ, Chu FK, Lutz H, Meli M, von Loewenich FD, Grzeszczuk A, Torina A, Caracappa S, Mangold AJ, Naranjo V, Stuen S....The causative agent of human granulocytic ehrlichiosis was recently reclassified as Anaplasma phagocytophilum, unifying previously described bacteria that cause disease in humans, horses, dogs, and ruminants. For the characterization of genetic heterogeneity in this species, the homologue of Anaplasma marginale major surface protein 4 gene (msp4) was identified, and the coding region was PCR amplified and sequenced from a variety of sources, including 50 samples from the United States, Germany, Poland, Norway, Italy, and Switzerland and 4 samples of A. phagocytophilum-like organisms obtained f...
Chandriani S, Skewes-Cox P, Zhong W, Ganem DE, Divers TJ, Van Blaricum AJ, Tennant BC, Kistler AL.Theiler's disease is an acute hepatitis in horses that is associated with the administration of equine blood products; its etiologic agent has remained unknown for nearly a century. Here, we used massively parallel sequencing to explore samples from a recent Theiler's disease outbreak. Metatranscriptomic analysis of the short sequence reads identified a 10.5-kb sequence from a previously undescribed virus of the Flaviviridae family, which we designate "Theiler's disease-associated virus" (TDAV). Phylogenetic analysis clusters TDAV with GB viruses of the recently proposed Pegivirus genus, altho...
Tulman ER, Delhon G, Afonso CL, Lu Z, Zsak L, Sandybaev NT, Kerembekova UZ, Zaitsev VL, Kutish GF, Rock DL.Here we present the genomic sequence of horsepox virus (HSPV) isolate MNR-76, an orthopoxvirus (OPV) isolated in 1976 from diseased Mongolian horses. The 212-kbp genome contained 7.5-kbp inverted terminal repeats and lacked extensive terminal tandem repetition. HSPV contained 236 open reading frames (ORFs) with similarity to those in other OPVs, with those in the central 100-kbp region most conserved relative to other OPVs. Phylogenetic analysis of the conserved region indicated that HSPV is closely related to sequenced isolates of vaccinia virus (VACV) and rabbitpox virus, clearly grouping to...
Doud MB, Ashenberg O, Bloom JD.Evolution drives changes in a protein's sequence over time. The extent to which these changes in sequence lead to shifts in the underlying preference for each amino acid at each site is an important question with implications for comparative sequence-analysis methods, such as molecular phylogenetics. To quantify the extent that site-specific amino acid preferences shift during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino acid identity. We found that only a modest fraction of sites exhibited shifts in amino acid preferences tha...
Bryant NA, Rash AS, Russell CA, Ross J, Cooke A, Bowman S, MacRae S, Lewis NS, Paillot R, Zanoni R, Meier H, Griffiths LA, Daly JM, Tiwari A....Equine influenza virus (EIV) surveillance is important in the management of equine influenza. It provides data on circulating and newly emerging strains for vaccine strain selection. To this end, antigenic characterisation by haemaggluttination inhibition (HI) assay and phylogenetic analysis was carried out on 28 EIV strains isolated in North America and Europe during 2006 and 2007. In the UK, 20 viruses were isolated from 28 nasopharyngeal swabs that tested positive by enzyme-linked immunosorbent assay. All except two of the UK viruses were characterised as members of the Florida sublineage w...
Knowles DP, Kappmeyer LS, Haney D, Herndon DR, Fry LM, Munro JB, Sears K, Ueti MW, Wise LN, Silva M, Schneider DA, Grause J, White SN, Tretina K....A novel apicomplexan parasite was serendipitously discovered in horses at the United States - Mexico border. Phylogenetic analysis based on 18S rDNA showed the erythrocyte-infective parasite to be related to, but distinct from, Theileria spp. in Africa, the most similar taxa being Theileria spp. from waterbuck and mountain zebra. The degree of sequence variability observed at the 18S rDNA locus also suggests the likely existence of additional cryptic species. Among described species, the genome of this novel equid Theileria parasite is most similar to that of Theileria equi, also a pathogen of...
Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM....The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further charact...
Lippold S, Matzke NJ, Reissmann M, Hofreiter M.DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. Results: In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds an...
Kappmeyer LS, Thiagarajan M, Herndon DR, Ramsay JD, Caler E, Djikeng A, Gillespie JJ, Lau AO, Roalson EH, Silva JC, Silva MG, Suarez CE, Ueti MW....Transmission of arthropod-borne apicomplexan parasites that cause disease and result in death or persistent infection represents a major challenge to global human and animal health. First described in 1901 as Piroplasma equi, this re-emergent apicomplexan parasite was renamed Babesia equi and subsequently Theileria equi, reflecting an uncertain taxonomy. Understanding mechanisms by which apicomplexan parasites evade immune or chemotherapeutic elimination is required for development of effective vaccines or chemotherapeutics. The continued risk of transmission of T. equi from clinically silent,...
Bhoora R, Franssen L, Oosthuizen MC, Guthrie AJ, Zweygarth E, Penzhorn BL, Jongejan F, Collins NE.A molecular epidemiological survey of the protozoal parasites that cause equine piroplasmosis was conducted using samples collected from horses and zebra from different geographical locations in South Africa. A total of 488 samples were tested for the presence of Theileria equi and/or Babesia caballi using the reverse line blot hybridization assay. Ten percent of the samples hybridized to the Theileria/Babesia genus-specific probe and not to the B. caballi or T. equi species-specific probes, suggesting the presence of a novel species or genotype. The small subunit of rRNA gene (18S; approximat...
Powers AM, Oberste MS, Brault AC, Rico-Hesse R, Schmura SM, Smith JF, Kang W, Sweeney WP, Weaver SC.Venezuelan equine encephalitis (VEE) epidemics and equine epizootics occurred periodically in the Americas from the 1920s until the early 1970s, when the causative viruses, subtypes IAB and IC, were postulated to have become extinct. Recent outbreaks in Columbia and Venezuela have renewed interest in the source of epidemic/epizootic viruses and their mechanism of interepizootic maintenance. We performed phylogenetic analyses of VEE virus isolates spanning the entire temporal and geographic range of strains available, using 857-nucleotide reverse transcription-PCR products including the E3 and ...
Venter M, Swanepoel R.West Nile virus (WNV) is widely distributed in South Africa, but since a few cases of neurological disease have been reported from this region, endemic lineage 2 strains were postulated to be of low virulence. Several cases of nonfatal encephalitis in humans as well as fatal cases in a foal, dog, and ostrich chicks have, however, been associated with lineage 2 WNV in South Africa. The pathogenesis of lineage 2 WNV strains was investigated using mouse neuroinvasive experiments, gene expression experiments, and genome sequence comparisons which indicated that lineage 2 strains that are highly pa...
Weaver SC, Hagenbaugh A, Bellew LA, Gousset L, Mallampalli V, Holland JJ, Scott TW.Evolution of viruses in the eastern equine encephalomyelitis (EEE) complex was studied by analyzing RNA sequences and oligonucleotide fingerprints from isolates representing the North and South American antigenic varieties. By using homologous sequences of Venezuelan equine encephalomyelitis virus as an outgroup, phylogenetic trees revealed three main EEE virus monophyletic groups. A North American variety group included all isolates from North America and the Caribbean. One South American variety group included isolates from the Amazon basin in Brazil and Peru, while the other included strain...
Schuffenecker I, Peyrefitte CN, el Harrak M, Murri S, Leblond A, Zeller HG.West Nile virus (WNV) reemerged in Morocco in September 2003, causing an equine outbreak. A WNV strain isolated from a brain biopsy was completely sequenced. On the basis of phylogenetic analyses, Moroccan WNV strains isolated during the 1996 and 2003 outbreaks were closely related to other strains responsible for equine outbreaks in the western Mediterranean basin.
Nagore D, García-Sanmartín J, García-Pérez AL, Juste RA, Hurtado A.Specific oligonucleotide probes were designed to develop a new and highly sensitive reverse line blot assay to detect and identify simultaneously different Theileria and Babesia species in horses. The amplified hypervariable V4 region of the 18S rRNA gene was hybridised against different generic and species-specific probes. The survey was conducted over 243 samples of equine blood divided into three different groups: group 1, 24 horses presented as possible clinical piroplasmosis; group 2, 181 clinically healthy free-ranging horses exposed to ticks; group 3, 38 riding horses with unrelated pat...
Asher RJ, Bennett N, Lehmann T.An unprecedented level of confidence has recently crystallized around a new hypothesis of how living placental mammals share a pattern of common descent. The major groups are afrotheres (e.g., aardvarks, elephants), xenarthrans (e.g., anteaters, sloths), laurasiatheres (e.g., horses, shrews), and euarchontoglires (e.g., humans, rodents). Compared with previous hypotheses this tree is remarkably stable; however, some uncertainty persists about the location of the placental root, and (for example) the position of bats within laurasiatheres, of sea cows and aardvarks within afrotheres, and of der...
Weaver SC, Bellew LA, Rico-Hesse R.We studied the evolution of alphaviruses in the Venezuelan equine encephalitis (VEE) complex using phylogenetic analysis of RNA nucleotide sequences from limited portions of the nsP4, E1, and 3' untranslated genome regions of representative strains. The VEE complex constituted a monophyletic group of viruses (descended from a common ancestor); some serologic VEE varieties such as subtype III formed monophyletic groups while subtype I did not. Subtype II Everglades and variety ID enzootic viruses formed a monophyletic group which also included all epizootic variety IAB and IC VEE isolates. Ever...
Martins LC, Silva EVPD, Casseb LMN, Silva SPD, Cruz ACR, Pantoja JAS, Medeiros DBA, Martins Filho AJ, Cruz EDRMD, Araújo MTF, Cardoso JF....Serological evidence of West Nile virus (WNV) infection has been reported in different regions of Brazil from equine and human hosts but the virus had never been isolated in the country. Objective: We sought to identify the viral etiology of equine encephalitis in Espírito Santo state. Methods: We performed viral culture in C6/36 cells, molecular detection of WNV genome, histopathology and immunohistochemistry from horse cerebral tissue. We also carried out sequencing, phylogenetic analysis and molecular clock. Results: Histopathologic analysis from horse cerebral tissue showed injury related...
Sharma M, Nunez-Garcia J, Kearns AM, Doumith M, Butaye PR, Argudín MA, Lahuerta-Marin A, Pichon B, AbuOun M, Rogers J, Ellis RJ, Teale C, Anjum MF.In recent years, there has been an increase in the number of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 recovered from S. aureus isolated animals in the UK. To determine possible origins of 12 LA-MRSA CC398 isolates collected after screening more than a thousand S. aureus animal isolates from the UK between 2013 and 2015, whole genome sequences (WGS) of CC398 European, including UK, and non-European isolates from diverse animal hosts were compared. Phylogenetic reconstruction applied to WGS data to assess genetic relatedness of all 89 iso...
Kolodziejek J, Dürrwald R, Herzog S, Ehrensperger F, Lussy H, Nowotny N.The aim of this study was to gain more detailed insights into the genetic evolution and variability of Borna disease virus (BDV). Phylogenetic analyses were performed on field viruses originating from naturally infected animals, the BDV vaccine strain 'Dessau', four widely used laboratory strains and the novel BDV subtype No/98. Four regions of the BDV genome were analysed: the complete p40, p10 and p24 genes and the 5'-untranslated region of the X/P transcript. BDV isolates from the same geographical area exhibited a clearly higher degree of identity to each other than to BDV isolates from ot...
Matthijnssens J, Miño S, Papp H, Potgieter C, Novo L, Heylen E, Zeller M, Garaicoechea L, Badaracco A, Lengyel G, Kisfali P, Cullinane A, Collins PJ....In this study, the complete genome sequences of seven equine group A rotavirus (RVA) strains (RVA/Horse-tc/GBR/L338/1991/G13P[18], RVA/Horse-wt/IRL/03V04954/2003/G3P[12] and RVA/Horse-wt/IRL/04V2024/2004/G14P[12] from Europe; RVA/Horse-wt/ARG/E30/1993/G3P[12], RVA/Horse-wt/ARG/E403/2006/G14P[12] and RVA/Horse-wt/ARG/E4040/2008/G14P[12] from Argentina; and RVA/Horse-wt/ZAF/EqRV-SA1/2006/G14P[12] from South Africa) were determined. Multiple novel genotypes were identified and genotype numbers were assigned by the Rotavirus Classification Working Group: R9 (VP1), C9 (VP2), N9 (NSP2), T12 (NSP3), ...
Bryant NA, Wilkie GS, Russell CA, Compston L, Grafham D, Clissold L, McLay K, Medcalf L, Newton R, Davison AJ, Elton DM.Equine herpesvirus 1 (EHV-1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV-1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term "neuropathic strain," even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understan...
Lau AN, Peng L, Goto H, Chemnick L, Ryder OA, Makova KD.Despite their ability to interbreed and produce fertile offspring, there is continued disagreement about the genetic relationship of the domestic horse (Equus caballus) to its endangered wild relative, Przewalski's horse (Equus przewalskii). Analyses have differed as to whether or not Przewalski's horse is placed phylogenetically as a separate sister group to domestic horses. Because Przewalski's horse and domestic horse are so closely related, genetic data can also be used to infer domestication-specific differences between the two. To investigate the genetic relationship of Przewalski's hors...
The Journal of heredityOctober 15, 2003
Volume 94, Issue 5 374-380 doi: 10.1093/jhered/esg079
Tozaki T, Takezaki N, Hasegawa T, Ishida N, Kurosawa M, Tomita M, Saitou N, Mukoyama H.The genetic relationships of seven Japanese and four mainland-Asian horse populations, as well as two European horse populations, were estimated using data for 20 microsatellite loci. Mongolian horses showed the highest average heterozygosities (0.75-0.77) in all populations. Phylogenetic analysis showed the existence of three distinct clusters supported by high bootstrap values: the European cluster (Anglo-Arab and thoroughbreds), the Hokkaido-Kiso cluster, and the Mongolian cluster. The relationships of these clusters were consistent with their geographical distributions. Basing our assumpti...
The climatic and cultural diversity of the Italian Peninsula triggered, over time, the development of a great variety of horse breeds, whose origin and history are still unclear. To clarify this issue, analyses on phenotypic traits and genealogical data were recently coupled with molecular screening. Methods: To provide a comprehensive overview of the horse genetic variability in Italy, we produced and phylogenetically analyzed 407 mitochondrial DNA (mtDNA) control-region sequences from ten of the most important Italian riding horse and pony breeds: Bardigiano, Esperia, Giara, Lipizzan, Maremm...
Tan Y, Lam TT, Heberlein-Larson LA, Smole SC, Auguste AJ, Hennigan S, Halpin RA, Fedorova N, Puri V, Stockwell TB, Shilts MH, Andreadis T....Eastern equine encephalitis virus (EEEV) has a high case-fatality rate in horses and humans, and Florida has been hypothesized to be the source of EEEV epidemics for the northeastern United States. To test this hypothesis, we sequenced complete genomes of 433 EEEV strains collected within the United States from 1934 to 2014. Phylogenetic analysis suggested EEEV evolves relatively slowly and that transmission is enzootic in Florida, characterized by higher genetic diversity and long-term local persistence. In contrast, EEEV strains in New York and Massachusetts were characterized by lower genet...
Rash A, Morton R, Woodward A, Maes O, McCauley J, Bryant N, Elton D.Equine influenza viruses (EIV) are a major cause of acute respiratory disease in horses worldwide and occasionally also affect vaccinated animals. Like other influenza A viruses, they undergo antigenic drift, highlighting the importance of both surveillance and virus characterisation in order for vaccine strains to be kept up to date. The aim of the work reported here was to monitor the genetic and antigenic changes occurring in EIV circulating in the UK from 2013 to 2015 and to identify any evidence of vaccine breakdown in the field. Virus isolation, reverse transcription polymerase chain rea...
Wallner B, Brem G, Müller M, Achmann R.The phylogenetic relationship between Equus przewalskii and E. caballus is often a matter of debate. Although these taxa have different chromosome numbers, they do not form monophyletic clades in a phylogenetic tree based on mtDNA sequences. Here we report sequence variation from five newly identified Y chromosome regions of the horse. Two fixed nucleotide differences on the Y chromosome clearly display Przewalski's horse and domestic horse as sister taxa. At both positions the Przewalski's horse haplotype shows the ancestral state, in common with the members of the zebra/ass lineage. We discu...
Munkhjargal T, Sivakumar T, Battsetseg B, Nyamjargal T, Aboulaila M, Purevtseren B, Bayarsaikhan D, Byambaa B, Terkawi MA, Yokoyama N, Igarashi I.Equine piroplasmosis represents a serious problem in horse industry. Although, researchers suggested the possible use of sub-unit vaccines to control equine piroplasmosis, the genetic diversity of vaccine candidate antigens was not properly investigated. In the present study, we screened 250 horses reared in three different districts of Tov province, Mongolia, for Babesia caballi and Theileria equi using ELISA and nested PCR (nPCR) assays. Among these animals, piroplasms were detected in 128 (51.2%) horses by nPCR assays (B. caballi, 42.4%; T. equi, 6.4%; and mixed infections, 2.4%), while 204...
