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Guan M, Sun N, Yau SST. Geometric analysis of SARS-CoV-2 variants. Gene 2024; 909:148291. [PMID: 38417688 DOI: 10.1016/j.gene.2024.148291] [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: 11/15/2023] [Revised: 01/23/2024] [Accepted: 02/14/2024] [Indexed: 03/01/2024]
Abstract
SARS-CoV-2 as a severe respiratory disease has been prevalent around the world since its first discovery in 2019.As a single-stranded RNA virus, its high mutation rate makes its variants manifold and enables some of them to have high pathogenicity, such as Omicron variant, the most prevalent virus now. Research on the relationship of these SARS-CoV-2 variants, especially exploring their difference is a hot issue. In this study, we constructed a geometric space to represent all SARS-CoV-2 sequences of different variants. An alignment-free method: natural vector method was utilized to establish genome space. The genome space of SARS-CoV-2 was constructed based on the 24-dimensional natural vector and the appropriate metric was determined through performing phylogenetic analysises. Phylogenetic trees of different lineages constructed under the selected natural vector and metric coincided with the lineage naming standards, which means lineages with same alphabetical prefix cluster in phylogenetic trees. Furthermore, the relationships between the various GISAID clades as depicted by the natural graph primarily matched the description provided in the GISAID clade naming.The validity of our geometric space was demonstrated by these phylogenetic analysis results. So in this research, we constructed a geometry space for the genomes of the novel coronavirus SARS-CoV-2, which allows us to compare the different variants. Our geometric space is valuable for resolving the issues insides the virus.
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Affiliation(s)
- Mengcen Guan
- Department of Mathematical Sciences, Tsinghua University, Beijing, China.
| | - Nan Sun
- Department of Mathematical Sciences, Tsinghua University, Beijing, China.
| | - Stephen S-T Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing, China; Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
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2
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Kim S, Cheng Y, Fang Z, Liu X, Zhongqi Q, Weidong Y, Yilmaz A, Yilmaz H, Umar S. Molecular epidemiology and phylogenetic analysis of feline calicivirus in Kunshan, China. Virol J 2024; 21:50. [PMID: 38414028 PMCID: PMC10900597 DOI: 10.1186/s12985-024-02319-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Feline calicivirus (FCV) is a highly contagious virus in cats, which typically causes respiratory tract and oral infections. Despite vaccination against FCV being a regular practice in China, new FCV cases still occur. Antigenic diversity of FCV hinders the effective control by vaccination. This is first report which aims to investigate the molecular epidemiology and molecular characteristics of FCV in Kunshan, China. The nasopharyngeal swabs were collected from cats showing variable clinical signs from different animal clinics in Kunshan from 2022 to 2023. Preliminary detection and sequencing of the FCV capsid gene were performed to study genetic diversity and evolutionary characteristics. FCV-RNA was identified in 52 (26%) of the samples using RT-PCR. A significant association was found between FCV-positive detection rate, age, gender, vaccination status and living environment, while a non-significant association was found with breed of cats. Nucleotide analysis revealed two genotypes, GI and GII. GII predominated in Kunshan, with diverse strains and amino acid variations potentially affecting vaccination efficacy and FCV detection. Notably, analysis pinpointed certain strains' association with FCV-virulent systemic disease pathotypes. This investigation sheds light on FCV dynamics, which may aid in developing better prevention strategies and future vaccine designs against circulating FCV genotypes.
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Affiliation(s)
- Semin Kim
- Global Health Research Center (GHRC), Duke Kunshan University, Suzhou, China
| | - Yixi Cheng
- Global Health Research Center (GHRC), Duke Kunshan University, Suzhou, China
| | - Zhenkun Fang
- Global Health Research Center (GHRC), Duke Kunshan University, Suzhou, China
| | - Xinyue Liu
- Global Health Research Center (GHRC), Duke Kunshan University, Suzhou, China
- Division of Natural & Applied Sciences (DNAS), Duke Kunshan University, Suzhou, China
| | - Qiu Zhongqi
- Simba Pet Hospital, Tinglin Park Branch), Maanshan Road, 215335, Kunshan, Suzhou, Jiangsu Province, China
| | - Yu Weidong
- Play Pi Kangkang Pet Hospital, Kunshan City Development Zone, 215300, Kunshan, Suzhou, Jiangsu Province, China
| | - Aysun Yilmaz
- Department of Virology, Veterinary Faculty, Istanbul University-Cerrahpasa, 35500, Büyükcekmece, Istanbul, Turkey
| | - Huseyin Yilmaz
- Department of Virology, Veterinary Faculty, Istanbul University-Cerrahpasa, 35500, Büyükcekmece, Istanbul, Turkey
| | - Sajid Umar
- Global Health Research Center (GHRC), Duke Kunshan University, Suzhou, China.
- Division of Natural & Applied Sciences (DNAS), Duke Kunshan University, Suzhou, China.
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3
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Hong JH, Seo M, Oh CS, Chai JY, Shin DH. Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty. J Parasitol 2021; 106:802-808. [PMID: 33351947 DOI: 10.1645/20-42] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/14/2022] Open
Abstract
Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics.
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Affiliation(s)
- Jong Ha Hong
- Institute of Korean Archaeology and Ancient History, Kyung Hee University, Seoul, South Korea.,Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea
| | - Min Seo
- Department of Parasitology, Dankook University College of Medicine, Cheonan, South Korea
| | - Chang Seok Oh
- Department of Mortuary Science, Eulji University, Seongnam-Si, Gyeonggi-Do, South Korea.,Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong-Yil Chai
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Parasitic Diseases, Korea Association of Health Promotion, Seoul, South Korea
| | - Dong Hoon Shin
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
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4
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Ghaffar A, Ijaz M, Ali A, Farooqi SH, Rehman A, Ali MM, Zafar MZ, Naeem MA. First Report on Molecular Characterization of Anaplasmosis in Small Ruminants in Pakistan. J Parasitol 2020; 106:360-368. [PMID: 32227225 DOI: 10.1645/19-90] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/20/2023] Open
Abstract
Anaplasmosis is caused by a Gram-negative obligate intracellular bacterium of the genus Anaplasma with the pathogen having a zoonotic impact. The study aimed to estimate the prevalence of anaplasmosis in Pakistan, to unravel the association of potential risk factors, and to investigate the effect on hematological parameters in affected small ruminants. A total of 150 (n = 75 sheep; n = 75 goats) blood samples were initially screened microscopically and then subjected to PCR targeting the amplification of the 16S rRNA gene fragment of Anaplasma. The PCR-based positive samples were then processed for sequencing. Statistical analysis regarding risk factors was performed using R software. The study revealed an overall 29.33% (44/150) prevalence of anaplasmosis in small ruminants. Sheep had higher (P > 0.05) prevalence (32%) as compared to goats (25.30%). The final statistical model resulting from backward elimination showed only tick infestation as a significant predictor of infection status. The phylogenetic analysis of 16S rRNA gene of Anaplasma spp. revealed 9 study isolates clustered together and showed a close resemblance (99%) with Anaplasma ovis isolate (DQ837600) from Hungary. One of the isolates showed (99%) similarity with the isolate of Anaplasma marginale (MH155594) from Iraq. Furthermore, the hematological parameters pack cell volume, red blood cells, hemoglobin, white blood cells, granulocytes, monocytes, lymphocytes, and platelet count were decreased in Anaplasma-positive animals. This is the first study at the molecular level to characterize Anaplasma spp. in small ruminants of Pakistan, and it will be useful in developing control strategies for anaplasmosis.
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Affiliation(s)
- Awais Ghaffar
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
| | - Muhammad Ijaz
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
| | - Ahmad Ali
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
| | - Shahid Hussain Farooqi
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
| | - Abdul Rehman
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
| | - Muhammad Muddassir Ali
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
| | - Muhammad Zeeshan Zafar
- Department of Microbiology, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
| | - Muhammad Anas Naeem
- Department of Microbiology, University of Veterinary and Animal Sciences, Lahore 54600, Pakistan
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Abstract
The novel coronavirus (SARS-COV-2) is generally referred to as Covid-19 virus has spread to 213 countries with nearly 7 million confirmed cases and nearly 400,000 deaths. Such major outbreaks demand classification and origin of the virus genomic sequence, for planning, containment, and treatment. Motivated by the above need, we report two alignment-free methods combing with CGR to perform clustering analysis and create a phylogenetic tree based on it. To each DNA sequence we associate a matrix then define distance between two DNA sequences to be the distance between their associated matrix. These methods are being used for phylogenetic analysis of coronavirus sequences. Our approach provides a powerful tool for analyzing and annotating genomes and their phylogenetic relationships. We also compare our tool to ClustalX algorithm which is one of the most popular alignment methods. Our alignment-free methods are shown to be capable of finding closest genetic relatives of coronaviruses.
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Affiliation(s)
- Dipendra C Sengupta
- Department of Mathematics, Computer Science & Engineering Technology, Elizabeth City State University, Elizabeth City, North Carolina, USA
| | - Matthew D Hill
- Department of Mathematics, Computer Science & Engineering Technology, Elizabeth City State University, Elizabeth City, North Carolina, USA
| | - Kevin R Benton
- Department of Mathematics, Computer Science & Engineering Technology, Elizabeth City State University, Elizabeth City, North Carolina, USA
| | - Hirendra N Banerjee
- Department Natural Sciences, Elizabeth City State University, Elizabeth City, North Carolina, USA
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Rezaee H, Ghalyanchi Langeroudi A, Karimi V, Fallah Mehrabadi MH, Motamed Chaboki P, Shayganmehr A, Esmaeelzadeh Dizaji R. Molecular Detection of Avian Infectious Bronchitis Viruses in Live Bird Markets, Gilan Province. Arch Razi Inst 2020; 75:155-162. [PMID: 32621443 DOI: 10.22092/ari.2018.122702.1226] [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] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 12/06/2018] [Indexed: 09/30/2022]
Abstract
Coronaviruses (AvCoV) which include infectious bronchitis virus (IBV) and other bird coronaviruses belong to the genus gammacoronavirus, subfamily Coronavirinae. One of the most prominent representatives of gammacoronavirus genus is infectious bronchitis virus (IBV) which is a highly contagious viral pathogen of chickens causing considerable economic losses to the poultry industry. IBVs mostly affect the respiratory, urinary, and reproductive tracts leading to a substantial drop in production. Backyard poultry in the villages usually share their food and water with free flight birds which puts them at serious risk of disease transmission. Furthermore, the poor hygienic measurements which are often used in backyard flocks make them a potential reservoir for diseases that can be transferred to commercial poultry flocks. Live bird markets (LBMs) which receive live poultry to be resold or slaughtered and sold onsite play a significant role in spreading infectious diseases among the different bird species. In the present study, a number of 354 cloacal swab samples were collected from different bird species from LBMs of Gilan province. Subsequently, after RNA extraction, reverse transcription-polymerase chain reaction (RT-PCR) technique was carried out using specific primers of S1 gene to detect coronavirus infectious bronchitis virus. Two samples from backyard chickens were reported to be positive to coronavirus which were named Iran/Backyardchicken 96/2017 and Iran/Backyardchicken 94/2017. The results of the phylogenetic analysis demonstrated that these two isolates are placed in QX and IS-1494 strains, respectively. On a final note, the obtained results highlighted the role of live birds offered in LBMs in the epidemiology of IBV and the transmission of the virus to the industrial flock.
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Affiliation(s)
- H Rezaee
- Department of Avian Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - A Ghalyanchi Langeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - V Karimi
- Department of Avian Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - M H Fallah Mehrabadi
- Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.,Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - P Motamed Chaboki
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - A Shayganmehr
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - R Esmaeelzadeh Dizaji
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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7
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Ruhnke TR, Daniel V, Jensen K. Four New Species of Paraorygmatobothrium (Eucestoda: Phyllobothriidea) From Sharks of the Gulf of Mexico and the Atlantic Ocean, with Comments on Their Host Specificity. J Parasitol 2020; 106:133-156. [PMID: 32048913] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
Four new species of Paraorygmatobothrium are described from carcharhinid shark species from the Gulf of Mexico and the U.S. coast of the northwestern Atlantic Ocean. Paraorygmatobothrium bullardi n. sp. is described from Carcharhinus brevipinna as its type host, and from Carcharhinus acronotus and Carcharhinus limbatus. Paraorygmatobothrium campbelli n. sp. is described from Rhizoprionodon terraenovae. Paraorygmatobothrium deburonae n. sp. is described from Carcharhinus isodon as its type host, as well as from C. brevipinna, C. limbatus, and R. terraenovae. Paraorygmatobothrium mattisi n. sp. is described from R. terraenovae as its type host, and from C. brevipinna and C. limbatus. These 4 species differ from other species of Paraorygmatobothrium and from each other in bothridial microthrix shape, and in various combinations of features such as the total length of the worm, apical sucker size, bothridial musculature, proglottid number, testes number, and genital pore position. Difficulty in differentiating these 4 species from one another, and from other species of Paraorygmatobothrium, points to limitations in the use of morphology alone to recognize species diversity in this genus. A phylogenetic analysis of Paraorygmatobothrium and related genera, based on partial (D1-D3) 28S rDNA sequence data, confirms that the genus is not monophyletic. Genetic distances of COI revealed that sequence divergence between species of Paraorygmatobothrium is generally at least an order of magnitude larger than COI divergence within a species. Patterns of host use for 3 of the new species are consistent with previous findings that point to a lack of host specificity in Paraorygmatobothrium.
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Affiliation(s)
- T R Ruhnke
- Department of Biology, Barron Drive, West Virginia State University, Institute, West Virginia 25112-1000
| | - V Daniel
- Department of Biology, Barron Drive, West Virginia State University, Institute, West Virginia 25112-1000
| | - K Jensen
- Department of Ecology and Evolutionary Biology and the Biodiversity Institute, 1200 Sunnyside Ave., University of Kansas, Lawrence, Kansas 66045
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Yaghoubi H, Ghalyanchi Langeroudi A, Karimi V, Ghafouri SA, Hashemzadeh M, Hosseini H, Fallah Mehrabadi MH, Sadat Mousavi F, Najafi H. Molecular Detection of Gamma Coronaviruses in Bird Parks of Iran. Arch Razi Inst 2019; 74:349-355. [PMID: 31939251 DOI: 10.22092/ari.2018.116786.1176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/22/2018] [Indexed: 09/30/2022]
Abstract
Gamma Coronaviruses (GCoVs) are distributed worldwide, affecting a wide range of bird species, the beluga whale, and bottlenose dolphins. Because of the limited proofreading capability in the viral encoded polymerase, they emerge genetically diverse. There has been no molecular surveillance data to describe the epidemiology of GCOVs in avian species. The present study was conducted to detect GCOVs in Tehran birds’ parks, 2015. Cloacal swabs (267 samples) from eight different bird species ((Chickens (Gallus gallus), Pheasant (Phasianus colchicus), Turkey (Meleagris gallopavo), Partridge (Perdix perdix), Quail (Coturnix coturnix), Duck (Anas platyrhynchos), Goose (Anserini),and Guinea fowl (Numididae)) were collected, the viral RNA was extracted, the RT-PCR was performed using QIAGEN one step RT-PCR kit and the primers targeting “3'-UTR” and “Nucleocapsid” genes. The detection rate was approximately 8.99%. GCOVs were detected in the chicken, quail, pheasant, turkey, and the partridge with different prevalence rates. Phylogenetic tree based on partial nucleotide sequences of the N gene clustered the samples into two groups. It is the first report of GCOVs in non-commercial birds in Iran. According to our results, GCOVs are circulating in different avian species, and further studies are needed to isolate these viruses and evaluate their pathogenesis.
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Affiliation(s)
- H Yaghoubi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - A Ghalyanchi Langeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.,Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - V Karimi
- Department of Avian Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - S A Ghafouri
- Department of clinical sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - M Hashemzadeh
- Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - H Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Karaj Branch, Islamic Azad University, Alborz, Iran
| | - M H Fallah Mehrabadi
- Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - F Sadat Mousavi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - H Najafi
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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9
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Hong JH, Oh CS, Chai JY, Seo M, Shin DH. Cytochrome C Oxidase Subunit 1, Internal Transcribed Spacer 1, Nicotinamide Adenine Dinucleotide Hydrogen Dehydrogenase Subunits 2 and 5 of Clonorchis sinensis Ancient DNA Retrieved from Joseon Dynasty Mummy Specimens. J Korean Med Sci 2019; 34:e149. [PMID: 31124326 PMCID: PMC6535405 DOI: 10.3346/jkms.2019.34.e149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.
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Affiliation(s)
- Jong Ha Hong
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Seok Oh
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Yil Chai
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul, Korea
- Institute of Parasitic Diseases, Korean Association of Health Promotion, Seoul, Korea
| | - Min Seo
- Department of Parasitology, Dankook University College of Medicine, Cheonan, Korea.
| | - Dong Hoon Shin
- Laboratory of Bioanthropology, Paleopathology and History of Diseases, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea.
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Eudy E, Caira JN, Jensen K. A New Species of Pentaloculum (Cestoda: "Tetraphyllidea") from the Taiwan Saddled Carpetshark, Cirrhoscyllium formosanum (Orectolobiformes: Parascylliidae). J Parasitol 2019; 105:303-312. [PMID: 30990771] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Collection of cestodes from the Taiwan saddled carpetshark, Cirrhoscyllium formosanum, for the first time led to the discovery of Pentaloculum hoi n. sp. This species provided important insights into the identity of the heretofore monotypic Pentaloculum-known previously only from the blind electric ray, Typhlonarke aysoni, in New Zealand. The new species differs from Pentaloculum macrocephalum in testis number, vitelline follicle and cirrus sac configuration, and in that it is hyperapolytic rather than euapolytic. Maximum-likelihood analysis of sequence data generated for the D1-D3 region of the 28S rDNA gene not only confirmed this generic placement but also confirmed the close affinities between both species of Pentaloculum and specimens previously referred to in the literature as new genus 7 n. sp. 1. Examination of limited material of the latter, including that of a second specimen from which partial 28S rDNA sequence data were generated here, led to the realization that new genus 7 n. sp. 1 represents an undescribed species of Pentaloculum, referred to here as Pentaloculum n. sp. 2. All 3 species share bothridia divided into 1 anterior and 2 consecutive pairs of loculi. Given that Pentaloculum n. sp. 2 parasitizes a member of the second and only other genus of parascylliid sharks (i.e., Parascyllium), we predict that the 4 other species of Parascyllium and the 2 other species of Cirrhoscyllium are likely to host other species of Pentaloculum. The factors that might account for the eclectic host associations of Pentaloculum, which include a torpediniform ray and 2 species of orectilobiform sharks, are currently unclear. The compilation of diet data for these elasmobranchs and determination of the final intermediate hosts for these cestodes would be interesting avenues of further investigation given that cestodes are trophically transmitted between their intermediate and definitive hosts. The phylogenetic affinities of Pentaloculum among elasmobranch cestodes remain unresolved.
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Affiliation(s)
- Elizabeth Eudy
- 1 Department of Ecology and Evolutionary Biology, 75 N. Eagleville Road Unit 3043, University of Connecticut, Storrs, Connecticut 06269-3043
| | - J N Caira
- 1 Department of Ecology and Evolutionary Biology, 75 N. Eagleville Road Unit 3043, University of Connecticut, Storrs, Connecticut 06269-3043
| | - K Jensen
- 2 Department of Ecology and Evolutionary Biology and the Biodiversity Institute, 1200 Sunnyside Avenue, University of Kansas, Lawrence, Kansas 66045
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11
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Charoensook R, Gatphayak K, Brenig B, Knorr C. Genetic diversity analysis of Thai indigenous pig population using microsatellite markers. Asian-Australas J Anim Sci 2019; 32:1491-1500. [PMID: 31010994 PMCID: PMC6718910 DOI: 10.5713/ajas.18.0832] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/16/2019] [Indexed: 11/27/2022]
Abstract
Objective European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results The results showed that Thai pig populations had a high genetic diversity with mean total and effective (Ne) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity (He) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher He compared to observed heterozygosity (Ho) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei’s genetic distance, mean FST estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.
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Affiliation(s)
- Rangsun Charoensook
- Division of Animal Science and Feed Technology, Department of Agricultural Sciences, Faculty of Agriculture Natural Resources and Environment, Naresuan University, Phitsanulok 65000, Thailand
| | - Kesinee Gatphayak
- Department of Animal and Aquatic Science, Faculty of Agriculture, Chiang Mai University, 50200 Chiang Mai, Thailand
| | - Bertram Brenig
- Division of Molecular Biology of Livestock and Molecular Diagnostics, Faculty of Agricultural Sciences, Georg-August University of Göttingen, Göttingen 37077, Germany
| | - Christoph Knorr
- Division of Livestock Biotechnology and Reproduction, Faculty of Agricultural Sciences, Georg-August University of Göttingen, Göttingen 37077, Germany
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Steinauer ML, Garcia-Vedrenne AE, Weinstein SB, Kuris AM. Acanthocephalan Parasites of the Oarfish, Regalecus russelii (Regalecidae), With A Description of A New Species of Gymnorhadinorhynchus (Acanthocephala: Gymnorhadinorhynchidae). J Parasitol 2019; 105:124-132. [PMID: 30807713] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Oarfish are rarely seen and seldom studied, which makes their parasite fauna even more enigmatic. Necropsy of 12 oarfish, Regalecus russelii (Regalecidae) (Cuvier, 1816), from Japan yielded 2 species of acanthocephalans. One species was found in 2 oarfish and a total of 76 specimens was collected, but only a single, immature specimen of the second species was found. The former represents an undescribed species from the order Echinorhynchida and is described here. Morphological and phylogenetic analyses of the small subunit ( SSU) rDNA place this species in the family Gymnorhadinorhynchidae, and genus Gymnorhadinorhynchus which is characterized by a cylindrical proboscis with longitudinal rows of hooks, basal circle of enlarged hooks, asymmetry of hook shape, 4 cement glands, and a spineless trunk. Diagnostic characters of this species within the genus are the number of longitudinal rows of hooks (14), smaller body size (males: 4.8-6.6 mm and females: 5.3-6.3 mm) and a number of molecular autapomorphies including a number of long insertions in both the SSU and large subunit rDNA (LSU). A single immature female of Bolbosoma sp. (Palaeacanthocephala: Plagiorhynchidae) was also found with its anterior end embedded in the mucosa of the pyloric ceca. The characters of this specimen are not consistent with any other known species of Bolbosoma; however, because only 1 immature specimen with a partially invaginated proboscis was recovered, it was not designated as a new species.
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Affiliation(s)
- Michelle L Steinauer
- 1 Department of Basic Medical Sciences, COMP-NW, Western University of Health Sciences, Lebanon, Oregon 97355
| | - Ana E Garcia-Vedrenne
- 2 Department of Ecology, Evolution and Marine Biology, and Marine Science Institute, University of California, Santa Barbara, California 93106
| | - Sara B Weinstein
- 2 Department of Ecology, Evolution and Marine Biology, and Marine Science Institute, University of California, Santa Barbara, California 93106
| | - Armand M Kuris
- 2 Department of Ecology, Evolution and Marine Biology, and Marine Science Institute, University of California, Santa Barbara, California 93106
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Xia Y, Qu H, Lu B, Zhang Q, Li H. Molecular cloning and expression analysis of annexin A2 gene in sika deer antler tip. Asian-Australas J Anim Sci 2017; 31:467-472. [PMID: 28823128 PMCID: PMC5838317 DOI: 10.5713/ajas.17.0280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/22/2017] [Accepted: 08/03/2017] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Molecular cloning and bioinformatics analysis of annexin A2 (ANXA2) gene in sika deer antler tip were conducted. The role of ANXA2 gene in the growth and development of the antler were analyzed initially. METHODS The reverse transcriptase polymerase chain reaction (RT-PCR) was used to clone the cDNA sequence of the ANXA2 gene from antler tip of sika deer (Cervus Nippon hortulorum) and the bioinformatics methods were applied to analyze the amino acid sequence of Anxa2 protein. The mRNA expression levels of the ANXA2 gene in different growth stages were examined by real time reverse transcriptase polymerase chain reaction (real time RT-PCR). RESULTS The nucleotide sequence analysis revealed an open reading frame of 1,020 bp encoding 339 amino acids long protein of calculated molecular weight 38.6 kDa and isoelectric point 6.09. Homologous sequence alignment and phylogenetic analysis indicated that the Anxa2 mature protein of sika deer had the closest genetic distance with Cervus elaphus and Bos mutus. Real time RT-PCR results showed that the gene had differential expression levels in different growth stages, and the expression level of the ANXA2 gene was the highest at metaphase (rapid growing period). CONCLUSION ANXA2 gene may promote the cell proliferation, and the finding suggested Anxa2 as an important candidate for regulating the growth and development of deer antler.
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Affiliation(s)
- Yanling Xia
- College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China.,Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin 150086, China
| | - Haomiao Qu
- College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Binshan Lu
- College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Qiang Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
| | - Heping Li
- College of Wildlife Resources, Northeast Forestry University, Harbin 150040, China
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Mortazavi M, Zarenezhad M, Alavian SM, Gholamzadeh S, Malekpour A, Ghorbani M, Torkzadeh Mahani M, Lotfi S, Fakhrzad A. Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus. Hepat Mon 2016; 16:e39196. [PMID: 27882066 PMCID: PMC5111459 DOI: 10.5812/hepatmon.39196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/16/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND The hepatitis C virus (HCV) has six major genotypes. The purpose of this study was to phylogenetically investigate the differences between the genotypes of HCV, and to determine the types of amino acid codon usage in the structure of the virus in order to discover new methods for treatment regimes. METHODS The codon usage of the six genotypes of the HCV nucleotide sequence was investigated through the online application available on the website Gene Infinity. Also, phylogenetic analysis and the evolutionary relationship of HCV genotypes were analyzed with MEGA 7 software. RESULTS The six genotypes of HCV were divided into two groups based on their codon usage properties. In the first group, genotypes 1 and 5 (74.02%), and in the second group, genotypes 2 and 6 (72.43%) were shown to have the most similarity in terms of codon usage. Unlike the results with respect to determining the similarity of codon usage, the phylogenetic analysis showed the closest resemblance and correlation between genotypes 1 and 4. The results also showed that HCV has a GC (guanine-cytosine) abundant genome structure and prefers codons with GC for translation. CONCLUSIONS Genotypes 1 and 4 demonstrated remarkable similarity in terms of genome sequences and proteins, but surprisingly, in terms of the preferred codons for gene expression, they showed the greatest difference. More studies are therefore needed to confirm the results and select the best approach for treatment of these genotypes based on their codon usage properties.
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Affiliation(s)
- Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran
| | - Mohammad Zarenezhad
- Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Disease, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Saeed Gholamzadeh
- Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
- Corresponding Authors: Saeed Gholamzadeh, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail: ; Abdorrasoul Malekpour, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail:
| | - Abdorrasoul Malekpour
- Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran
- Corresponding Authors: Saeed Gholamzadeh, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail: ; Abdorrasoul Malekpour, Legal Medicine Research Center, Legal Medicine Organization of Iran, Tehran, IR Iran. Tel: +98-7136324100, E-mail:
| | - Mohammad Ghorbani
- Department of Pathology, School of Medicine, Fasa University of Medical Sciences, Fasa, IR Iran
| | - Masoud Torkzadeh Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran
| | - Safa Lotfi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, IR Iran
| | - Ali Fakhrzad
- Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
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Muller SK, Assenga JA, Matemba LE, Misinzo G, Kazwala RR. Human leptospirosis in Tanzania: sequencing and phylogenetic analysis confirm that pathogenic Leptospira species circulate among agro-pastoralists living in Katavi-Rukwa ecosystem. BMC Infect Dis 2016; 16:273. [PMID: 27287703 PMCID: PMC4902944 DOI: 10.1186/s12879-016-1588-x] [Citation(s) in RCA: 6] [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: 10/21/2015] [Accepted: 05/21/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Leptospirosis is a neglected zoonotic disease of worldwide public health importance. The disease affects humans, domestic animals and wildlife. However, leptospirosis is challenging in its diagnosis in humans. Culture technique, which is time consuming, is not recommended for clinical diagnosis. For these reasons, serological and molecular techniques remain the test of choice. The major objective of this study was to explore the genetic characteristic of Leptospira species which are prevalent among agro-pastoralists living in Katavi-Rukwa Ecosystem, Tanzania. METHODS A cross-sectional epidemiological study was carried out in the Katavi-Region South-west, Tanzania between August, 2013 and November, 2014. A total of 267 participants were randomly recruited for the study. Microscopic agglutination test (MAT) was used to detect antibody against six Leptospira antigens including local serogroups Icterohaemorrhagiae, Ballum, Grippotyphosa, Sejroe and reference serogroups Hebdomadis, and Australis. Samples with MAT titers ≥ 1:160 were scored as positive, samples with MAT titers ranging from 1:20 to 1:80 were scored as exposed to Leptospira, and absence of agglutination titers was scored as negative. All MAT positive samples, including the low titre samples were subjected to PCR using the respective 16S rRNA primers for the pathogenic and non-pathogenic species. RESULTS Out of 267 samples tested, 80 (29.9 %) were positive with MAT. The major circulating leptospiral serogroups were Sejroe (15.7 %,), Icterohaemorrhagiae (8.9 %), Grippotyphosa (4.8 %), Hebdomadis (3.37 %), Australis (1.49 %) and Ballum (1.19 %). By using PCR, 33 (15.7 %) out of 210 samples were pathogenic Leptospira while no saprophytic Leptospira spp. was detected. Partial 16S rRNA gene sequences of Leptospira species which were obtained from this study were submitted to GenBank and acquired accession numbers KP313246 and KP313247. Phylogenetic analysis of the nucleotide sequences revealed that species obtained from Katavi-Rukwa ecosystem clustered in the same group with several published pathogenic Leptospira specifically Leptospira interrogans and Leptospira kirschneri. To the best of the authors' knowledge(,) this is the first study from Tanzania to confirm pathogenic Leptospira in human subjects using genomic typing technique. CONCLUSION These findings provide ultimate evidence of pathogenic Leptospira species circulating among agro-pastoralists living in Katavi-Rukwa Ecosystem suggesting that active disease surveillance should be undertaken in order to achieve greater protection of the agro-pastoral communities in Tanzania.
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Affiliation(s)
- Shabani K Muller
- Sokoine University of Agriculture, Morogoro, Tanzania.
- National Institute for Medical Research (NIMR), MOMS clinical Trial, Morogoro, Tanzania.
| | | | - Lucas E Matemba
- National Institute for Medical Research (NIMR), MOMS clinical Trial, Morogoro, Tanzania
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Abstract
The free available eutherian genomic sequence data sets advanced scientific field of genomics. Of note, future revisions of gene data sets were expected, due to incompleteness of public eutherian genomic sequence assemblies and potential genomic sequence errors. The eutherian comparative genomic analysis protocol was proposed as guidance in protection against potential genomic sequence errors in public eutherian genomic sequences. The protocol was applicable in updates of 7 major eutherian gene data sets, including 812 complete coding sequences deposited in European Nucleotide Archive as curated third party data gene data sets.
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Fateh R, Zaini F, Kordbacheh P, Falahati M, Rezaie S, Daie Ghazvini R, Borhani N, Safara M, Fattahi A, Kanani A, Farahyar S, Bolhassani M, Heidari M. Identification and Sequencing of Candida krusei Aconitate Hydratase Gene Using Rapid Amplification of cDNA Ends Method and Phylogenetic Analysis. Jundishapur J Microbiol 2015; 8:e25218. [PMID: 26855741 PMCID: PMC4736022 DOI: 10.5812/jjm.25218] [Citation(s) in RCA: 3] [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: 11/09/2014] [Revised: 12/29/2014] [Accepted: 02/10/2015] [Indexed: 11/28/2022] Open
Abstract
Background: The production and development of an effective fungicidal drug requires the identification of an essential fungal protein as a drug target. Aconitase (ACO) is a mitochondrial protein that plays a vital role in tricarboxylic acid (TCA) cycle and thus production of energy within the cell. Objectives: The current study aimed to sequence Candida krusei ACO gene and determine any amino acid residue differences between human and fungal aconitases to obtain selective inhibition. Materials and Methods: Candida krusei (ATCC: 6258) aconitase gene was determined by 5’Rapid Amplification of cDNA Ends (RACE) method and degenerate Polymerase Chain Reaction (PCR) and analyzed using bioinformatics softwares. Results: One thousand-four hundred-nineteen nucleotide of C. krusei aconitase gene were clarified and submitted in Genbank as a partial sequence and then taxonomic location of C. krusei was determined by nucleotide and amino acid sequences of this gene. The comparison of nucleotide and amino acid sequences of Candida species ACO genes showed that C. krusei possessed characteristic sequences. No significant differences were observed between C. krusei and human aconitases within the active site amino acid residues. Conclusions: Results of the current study indicated that aconitase was not a suitable target to design new anti-fungal drugs that selectively block this enzyme.
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Affiliation(s)
- Roohollah Fateh
- Department of Microbiology and Immunology, Faculty of Medicine, Qom University of Medical Sciences, Qom, IR Iran
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Farideh Zaini
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
- Corresponding authors: Farideh Zaini, Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran. Tel: +98-2142933141, Fax: +98-2188951392, E-mail:
| | - Parivash Kordbacheh
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Mehraban Falahati
- Department of Medical Mycology and Parasitology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, IR Iran
| | - Sasan Rezaie
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Roshanak Daie Ghazvini
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Nahid Borhani
- Department of Parasitology, Pasteur Institute of Iran, Tehran, IR Iran
| | - Mahin Safara
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Azam Fattahi
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Ali Kanani
- Department of Medical Mycology and Parasitology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Shirin Farahyar
- Department of Medical Mycology and Parasitology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, IR Iran
| | - Manzar Bolhassani
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Mansour Heidari
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, IR Iran
- Experimental Research Center, Tehran University of Medical Sciences, Tehran, IR Iran
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Khoshnood S, Rafiei A, Saki J, Alizadeh K. Prevalence and Genotype Characterization of Blastocystis hominis Among the Baghmalek People in Southwestern Iran in 2013 - 2014. Jundishapur J Microbiol 2015; 8:e23930. [PMID: 26587213 PMCID: PMC4644266 DOI: 10.5812/jjm.23930] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 10/03/2014] [Revised: 01/30/2015] [Accepted: 02/16/2015] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Blastocystis hominis is a common globally distributed parasite. The prevalence of this parasite has been shown to vary among different countries. Molecular studies have also shown that there is a high level of genetic diversity among Blastocystis spp. isolated from humans and animals. Extensive information on parasitic genotypes will aid in devising more effective strategies for the identification and potential control of these pathogenic parasites. OBJECTIVES This study aimed to gain information on the prevalence and abundance of Blastocystis subtypes in Iran. MATERIALS AND METHODS Over a period of 3 months, 1,410 stool samples were collected and examined by microscopy. Samples found to be positive for B. hominis were concentrated and phylogenetic analysis was subsequently performed. A questionnaire was completed by all study participants. RESULTS Blastocystis hominis was found to have a prevalence of 3.33% in the study population. There was no significant association of Blastocystis infection with age (P = 0.3) or gender (P = 0.57). The Blastocystis subtypes (ST) identified in this study were ST3, ST4, ST5, and ST7 with the most prevalent being ST4 (40.9%). CONCLUSIONS The prevalence of B. hominis in the study area was lower than that reported for most developed countries, and unlike in other countries in the Middle East, ST4 was the most prevalent subtype.
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Affiliation(s)
- Saleh Khoshnood
- Parasitology Department, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Abdollah Rafiei
- Parasitology Department, Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Jasem Saki
- Parasitology Department, Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Kobra Alizadeh
- Department of Occupational Health, Faculty of Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
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Dadmanesh M, Ranjbar MM, Alavian SM, Ghorban K. Sequencing and Phylogenetic Study of Partial NS3 Gene of Iranian GB Virus C/Hepatitis G Virus (HGV) Originated From Hemodialysis Patients in Tehran. Hepat Mon 2015; 15:e24173. [PMID: 25838830 PMCID: PMC4379489 DOI: 10.5812/hepatmon.24173] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/01/2015] [Accepted: 02/23/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis viruses are one of the most important concerns in the patients on hemodialysis who are at high risk for blood-borne infections. GB virus C (GBV-C)/hepatitis G virus (HGV) is positive-stranded RNA virus with global distribution, which codes structural and nonstructural proteins (such as NS3). OBJECTIVES Review on literature about Iranian HGV isolates showed that there was no report on sequencing and phylogenetic characteristics of NS3 gene and therefore, this study attempted to answers these challenges. MATERIALS AND METHODS Briefly, steps followed were as follows: preparation of nucleic acids from three Iranian hemodialysis HGV-positive samples and RNA extraction; reverse transcriptase-PCR (RT-PCR) for amplification of NS3 gene and gel electrophoresis; sequencing and analyzing sequencing data; NCBI Registering; blasting and alignment of sequences; and finally constructing the phylogenetic tree. RESULTS Nucleotide BLAST results emphasized that most similar sequences to Ir NS3 sequences were those from Europe (Spain, Germany, and the United Kingdom) and the United states and IR sequences were located with five leaves in a branch. In addition, homology of Ir sequences showed96.4% (between IR1 and IR2), 94.9% identity (between IR1 and IR3), and 96.5% identity (between IR2 and IR3).Furthermore, highly variation and significance differences in NS3 between GBC isolates from geographical regions and some little changes in IR sequences were seen. Finally, phylogenetic tree revealed that NS3 genotype of Iranian isolates was probably similar to European countries and USA. CONCLUSIONS Overall, results of present study were consistent with the data reported earlier base on 5' NTR in Iranian isolates and revealed genotype IR2 is major genotype in Iranian HGV-positive patient. It means there are higher similarities between Iranian and Europe-USA in HGV NS3 gene.
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Affiliation(s)
- Maryam Dadmanesh
- Department of Infectious Diseases, School of Medicine, AJA University of Medical Sciences, Tehran, IR Iran
| | - Mohammad Mehdi Ranjbar
- Department of Immunology, School of Medicine, AJA University of Medical Sciences, Tehran, IR Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran ; Middle East Liver Diseases Research Center (MELD), Tehran, IR Iran ; Iran Hepatitis Network, Tehran, IR Iran
| | - Khodayar Ghorban
- Department of Immunology, School of Medicine, AJA University of Medical Sciences, Tehran, IR Iran
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Joshi J, Salar RK, Banerjee P, S U, Tantia MS, Vijh RK. Genetic variation and phylogenetic relationships of Indian buffaloes of uttar pradesh. Asian-Australas J Anim Sci 2014; 26:1229-36. [PMID: 25049904 PMCID: PMC4093408 DOI: 10.5713/ajas.2012.12669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/05/2013] [Accepted: 02/17/2013] [Indexed: 11/27/2022]
Abstract
India possesses a total buffalo population of 105 million out of which 26.1% inhabit Uttar Pradesh. The buffalo of Uttar Pradesh are described as nondescript or local buffaloes. Currently, there is no report about the genetic diversity, phylogenetic relationship and matrilineal genetic structure of these buffaloes. To determine the origin and genetic diversity of UP buffaloes, we sequenced and analysed the mitochondrial DNA D-loop sequences in 259 samples from entire Uttar Pradesh. One hundred nine haplotypes were identified in UP buffaloes that were defined by 96 polymorphic sites. We implemented neutrality tests to assess signatures of recent historical demographic events like Tajima’s D test and Fu’s Fs test. The phylogenetic studies revealed that there was no geographic differentiation and UP buffaloes had a single maternal lineage while buffaloes of Eastern UP were distinctive from rest of the UP buffaloes.
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Affiliation(s)
- Jyoti Joshi
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - R K Salar
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - Priyanka Banerjee
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - Upasna S
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - M S Tantia
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
| | - R K Vijh
- Department of Animal Genetics, National Bureau of Animal Genetic Resources, POBox 129, GTBypass Road Karnal - 132001, Haryana, India
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Kim JH, Byun MJ, Kim MJ, Suh SW, Ko YG, Lee CW, Jung KS, Kim ES, Yu DJ, Kim WH, Choi SB. mtDNA Diversity and Phylogenetic State of Korean Cattle Breed, Chikso. Asian-Australas J Anim Sci 2014; 26:163-70. [PMID: 25049772 PMCID: PMC4093160 DOI: 10.5713/ajas.2012.12499] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 11/19/2012] [Accepted: 10/11/2012] [Indexed: 11/27/2022]
Abstract
In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1–C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3–C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed.
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Affiliation(s)
- Jae-Hwan Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Mi Jeong Byun
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Myung-Jick Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Sang Won Suh
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Yeoung-Gyu Ko
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Chang Woo Lee
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Kyoung-Sub Jung
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Eun Sung Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Dae Jung Yu
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Woo Hyun Kim
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
| | - Seong-Bok Choi
- Animal Genetic Resources Station, National Institute of Animal Science, RDA, Namwon 590-832, Korea
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Frutos MC, Monetti MS, Ré VE, Cuffini CG. Molecular evidence of Chlamydophila pneumoniae infection in reptiles in Argentina. Rev Argent Microbiol 2014; 46:45-8. [PMID: 24721274 DOI: 10.1016/s0325-7541(14)70047-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 08/06/2013] [Accepted: 02/14/2014] [Indexed: 11/26/2022] Open
Abstract
In the central area of Argentina, the epidemiological and molecular characteristics of Chlamydophila pneumoniae infections in reptiles are still unknown. A nested polymerase chain reaction of the rpoB gene was used to detect C. pneumoniae in cloacal swab samples from 19 reptiles at a recreational area. Eleven (57.89%) reptiles were positive; the sequencing and phylogenetic analysis confirmed the presence of this bacterium. Neither C. pneumoniae DNA in the caregivers pharynges nor IgM antibodies anti-C. pneumoniae in their serum samples were detected; however, caregivers presented very high titers of IgG anti-C. pneumoniae. The detection of C. pneumoniae DNA in reptiles demonstrated the circulation of this agent in the recreational area and could be responsible for the exacerbated immune response of the personnel handling the reptiles, which suggests a potential zoonotic cycle. This is the first report of the detection of C. pneumoniae in reptiles in Argentina.
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Affiliation(s)
- María C Frutos
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Marina S Monetti
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Viviana E Ré
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Cecilia G Cuffini
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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Omran MH, Nabil W, Youssef SS, El-Sayed M, El Awady MK. Heterogeneity and new epitopes of hepatitis C virus genotype 4. Hepat Mon 2013; 13:e10521. [PMID: 24130599 PMCID: PMC3796197 DOI: 10.5812/hepatmon.10521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/14/2013] [Accepted: 06/20/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatitis C virus (HCV) was found to have a major role in human liver disease by its ability to face the host-cell defenses and the immune system. Heterogeneity of HCV was the key for its adaptation to its host and represented a significant hurdle for the development of both effective vaccines as well as for novel therapeutic interventions. OBJECTIVES Due to the heterogeneity of HCV virus because of both high replication and high mutation rate in vivo, this study was conducted to analyze different isolates of Egyptian patients of genotype 4, of the most mutant regions of the virus (E1 and E2) as they played an important role in viral persistence by escaping from the immune system of the host body. PATIENTS AND METHODS This study was conducted through PCR amplification of E1 and E2 regions, sequencing and phylogenetic analysis, calculating synonyms and non-synonyms substitutions, finding the possible glycosylation sites and different epitope domains. RESULTS The present work figured out that the heterogeneity of the quasispecies of our local strains 4a was high showing up 15% diversity. This study also showed four glycosylation sites that play an important role in the entry of the virus and protein folding. Besides, different epitpoes were identified in different regions of the E1 and E2 domains; a finding which would help in determining the neutralizing and non- neutralizing antibodies. CONCLUSIONS This study would help in understanding the driving forces of genetic diversity and would be fundamental for representing potential candidate targets for antibodies and the development of vaccine trials.
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Affiliation(s)
- Moataza H. Omran
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Dokki Cairo, Egypt
- Corresponding author: Moataza H. Omran, Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Dokki Cairo, Egypt. Tel: +20-1223735450, Fax: +20-233370931, E-mail: ,
| | - Wael Nabil
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Dokki Cairo, Egypt
| | - Samar S. Youssef
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Dokki Cairo, Egypt
| | - Mervat El-Sayed
- Chemistry Department, Faculty of Science, Cairo University, Dokki Cairo, Egypt
| | - Mostafa K. El Awady
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Dokki Cairo, Egypt
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Kamarudin KR, Ngah N, Hamid THTA, Susanti D. Isolation of a Pigment-producing Strain of Staphylococcus kloosii from the Respiratory Tree of Holothuria (Mertensiothuria) leucospilota () from Malaysian Waters. Trop Life Sci Res 2013; 24:85-100. [PMID: 24575244 PMCID: PMC3799409] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
Staphylococcus kloosii, an orange pigment-producing bacterium, was isolated from the respiratory tree of Holothuria (Mertensiothuria) leucospilota (Brandt 1835) from Teluk Nipah, Pangkor Island, Perak, Malaysia. This report is the first documentation of this Gram-positive strain, referred to as Strain 68 in Malaysia. A partial 16S ribosomal RNA gene sequence of the mesophilic strain has been registered with GenBank (National Center for Biotechnology Information, US National Library of Medicine) with accession number JX102547. Phylogenetic analysis using the neighbour-joining method further supported the identification of Strain 68 as S. kloosii. The circular strain produced orange pigments on tryptone glucose yeast extract agar (TGYEA) and in nutrient broth (NB) at approximately pH 7. The visible spectra of ethanolic and methanolic pigment extracts of the bacterial strain were considered identical with λmax at 426, 447 and 475 nm and λmax at 426, 445 and 473 nm, respectively. Both visible spectra resemble the visible spectra of lutein, which is a commercial carotenoid; however, further analyses are required to confirm the identity of this pigment. The methanolic extracts of the intracellular pigments comprised at least three pigment compounds: an orange pigment compound (major compound), a yellow pigment compound (the least polar) and a pink pigment compound (the most polar). These findings are the first documentation of the pigment composition of S. kloosii as no such record could be found to date.
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Habibi GH. Phylogenetic Analysis of Theileria annulata Infected Cell Line S15 Iran Vaccine Strain. Iran J Parasitol 2012; 7:73-81. [PMID: 23109949 PMCID: PMC3469191] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Accepted: 04/18/2012] [Indexed: 11/25/2022]
Abstract
BACKGROUND Bovine theileriosis results from infection with obligate intracellular protozoa of the genus Theileria. The phylogenetic relationships between two isolates of Theileria annulata, and 36 Theileria spp., as well as 6 outgroup including Babesia spp. and coccidian protozoa were analyzed using the 18S rRNA gene sequence. METHODS The target DNA segment was amplified by PCR. The PCR product was used for direct sequencing. The length of the 18S rRNA gene of all Theileria spp. involved in this study was around 1,400 bp. RESULTS A phylogenetic tree was inferred based on the 18S rRNA gene sequence of the Iran and Iraq isolates, and other species of Theileria available in GenBank. In the constructed tree, Theileria annulata (Iran vaccine strain) was closely related to other T. annulata from Europe, Asia, as well as T. lestoquardi, T. parva and T. taurotragi all in one clade. CONCLUSION Phylogenetic analyses based on small subunit ribosomal RNA gene suggested that the percent identity of the sequence of Iran vaccine strain was completely the same as Iraq sequence (100% identical), but the similarity of Iran vaccine strain with other T. annulata reported from China, Spain and Italy determined the 97.9 to 99.9% identity.
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Affiliation(s)
- GH Habibi
- Corresponding author:Tel: 026 4457 0038 (2098), E-mail:
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26
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Srivastava P, Trivedi AC, Tiwari A, Verma A, Pant A. Phylogenetic analysis of poly and non structural protein in Japanese Encephalitis virus with other related viral families. Ann Neurosci 2010; 17:74-9. [PMID: 25205875 PMCID: PMC4117001 DOI: 10.5214/ans.0972-7531.1017205] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/26/2010] [Accepted: 07/28/2010] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Japanese encephalitis (JE) causes inflammation of brain. The mortality rate due to JE is 30% while 10 -15 % of patients make full recovery. The disease spreads through infected mosquito bites breeding in rice fields and feeds on pigs, birds, and ducks. PURPOSE As proteins show important structure to function relationship the study was designed to carry out the identification of poly and non-structural proteins in the infective virus group using different strains of Japanese encephalitis virus i.e. JAOARS982, Nakayama Strain SA (V), Strain SA-14. METHODS With reference to non structural proteins we obtained protein sequences of the following Japanese encephalitis virus groups: Japanese encephalitis virus, Weatnile virus, Kunjin virus. Further comparative and phylogenetic analysis was performed to explore evolutionary relationship among these groups. RESULTS Results of phylogeny of alignment score was found to be 375184 using multiple alignment, Jal view, ClustalW (1.83) and ClustalW2. However, the analysis among the non-structural proteins of Japanese Encephalitis Virus, Westnile Virus, and Kunjin Virus revealed the phylogeny alignment score to be 875 through multiple sequence alignment and Tree view respectively. CONCLUSION Phylogenetic analysis revealed that these four strains are interrelated as well as showing high similarity with the other viruses of this group due to conserved regions among their sequences.
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Affiliation(s)
| | | | - Anshul Tiwari
- Amity Institute of Biotechnology, Amity University Lucknow Campus, UP
| | - Alpha Verma
- Department of Microbiology, International Medical &' Technological University, Dares–Salaam, TANZANIA
| | - A.B. Pant
- Invitro Toxicology division, Indian Institute of Toxicology Research, Lucknow, UP
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