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Baghi FR, Harzandi N, Moniri A, Nadji SA. Phylogenetic analysis of BKV genetic variations, based on the whole sequence of the genome and different genomic sections. J Med Virol 2022; 94:3930-3945. [PMID: 35437782 DOI: 10.1002/jmv.27791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/05/2022] [Accepted: 04/12/2022] [Indexed: 11/07/2022]
Abstract
OBJECTIVE(S) BK polyomavirus virus primarily infects humans in their early life stages, and in later life stages, immunosuppressed patients may develop asymptomatic infections. The nucleotides 1744-1812 in the VP1 gene are traditionally used to determine this virus's genotype. MATERIALS AND METHODS The complete genome of the BKV samples from patients referred to Masih Daneshvari Hospital's virology research center was amplified by previously known primer sets. The phylogenetic diversity of the whole genome, different genomic sections, and the non-coding control region of BK virus samples were investigated. Using software Mega X and references, the samples' genotype was determined in separate genomic fragments and the whole genome. RESULTS The samples were classified into two genotypes (I and IV) and five subtypes (Ia, Ib-2, IVc-1, and IVc-2), but none of the isolates belonged to genotype II, III, V, or VI. The Large T antigen-based phylogenetic tree provided 100% bootstrap values for these divisions, which were superior to those (96-100%) used in the VP1 sequence. Among the genomic segments, LTag and VP1 had the most mutations. The non-coding control area contained mutations at the O41 position in the granulocyte/macrophage stimulus gene and the P31 position in the NF-1 gene. CONCLUSION The validity of the phylogenetic analysis was supported by sequence analysis, which found SNPs that could be useful for sub-classifying isolates. More research with a large number of samples and in the wider geographical areas is needed to understand the genetic diversity of the BKV in Iran and also to determine these SNPs' clinical significance in terms of patient outcome and viral load dynamics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Naser Harzandi
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Afshin Moniri
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Alireza Nadji
- Virology Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Takahashi M, Nishizono A, Kawakami M, Fukui E, Isogai E, Matsuoka H, Yamamoto S, Mizuo H, Nagashima S, Murata K, Okamoto H. Identification of hepatitis E virus in wild sika deer in Japan. Virus Res 2022; 308:198645. [PMID: 34822952 DOI: 10.1016/j.virusres.2021.198645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
Hepatitis E virus (HEV) is a zoonotic agent mainly transmitted through the consumption of uncooked or undercooked meat products derived from infected animals. In Japan, domestic pigs and wild boars are the major animal reservoirs, and whether or not deer are an HEV reservoir remains controversial. We analyzed 395 serum and 199 liver samples from 405 sika deer (Cervus nippon) caught in the wild between 1997 and 2020 in 11 prefectures of Japan for markers of HEV infection. Overall, 17 deer had anti-HEV IgG (4.3%), while 1 (0.2%) had HEV RNA (genotype 3b), indicating the occurrence of ongoing HEV infection in wild deer in Japan. An analysis of the complete HEV genome (deJOI_14) recovered from a viremic deer in Oita Prefecture revealed only 88.8% identity with the first HEV strain in sika deer (JDEER-Hyo03L) in Japan, being closest (96.3%) to the HEV obtained from a hepatitis patient living in the same prefecture. Of note, the deJOI_14 strain was 8.7-9.0% different from the wild boar HEV strains obtained in the same habitat and the same year, suggesting that difference in infected HEV strains between boar and deer may be explained by the limited possibility of close contact with each other, although boars are a known source of HEV infection. Increased numbers of hepatitis E cases after consumption of raw or undercooked meat products of wild deer have been reported in Japan. These results suggest a low but nonnegligible zoonotic risk of HEV infection in wild deer in this country.
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Filioussis G, Bramis G, Petridou E, Giadinis ND, Nouvel LX, Citti C, Frey J. Mycoplasma agalactiae ST35: a new sequence type with a minimal accessory genome primarily affecting goats. BMC Vet Res 2022; 18:29. [PMID: 35016679 PMCID: PMC8751087 DOI: 10.1186/s12917-021-03128-w] [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: 09/21/2021] [Accepted: 12/20/2021] [Indexed: 05/31/2023] Open
Abstract
Background Mycoplasma agalactiae, causing agent of contagious agalactia, infects domestic small ruminants such as sheep and goats but also wild Caprinae. M. agalactiae is highly contagious and transmitted through oral, respiratory, and mammary routes spreading rapidly in an infected herd. Results In an outbreak of contagious agalactia in a mixed herd of sheep and goats, 80% of the goats were affected displaying swollen udders and loss of milk production but no other symptom such as kerato-conjunctivitis, arthritis or pulmonary distress commonly associated to contagious agalactia. Surprisingly, none of the sheep grazing on a common pasture and belonging to the same farm as the goats were affected. Whole genome sequencing and analysis of M. agalactiae strain GrTh01 isolated from the outbreak, revealed a previously unknown sequence type, ST35, and a particularly small, genome size of 841′635 bp when compared to others available in public databases. Overall, GrTh01 displayed a reduced accessory genome, with repertoires of gene families encoding variable surface proteins involved in host-adhesion and variable antigenicity being scaled down. GrTh01 was also deprived of Integrative Conjugative Element or prophage, and had a single IS element, suggesting that GrTh01 has a limited capacity to adapt and evolve. Conclusions The lack of most of the variable antigens and the Integrative Conjugative Element, both major virulence- and host specificity factors of a M. agalactiae strain isolated from an outbreak affecting particularly goats, indicates the implication of these factors in host specificity. Whole genome sequencing and full assembly of bacterial pathogens provides a most valuable tool for epidemiological and virulence studies of M. agalactiae without experimental infections.
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Affiliation(s)
- George Filioussis
- Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, School of Health Science, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloniki, Greece
| | - Georgios Bramis
- Laboratory of Animal Husbandry, Faculty of Veterinary Medicine, School of Health Science, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloniki, Greece
| | - Evanthia Petridou
- Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, School of Health Science, Aristotle University of Thessaloniki, University Campus, 54124, Thessaloniki, Greece
| | - Nektarios D Giadinis
- Clinic of Farm Animals, Faculty of Veterinary Medicine, School of Health Science, Aristotle University of Thessaloniki, St. Voutyra 11, 54627, Thessaloniki, Greece
| | | | | | - Joachim Frey
- Vetsuisse Faculty, University of Bern, Laenggasstrasse 120, 3001, Bern, Switzerland.
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Avila E, Speransa PA, Lindholz CG, Kahmann A, Alho CS. Haplotype distribution in a forensic full mtDNA genome database of admixed Southern Brazilians and its association with self-declared ancestry and pigmentation traits. Forensic Sci Int Genet 2021; 57:102650. [PMID: 34972071 DOI: 10.1016/j.fsigen.2021.102650] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/01/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND The advent of massively parallel sequencing (MPS) applications focused on the generation of forensic-quality full mitochondrial genome sequences led to a popularization of the technique on a global scale. However, the lack of forensic-graded population databases has refrained a wider adoption of full genome sequences as the industry standard, despite its better discrimination capacity of individual maternal lineages. PURPOSE This work describes a forensic-oriented full mtDNA genome database comprised of 480 samples from a Southern Brazilian population. METHODS A collection of mitochondrial sequences were obtained from low-pass, full genome DNA sequencing results. The complete sample set was evaluated regarding haplotype composition and distribution. Summary statistics and forensic parameters were calculated and are presented for the database, with detailed information concerning the impact of removing genetic information in the form of specific variants or increasingly larger genomic regions. Interpopulational analysis comparing haplotypical diversity in Brazilian and 26 worldwide populations was also performed. The association between mitochondrial genetic variability and phenotypic diversity was also evaluated in populations, with self-declared ancestry and three distinct phenotypic pigmentation traits (eyes, skin and hair colors) as parameters. RESULTS The presented database can be used to evaluate mitochondrial-related genetic evidence, providing LR values of up to 20,465 for unobserved haplotypes. Haplotype distribution in Southern Brazil seems to be different than the remaining of the country, with a larger contribution of maternal lines with European origin. Despite association can be found between lighter and darker phenotypes or self-declared ancestry and haplotype distribution, prediction models cannot be reliably proposed due to the admixed nature of the Brazilian population. CONCLUSIONS The proposed database provides a basis for statistical calculation and frequency estimation of full mitochondrial genomes, and can be part of an integrated, representative, national database comprising most of the genetic diversity of maternal lineages in the country.
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Affiliation(s)
- Eduardo Avila
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
| | - Pietro Augusto Speransa
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Catieli Gobetti Lindholz
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Alessandro Kahmann
- National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil; Institute of Mathematics, Statistics and Physics, Federal University of Rio Grande, Rio Grande, RS, Brazil.
| | - Clarice Sampaio Alho
- Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil.
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Sofy AR, El-Dougdoug NK, Refaey EE, Dawoud RA, Hmed AA. Characterization and Full Genome Sequence of Novel KPP-5 Lytic Phage against Klebsiella pneumoniae Responsible for Recalcitrant Infection. Biomedicines 2021; 9:342. [PMID: 33800632 DOI: 10.3390/biomedicines9040342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 01/21/2023] Open
Abstract
Klebsiella pneumoniae is a hazardous opportunistic pathogen that is involved in many serious human diseases and is considered to be an important foodborne pathogen found in many food types. Multidrug resistance (MDR) K. pneumoniae strains have recently spread and increased, making bacteriophage therapy an effective alternative to multiple drug-resistant pathogens. As a consequence, this research was conducted to describe the genome and basic biological characteristics of a novel phage capable of lysing MDR K. pneumoniae isolated from food samples in Egypt. The host range revealed that KPP-5 phage had potent lytic activity and was able to infect all selected MDR K. pneumoniae strains from different sources. Electron microscopy images showed that KPP-5 lytic phage was a podovirus morphology. The one-step growth curve exhibited that KPP-5 phage had a relatively short latent period of 25 min, and the burst size was about 236 PFU/infected cells. In addition, KPP-5 phage showed high stability at different temperatures and pH levels. KPP-5 phage has a linear dsDNA genome with a length of 38,245 bp with a GC content of 50.8% and 40 predicted open reading frames (ORFs). Comparative genomics and phylogenetic analyses showed that KPP-5 is most closely associated with the Teetrevirus genus in the Autographviridae family. No tRNA genes have been identified in the KPP-5 phage genome. In addition, phage-borne virulence genes or drug resistance genes were not present, suggesting that KPP-5 could be used safely as a phage biocontrol agent.
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Hosseini H, Majidi S, Ziafati Kafi Z, Esmaeelzadeh Dizaji R, Ghalyanchilangeroudi A. Molecular characterization and the first full sequencing genome of chicken infectious anemia virus (CIAV) in Iran. Iran J Vet Res 2021; 22:331-336. [PMID: 35126541 PMCID: PMC8806177 DOI: 10.22099/ijvr.2021.38455.5593] [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: 09/13/2020] [Revised: 06/07/2021] [Accepted: 06/21/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND The chicken infectious anemia virus (CIAV) is an important pathogen that causes severe immunosuppression in young chickens. AIMS The study aims to characterize the genotype and full-length sequencing of CIAV strains in Iran. METHODS First, the collected thymus samples were investigated by conventional PCR for CIAV detection. Second, one of the CIAV positive samples (UT-Zahraee) was chosen for full genome sequencing. RESULTS Throughout 2017, we detected 13 CIAVs isolated from 40 broiler flocks of different provinces of Iran. A comparison of the complete sequences of the genome and homologies of the nucleotides revealed that UT-Zahraee had a high similarity with American and Egyptian CIAV isolates. Moreover, VP1 sequence analysis showed that UT-Zahraee shared high homology with previously reported Iranian CIAV strains, Chinese, and Egyptian isolates. CONCLUSION This study is the first report of full genome sequencing of CIAV strain from Iran. It will be beneficial to understand better the epidemiology and molecular characteristics of CIAV circulating in Iran.
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Affiliation(s)
- H. Hosseini
- Department of Clinical Science, Karaj Branch, Islamic Azad University, Karaj, Iran;
| | - S. Majidi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Z. Ziafati Kafi
- 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
| | - A. Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran,Correspondence: A. Ghalyanchilangeroudi, Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran. E-mail:
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Cunha MS, Luchs A, da Costa AC, Ribeiro GDO, Dos Santos FCP, Nogueira JS, Komninakis SV, Marinho RDSS, Witkin SS, Villanova F, Deng X, Sabino EC, Delwart E, Leal É, Nogueira ML, Maiorka PC. Detection and characterization of Ilheus and Iguape virus genomes in historical mosquito samples from Southern Brazil. Acta Trop 2020; 205:105401. [PMID: 32081658 DOI: 10.1016/j.actatropica.2020.105401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/10/2020] [Accepted: 02/16/2020] [Indexed: 11/30/2022]
Abstract
In Brazil, flaviviruses have caused massive outbreaks. Surveillance programs designed to monitor virus activity in vectors provides a system for mapping disease distribution and for identifying specific vector species for targeted control. The present study aimed to describe the detection, whole genome characterization and phylogenetic analysis of Ilheus virus (ILHV) and Iguape virus (IGUV) strains obtained from historical mosquito's samples. Twelve isolates of pooled mosquito specimens (inoculated in neonate mouse brain) collected in the state of São Paulo, Brazil, in 1993, 1994 and 1997 were investigated. Viral RNA was extracted and analyzed by qRT-PCR using Flavivirus genus-specific primers. Positive samples were sequenced and underwent phylogenetic analyses. Flavivirus was detected in 50% of the specimens. Positive samples were successfully Sanger sequenced. Three Anopholes cruzii pools collected in 1994 were positive for IGUV. One Culex sp. pool, one Anopheles triannulatus pool, and one Coquillettidia juxtamansonia pool, collected in 1994, were positive for ILHV. Metagenomic sequencing successfully characterize one ILHV and four IGUV full genomes, and revealed a high degree of homology between the Brazilian ILHV and IGUV strains and isolates available in GenBank. Phylogenetic analysis of partial ILHV NS5 gene revealed three distinct lineages (clades), an indication of genetic heterogeneity in strains circulating in Brazil. Nucleotide insertions and a high-level of nucleotide diversity were observed in the NS1 protein and capsid region of IGUV strains, respectively. Detection of ILHV and IGUV in mosquitoes from Southeastern Brazil confirms the historical circulation of these viruses in this area. Furthermore, this first evidence of ILHV in Anopheles triannulatus suggests the potential importance of Anopheles mosquitoes in the IGUV transmission cycle. Genomic and phylogenetic analysis of these viruses provided insights into their diversity and evolution, which are important for the emergence patterns of flaviviruses and their evolutionary trends in Brazil, an endemic country for several arbovirus. in In-depth studies of ILHV and IGUV including vector competence and molecular studies are needed to shed light on their epidemiology and potential risk of future emergence.
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Affiliation(s)
- Mariana Sequetin Cunha
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil.
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | - Juliana Silva Nogueira
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Shirley Vasconcelos Komninakis
- Postgraduate Program in Health Science, Faculty of Medicine of ABC, Santo Andre, Brazil; Retrovirology Laboratory, Federal University of Sao Paulo, Sao Paulo, Brazil
| | | | - Steven S Witkin
- Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil; Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA
| | - Fabiola Villanova
- Biological Sciences Institute, Federal University of Para, Belém, Brazil
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ester Cerdeira Sabino
- Tropical Medicine Institute of São Paulo, University of São Paulo, São Paulo, Brazil; School of Medicine, LIM/46, University of São Paulo, Sao Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Élcio Leal
- Biological Sciences Institute, Federal University of Para, Belém, Brazil
| | | | - Paulo César Maiorka
- Department of Pathology, School of Veterinary Medicine, University of Sao Paulo, Sao Paulo, Brazil
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Hosseini H, Langeroudi AG, FallahMehrabadi MH, Ziafati Kafi Z, Dizaji RE, Ghafouri SA, Hamadan AM, Aghaiyan L, Hajizamani N. The fowl adenovirus (Fadv-11) outbreak in Iranian broiler chicken farms: The first full genome characterization and phylogenetic analysis. Comp Immunol Microbiol Infect Dis 2019; 70:101365. [PMID: 31610890 DOI: 10.1016/j.cimid.2019.101365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/28/2019] [Accepted: 09/29/2019] [Indexed: 02/03/2023]
Abstract
Fowl adenoviruses D and E (FAdV-D and E) can cause inclusion body hepatitis (IBH) in commercial chicken flocks. Recently, IBH outbreaks have been increasingly reported in different regions of Iran, particularly in broiler farms. The present study was conducted to perform, for the first time, a complete genome characterization of a FAdV isolate from an IBH outbreak in Iran. Briefly, liver samples were collected from affected broiler flocks and following viral DNA extraction and confirming by PCR technique; one positive sample was selected from an affected flock to conduct a complete genome sequencing. The current FAdV, named "Fowl_Adenovirus_D_isolate_iran/UT-Kiaee_2018", was placed into FAdV-11 serotype (D species). According to the complete genome sequence analysis, UT-Kiaee had high homology with Chinese and Canadian FAdV. The partial sequence of the hexon gene revealed that UT-Kiaee shared 100% identity with previous Iranian FAdVs. The present study was the first to report full genome FAdV in Iran and complete the puzzle of molecular epidemiology of FAdV in Iran through determining the possible origin of Iranian FAdvs, which are the causative agents of recent IBH outbreaks in Iran.
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Affiliation(s)
- Hossein Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Karaj Branch, Karaj, Iran
| | - Arash Ghalyanchi Langeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Mohammad Hossein FallahMehrabadi
- Department of Poultry Diseases, RAZI Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Zahra Ziafati Kafi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Reza Esmaeelzadeh Dizaji
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Seyed Ali Ghafouri
- Department of Clinical Sciences, Faculty of Veterinary Vedicine, Ferdowsi University of Mashhad, Tehran, Iran
| | - Amir Modiri Hamadan
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Leila Aghaiyan
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Niusha Hajizamani
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Kruse T, Ratnadevi CM, Erikstad HA, Birkeland NK. Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph "Candidatus Methylacidiphilum kamchatkense" strain Kam1 and comparison with its closest relatives. BMC Genomics 2019; 20:642. [PMID: 31399023 PMCID: PMC6688271 DOI: 10.1186/s12864-019-5995-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The candidate genus "Methylacidiphilum" comprises thermoacidophilic aerobic methane oxidizers belonging to the Verrucomicrobia phylum. These are the first described non-proteobacterial aerobic methane oxidizers. The genes pmoCAB, encoding the particulate methane monooxygenase do not originate from horizontal gene transfer from proteobacteria. Instead, the "Ca. Methylacidiphilum" and the sister genus "Ca. Methylacidimicrobium" represent a novel and hitherto understudied evolutionary lineage of aerobic methane oxidizers. Obtaining and comparing the full genome sequences is an important step towards understanding the evolution and physiology of this novel group of organisms. RESULTS Here we present the closed genome of "Ca. Methylacidiphilum kamchatkense" strain Kam1 and a comparison with the genomes of its two closest relatives "Ca. Methylacidiphilum fumariolicum" strain SolV and "Ca. Methylacidiphilum infernorum" strain V4. The genome consists of a single 2,2 Mbp chromosome with 2119 predicted protein coding sequences. Genome analysis showed that the majority of the genes connected with metabolic traits described for one member of "Ca. Methylacidiphilum" is conserved between all three genomes. All three strains encode class I CRISPR-cas systems. The average nucleotide identity between "Ca. M. kamchatkense" strain Kam1 and strains SolV and V4 is ≤95% showing that they should be regarded as separate species. Whole genome comparison revealed a high degree of synteny between the genomes of strains Kam1 and SolV. In contrast, comparison of the genomes of strains Kam1 and V4 revealed a number of rearrangements. There are large differences in the numbers of transposable elements found in the genomes of the three strains with 12, 37 and 80 transposable elements in the genomes of strains Kam1, V4 and SolV respectively. Genomic rearrangements and the activity of transposable elements explain much of the genomic differences between strains. For example, a type 1h uptake hydrogenase is conserved between strains Kam1 and SolV but seems to have been lost from strain V4 due to genomic rearrangements. CONCLUSIONS Comparing three closed genomes of "Ca. Methylacidiphilum" spp. has given new insights into the evolution of these organisms and revealed large differences in numbers of transposable elements between strains, the activity of these explains much of the genomic differences between strains.
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Affiliation(s)
- Thomas Kruse
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway.
| | | | - Helge-André Erikstad
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway.
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Liu CC, Ji H. PCR Amplification Strategies Towards Full-length HIV-1 Genome Sequencing. Curr HIV Res 2019; 16:98-105. [PMID: 29943704 DOI: 10.2174/1570162x16666180626152252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/15/2018] [Revised: 05/05/2018] [Accepted: 06/20/2018] [Indexed: 11/22/2022]
Abstract
The advent of next-generation sequencing has enabled greater resolution of viral diversity and improved feasibility of full viral genome sequencing allowing routine HIV-1 full genome sequencing in both research and diagnostic settings. Regardless of the sequencing platform selected, successful PCR amplification of the HIV-1 genome is essential for sequencing template preparation. As such, full HIV-1 genome amplification is a crucial step in dictating the successful and reliable sequencing downstream. Here we reviewed existing PCR protocols leading to HIV-1 full genome sequencing. In addition to the discussion on basic considerations on relevant PCR design, the advantages as well as the pitfalls of the published protocols were reviewed.
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Affiliation(s)
- Chao Chun Liu
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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Ghafouri SA, Fallah Mehrabadi MH, Talakesh SF, Hosseini H, Ziafati Z, Malekan M, Aghaeean L, Ghalyanchilangeroudi A. Full genome characterization of Iranian H5N8 highly pathogenic avian influenza virus from Hooded Crow (Corvus cornix), 2017: The first report. Comp Immunol Microbiol Infect Dis 2019; 64:73-80. [PMID: 31174704 DOI: 10.1016/j.cimid.2019.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 12/29/2018] [Accepted: 03/04/2019] [Indexed: 11/19/2022]
Abstract
During 2014-2017 Clade 2.3.4.4 H5N8 highly pathogenic avian influenza viruses (HPAIVs) have spread worldwide. In 2016, an epidemic of HPAIV H5N8 in Iran caused mass deaths among wild birds, and several commercial poultry farms and captive bird holdings were affected and continue to experience problems. Several outbreaks were reported in 2017. One of them is related to Hooded crow (Corvus cornix) in a national park in Esfahan province in 2017. Whole genome sequencing and characterization have been done on the detected H5N8 sample. Based on HA sequencing results, it belongs to 2.3.4.4 clade, and the cleavage site is (PLREKRRKR/G). Phylogenetic analysis of the HA gene showed that the Iran 2017 H5N8 virus clustered within subgroup Russia 2016 2.3.4.4 b of group B in H5 clade 2.3.4.4 HPAIV. On the other hand, the NA gene of the virus is placed in group C of Eurasian lineage. Complete genome characterization of this virus revealed probable reassortment of the virus with East-Asian low-pathogenic influenza viruses. Furthermore, the virus possessed some phenotypic markers related to the increased potential for transmission and pathogenicity to mammals at internal segments. This study is the first full genome characterization H5N8 HPAIV in Iran. The data complete the puzzle of molecular epidemiology of H5N8 HPAIV in Iran and the region. Our study provides evidence for fast and continuing reassortment of H5 clade 2.3.4.4 viruses, that might lead to changes in virus structural and functional characteristics such as the route and method of transmission of the virus and virus infective, pathogenic and zoonotic potential.
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Affiliation(s)
| | - Mohammad Hossein Fallah Mehrabadi
- Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | | | - Hossein Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Karaj Branch, Karaj, Iran
| | - Zahra Ziafati
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mohammad Malekan
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Leila Aghaeean
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
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Vidal A, Clilverd H, Cortey M, Martín-Valls GE, Franzo G, Darwich L, Martín M, Mateu E. Full-genome characterization by deep sequencing of rotavirus A isolates from outbreaks of neonatal diarrhoea in pigs in Spain. Vet Microbiol 2018; 227:12-19. [PMID: 30473342 DOI: 10.1016/j.vetmic.2018.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 07/17/2018] [Revised: 09/18/2018] [Accepted: 10/10/2018] [Indexed: 10/28/2022]
Abstract
Since early 2017, in Spain there was an apparent increase in reports on rotavirus involvement in neonatal diarrhoea outbreaks, affecting also adult sows. In this study, 16 unrelated outbreaks of diarrhoea in suckling pigs and sows, where rotavirus A was the only pathogen detected, were investigated. Deep-sequencing was performed on total RNA from twenty-four positive faecal samples. Genotyping, phylogenetic and bayesian analyses showed that all isolates had a common ancestor of porcine, or human porcine-like, origin. The new strain was introduced in the population shortly before the onset of the outbreaks. Besides, a high diversification of the VP7 and VP4 genes occurred in a short time. Isolates presented a high number of amino acid changes in the neutralizing epitopes compared to vaccine sequences. The present report illustrates how a new rotavirus A strain may disseminate rapidly and the extremely high diversification that this pathogen may undergo in a short period.
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Affiliation(s)
- Anna Vidal
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Hepzibar Clilverd
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain.
| | - Martí Cortey
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Gerard E Martín-Valls
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Laila Darwich
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Marga Martín
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Enric Mateu
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
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De Sabato L, Vaccari G, Lemey P, Amoroso MG, Fusco G, Ianiro G, Di Bartolo I. Phylogenetic analysis of two genotype 3 Hepatitis E viruses from wild boar, Italy. Virus Genes 2018; 54:812-7. [PMID: 30203361 DOI: 10.1007/s11262-018-1597-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/31/2018] [Indexed: 12/27/2022]
Abstract
The complete and near-complete genome sequences (7206 nt and 7229 nt) of two wild boar HEV strains detected in Southern Italy were obtained by the next generation sequencing. Phylogenetic analysis and p distance comparisons of one of the strains with HEV-3 reference subtype strains confirmed the detection of a subtype 3i (p distance = 0.110) strain in wild boar, never detected in Italy either in wild boar or pigs. The sequence of the second strain was not classifiable in any of the subtypes defined to date, showing a p distance > 0.138 and a low nucleotide identity with all HEV reference strains. The virus may represent a novel subtype, with a low relationship to other strains of genotype 3 detected in wild boar, pigs, or humans in Europe. This result suggests the circulation in Italy of an emerging or uncommon HEV strain. Sequencing followed by phylogenetic analyses of the complete HEV coding regions are important tools for understanding the evolutionary and epidemiological dynamics underlying the wide genetic diversity of HEV strains.
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Yahiro T, Takaki M, Chandrasena TGAN, Rajindrajith S, Iha H, Ahmed K. Human-porcine reassortant rotavirus generated by multiple reassortment events in a Sri Lankan child with diarrhea. Infect Genet Evol 2018; 65:170-186. [PMID: 30055329 DOI: 10.1016/j.meegid.2018.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/22/2023]
Abstract
A human-porcine reassortant rotavirus, strain R1207, was identified from 74 group A rotaviruses detected in 197 (37.6%) stool samples collected from patients who attended a tertiary care hospital in Ragama, Sri Lanka. This is the first report of a human-porcine reassortant rotavirus in Sri Lanka. The patient was a 12-month-old boy who had been hospitalized with fever and acute diarrhea with a duration of 6 days. The family had pigs at home before the birth of this boy. However, the neighbors still practice pig farming. The genotype constellation of R1207 was G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1. This is based on the assignment of all the eleven gene segments a full genome-based genotyping system. R1207 showed a 4-2-3-2 genomic electrophoretic migration pattern, which is characteristic of group A rotaviruses. Our analyses revealed that five (NSP2, NSP4, VP1, VP2, and VP7) of the 11 genes were closely related to the respective genes of porcine strains. Although the remaining six genes (NSP1, NSP3, NSP5, VP3, VP4, and VP6) were related to human strains, with the exception of the gene sequence of NSP1, all of these human strains were human-porcine reassortants. With a genogroup 1 genetic backbone, this strain was possibly formed via multiple genetic reassortments. We do not know whether this strain is circulating in pigs, as no data are available on porcine rotaviruses in Sri Lanka. Surveillance should be strengthened to determine the epidemiology of this genotype of rotavirus in Sri Lanka and to assess whether the infection was limited or sustained by ongoing human-to-human transmission.
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Affiliation(s)
- Takaaki Yahiro
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Minako Takaki
- Department of Microbiology, Oita University, Yufu-shi, Oita, Japan
| | | | | | - Hidekatsu Iha
- Department of Microbiology, Oita University, Yufu-shi, Oita, Japan
| | - Kamruddin Ahmed
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia; Borneo Medical and Health Research Centre, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia.
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Erfan AM, Selim AA, Naguib MM. Characterization of full genome sequences of chicken anemia viruses circulating in Egypt reveals distinct genetic diversity and evidence of recombination. Virus Res 2018; 251:78-85. [PMID: 29751020 DOI: 10.1016/j.virusres.2018.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/06/2018] [Accepted: 05/07/2018] [Indexed: 11/20/2022]
Abstract
Chicken anemia virus (CAV) is one of the commercially important diseases of poultry worldwide. In Egypt, CAV has been reported to be a potential threat to the commercial poultry sectors. Hence, this study was aimed at isolation and full genomic analysis of CAVs circulating in chicken populations in different geographical location in Egypt. A total of 42 samples were collected from broiler chicken flocks in 9 governorates in Egypt from 12 to 42 days of age. The mortality rate observed among chickens was ranging from 3% to 22%. Nineteen out of 42 farms were found positive for the CAV genome by polymerase chain reaction (PCR). Full genome sequencing was conducted for 18 positive samples. Genetic analysis revealed a high similarity of >99% in 11 viruses with the vaccine strain Del-Ros; while the other seven samples shared close similarity to CAV field strains isolated from China, Taiwan, and Brazil. The data also indicated Q139 and Q144 amino acids substitutions among the VP1 of Egyptian field strains, which are known to be important in virus replication and spread. Phylogenetic analysis of the sequenced viruses (n = 18) based on either the full gene nucleotide sequence or VP1 coding sequence, suggested the circulation of four distinct genotypes in Egypt designated as group A, B, C and D. Moreover, evidence of recombination was detected among four Egyptian CAVs located within group A. The findings of this study succeeded to elucidate the epidemiological and genetic features of CAVs circulating in Egypt, and underscores the important of CAVs surveillance.
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Lopes AM, Blanco-Aguiar J, Martín-Alonso A, Leitão M, Foronda P, Mendes M, Gonçalves D, Abrantes J, Esteves PJ. Full genome sequences are key to disclose RHDV2 emergence in the Macaronesian islands. Virus Genes 2017; 54:1-4. [PMID: 29151222 DOI: 10.1007/s11262-017-1523-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 11/27/2022]
Abstract
A recent publication by Carvalho et al. in "Virus Genes" (June 2017) reported the presence of the new variant of rabbit hemorrhagic disease virus (RHDV2) in the two larger islands of the archipelago of Madeira. Based on the capsid protein sequence, the authors suggested that the high sequence identity, along with the short time spanning between outbreaks, points to dissemination from Porto Santo to Madeira. By including information of the full RHDV2 genome of strains from Azores, Madeira, and the Canary Islands, we confirm the results obtained by Carvalho et al., but further show that several subtypes of RHDV2 circulate in these islands: non-recombinant RHDV2 in the Canary Islands, G1/RHDV2 in Azores, Porto Santo and Madeira, and NP/RHDV2 also in Madeira. Here we conclude that RHDV2 has been independently introduced in these archipelagos, and that in Madeira at least two independent introductions must have occurred. We provide additional information on the dynamics of RHDV2 in the Macaronesian archipelagos of Azores, Madeira, and the Canary Islands and highlight the importance of analyzing RHDV2 complete genome.
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Affiliation(s)
- Ana M Lopes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
- Department of Anatomy and Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Jose Blanco-Aguiar
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
- Instituto de Investigación en Recursos Cinegéticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo, s/n, 13071, Ciudad Real, Spain
| | - Aaron Martín-Alonso
- Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Avda. Fco. Sanchez s/n, 38203, Tenerife, Canary Islands, Spain
| | - Manuel Leitão
- Direção Regional dos Recursos Florestais, Rua do Contador 23, 9500-050, Ponta Delgada, Açores, Portugal
| | - Pilar Foronda
- Institute of Tropical Diseases and Public Health of the Canary Islands, Universidad de La Laguna, Avda. Fco. Sanchez s/n, 38203, Tenerife, Canary Islands, Spain
| | - Marco Mendes
- Quinta Vila Passos, Instituto das Florestas e Conservação da Natureza, Rua Alferes Veiga Pestana, 15, 9054-505, Funchal, Madeira, Portugal
| | - David Gonçalves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Joana Abrantes
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
- Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (CESPU), Gandra, Portugal.
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17
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Xin M, Cao M, Liu W, Ren Y, Lu C, Wang X. The genomic and biological characterization of Citrullus lanatus cryptic virus infecting watermelon in China. Virus Res 2017; 232:106-112. [PMID: 28238875 DOI: 10.1016/j.virusres.2017.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 11/09/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/23/2022]
Abstract
A dsRNA virus was detected in the watermelon (Citrullus lanatus) samples collected from Kaifeng, Henan province, China through the use of next generation sequencing of small RNAs. The complete genome of this virus is comprised of dsRNA-1 (1603nt) and dsRNA-2 (1466nt), both of which are single open reading frames and potentially encode a 54.2kDa RNA-dependent RNA polymerase (RdRp) and a 45.9kDa coat protein (CP), respectively. The RdRp and CP share the highest amino acid identities 85.3% and 75.4% with a previously reported Israeli strain Citrullus lanatus cryptic virus (CiLCV), respectively. Genome comparisons indicate that this virus is the same species with CiLCV, whereas the reported sequences of the Israeli strain of CiLCV are partial, and our newly identified sequences can represent the complete genome of CiLCV. Futhermore, phylogenetic tree analyses based on the RdRp sequences suggest that CiLCV is one member in the genus Deltapartitivirus, family Partitiviridae. In addition, field investigation and seed-borne bioassays show that CiLCV commonly occurs in many varieties and is transmitted though seeds at a very high rate.
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Affiliation(s)
- Min Xin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400715, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingdang Ren
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Chuantao Lu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Boussini H, Chitsungo E, Bodjo SC, Diakite A, Nwankpa N, Elsawalhy A, Anderson JR, Diallo A, Dundon WG. First report and characterization of peste des petits ruminants virus in Liberia, West Africa. Trop Anim Health Prod 2016; 48:1503-7. [PMID: 27315206 DOI: 10.1007/s11250-016-1101-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/13/2016] [Indexed: 01/14/2023]
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El-Kafrawy SA, Sohrab SS, Ela SA, Abd-Alla AMM, Alhabbab R, Farraj SA, Othman NA, Hassan AM, Bergoin M, Klitting R, Charrel RN, Hashem AM, Madani TA, Azhar EI. Multiple Introductions of Dengue 2 Virus Strains into Saudi Arabia from 1992 to 2014. Vector Borne Zoonotic Dis 2016; 16:391-9. [PMID: 27135750 DOI: 10.1089/vbz.2015.1911] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 11/13/2022] Open
Abstract
INTRODUCTION Dengue is a significant arboviral infection that represents a major public health concern worldwide. The infection is endemic in most parts of South East Asia, sub-Saharan Africa, and Latin America. Among the four dengue virus (DENV) serotypes, DENV-2 has been reported to be the predominant serotype in Saudi Arabia since 1992. However, virological and epidemiological data of DENV-2 from Saudi Arabia are severely deficient and require further investigations. METHODS Full genome sequencing of a recent DENV-2 isolate and phylogenetic analysis of all available DENV-2 sequences from Saudi Arabia. RESULTS Based on full genome and envelope (E) gene sequence, we show that a recent isolate (DENV-2-Jeddah-2014) belongs to the Indian subcontinent lineage of the Cosmopolitan genotype with close similarity to recent strains from Pakistan. Interestingly, the E gene sequence of DENV-2-Jeddah-2014 isolate was slightly divergent from those previously identified in Saudi Arabia between 1992 and 2004 with three to nine amino acid (aa) substitutions. While our data show that the Cosmopolitan genotype is still circulating in Saudi Arabia, they highlight four distinct genetic groups suggesting at least four independent introductions into the Kingdom. CONCLUSIONS The close clustering of DENV-2 isolates reported from Saudi Arabia between 1992 and 2014 with strains from countries providing the highest numbers of pilgrims attending either Hajj or Umrah pilgrimages (Indonesia, Pakistan, India) clearly suggests a role for pilgrims or expatriates coming from DENV endemic countries in DENV-2 importation into Saudi Arabia. Accordingly, continuous monitoring of the circulation of DENVs in Saudi Arabia must be implemented to undertake effective control and management strategies in the Kingdom. Screening of the pilgrims coming to perform Hajj and Umrah might help prevent the introduction of new DENV strains, which is expected to increase the burden of the disease not only in Saudi Arabia but also in other countries.
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Affiliation(s)
- Sherif A El-Kafrawy
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Sayed S Sohrab
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Said Abol Ela
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Adly M M Abd-Alla
- 2 Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture , Vienna, Austria .,3 Pests and Plant Protection Department, National Research Center , Cairo, Egypt
| | - Rowa Alhabbab
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia .,4 Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Suha A Farraj
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Norah A Othman
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Ahmed M Hassan
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Max Bergoin
- 5 Laboratoire de Pathologie Comparée, Université Montpellier 2 , Montpellier, France
| | - Raphaelle Klitting
- 6 Aix Marseille Université, IRD French Institute of Research for Development , EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", and IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Remi N Charrel
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia .,6 Aix Marseille Université, IRD French Institute of Research for Development , EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", and IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Anwar M Hashem
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia .,7 Department of Medical Microbiology and Parasitology Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Tariq A Madani
- 8 Department of Medicine, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Esam I Azhar
- 1 Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University , Jeddah, Saudi Arabia .,4 Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University , Jeddah, Saudi Arabia
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Suzuki T, Murakami S, Takahashi O, Kodera A, Masuda T, Itoh S, Miyazaki A, Ohashi S, Tsutsui T. Molecular characterization of pig epidemic diarrhoea viruses isolated in Japan from 2013 to 2014. Infect Genet Evol 2015; 36:363-368. [PMID: 26477934 DOI: 10.1016/j.meegid.2015.10.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/17/2015] [Accepted: 10/13/2015] [Indexed: 11/30/2022]
Abstract
Since October 2013, approximately 1000 outbreaks of porcine epidemic diarrhoea (PED) have occurred, spanning almost all prefectures of Japan, after a period of seven years without a reported case. In order to consider occurrence factor of PED outbreaks, we determined the whole-genome sequences of 38 PED virus (PEDV) strains from diarrheal samples collected at swine farms in 18 prefectures between 2013 and 2014 using next-generation sequencing technology. Using these data, we investigated genetic variation among the recent Japanese PEDV strains and the genetic relationships between these strains and global PEDV strains isolated recently from multiple swine-industrial countries. Eleven out of 38 PEDV strains were isolated successfully on Vero cells with trypsin treatment and subjected to genome sequence analysis. In a comparative genome analysis, we detected two novel PEDV variants, TTR-2/JPN/2014 and MYG-1/JPN/2014, with large deletions in the spike and ORF3 genes, respectively. A phylogenetic analysis based on the spike gene showed that the 38 Japanese PEDV strains were classified into two PEDV types: the North American type with high virulence (n=34) and the INDEL type (n=4). In addition, the recent Japanese PEDV isolates had a close relationship to global PEDV strains isolated in recent years than to the classical PEDV strains detected in Japan the past decades ago. Moreover, the phylogenetic dendrogram of the complete genomes also indicated that the 38 Japanese PEDV strains, including the two novel PEDV variants discovered in this study, are closely related to the PEDV strains that were widespread in the United States and Korea in 2013-2014. These findings suggest that the re-emergence of PED outbreaks since the last reported case in 2006 was caused by the introduction of recent PEDV strains to Japan from overseas.
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Affiliation(s)
- Tohru Suzuki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan.
| | - Satoshi Murakami
- Life Technologies Japan ltd., Thermo Fisher Scientific, 4-2-8 Shibaura, Minato-ku, Tokyo 108-0023, Japan
| | - Osamu Takahashi
- Life Technologies Japan ltd., Thermo Fisher Scientific, 4-2-8 Shibaura, Minato-ku, Tokyo 108-0023, Japan
| | - Aya Kodera
- Sendai Livestock Hygiene Service Center, 3-11-22 Sendai, Miyagi 983-0832, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, 2-132 Kurayoshi, Tottori 682-0017, Japan
| | - Sakie Itoh
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan
| | - Ayako Miyazaki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan
| | - Seiichi Ohashi
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, NARO, 3-1-5 Tsukuba, Ibaraki 305-0856, Japan
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21
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Valdazo-González B, Kim JT, Soubeyrand S, Wadsworth J, Knowles NJ, Haydon DT, King DP. The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus. Infect Genet Evol 2015; 32:440-8. [PMID: 25861750 PMCID: PMC7106308 DOI: 10.1016/j.meegid.2015.03.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/05/2015] [Accepted: 03/26/2015] [Indexed: 11/26/2022]
Abstract
45 full FMDV genomes were analysed from farms infected in the UK during 2007. Analyses revealed intra-herd clustering consistent with virus transmission events. Inter-herd sequence differences were estimated to be 4.6 nucleotides. Random selection of 1 sequence from each herd generated similar transmission trees. These results will help to design cost-effective approaches for the control of FMD.
Full-genome sequences have been used to monitor the fine-scale dynamics of epidemics caused by RNA viruses. However, the ability of this approach to confidently reconstruct transmission trees is limited by the knowledge of the genetic diversity of viruses that exist within different epidemiological units. In order to address this question, this study investigated the variability of 45 foot-and-mouth disease virus (FMDV) genome sequences (from 33 animals) that were collected during 2007 from eight premises (10 different herds) in the United Kingdom. Bayesian and statistical parsimony analysis demonstrated that these sequences exhibited clustering which was consistent with a transmission scenario describing herd-to-herd spread of the virus. As an alternative to analysing all of the available samples in future epidemics, the impact of randomly selecting one sequence from each of these herds was used to assess cost-effective methods that might be used to infer transmission trees during FMD outbreaks. Using these approaches, 85% and 91% of the resulting topologies were either identical or differed by only one edge from a reference tree comprising all of the sequences generated within the outbreak. The sequence distances that accrued during sequential transmission events between epidemiological units was estimated to be 4.6 nucleotides, although the genetic variability between viruses recovered from chronic carrier animals was higher than between viruses from animals with acute-stage infection: an observation which poses challenges for the use of simple approaches to infer transmission trees. This study helps to develop strategies for sampling during FMD outbreaks, and provides data that will guide the development of further models to support control policies in the event of virus incursions into FMD free countries.
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Affiliation(s)
| | - Jan T Kim
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Samuel Soubeyrand
- INRA, UR546 Biostatistics and Spatial Processes, F-84914 Avignon, France
| | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom.
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22
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Xu L, Wu J, He B, Qin S, Xia L, Qin M, Li N, Tu C. Novel hantavirus identified in black-bearded tomb bats, China. Infect Genet Evol 2015; 31:158-60. [PMID: 25643870 DOI: 10.1016/j.meegid.2015.01.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 12/14/2022]
Abstract
The full genome sequence of a bat hantavirus was determined. It provides reference data for determining bat hantavirus’ full genomes. Genomic analysis shows that it is distantly related to all known bat hantaviruses.
Hantaviruses cause life-threatening diseases in human worldwide. Rodents, insectivores and bats are known hantaviral reservoirs, but lack of complete genomic sequences of bat-borne hantaviruses impedes phylogenetic and evolutionary comparison with those of rodents and insectivores. Here, a novel bat-borne hantavirus, Laibin virus (LBV), has been identified in a black-bearded tomb bat in China. The complete genomic sequence shows that LBV is only distantly related to all previously known bat-borne hantaviruses.
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23
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Balka G, Wang X, Olasz F, Bálint Á, Kiss I, Bányai K, Rusvai M, Stadejek T, Marthaler D, Murtaugh MP, Zádori Z. Full genome sequence analysis of a wild, non-MLV-related type 2 Hungarian PRRSV variant isolated in Europe. Virus Res 2015; 200:1-8. [PMID: 25616050 DOI: 10.1016/j.virusres.2015.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 10/06/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 11/15/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a widespread pathogen of pigs causing significant economic losses to the swine industry. The expanding diversity of PRRSV strains makes the diagnosis, control and eradication of the disease more and more difficult. In the present study, the authors report the full genome sequencing of a type 2 PRRSV strain isolated from piglet carcasses in Hungary. Next generation sequencing was used to determine the complete genome sequence of the isolate (PRRSV-2/Hungary/102/2012). Recombination analysis performed with the available full-length genome sequences showed no evidence of such event with other known PRRSV. Unique deletions and an insertion were found in the nsp2 region of PRRSV-2/Hungary/102/2012 when it was compared to the highly virulent VR2332 and JXA-1 prototype strains. The majority of amino acid alterations in GP4 and GP5 of the virus were in the known antigenic regions suggesting an important role for immunological pressure in PRRSV-2/Hungary/102/2012 evolution. Phylogenetic analysis revealed that it belongs to lineage 1 or 2 of type 2 PRRSV. Considering the lack of related PRRSV in Europe, except for a partial sequence from Slovakia, the ancestor of PRRSV-2/Hungary/102/2012 was most probably transported from North-America. It is the first documented type 2 PRRSV isolated in Europe that is not related to the Ingelvac MLV.
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Affiliation(s)
- Gyula Balka
- Department of Pathology, Faculty of Veterinary Science, Szent István University, István u. 2, H-1078 Budapest, Hungary.
| | - Xiong Wang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA
| | - Ferenc Olasz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Ádám Bálint
- National Food Chain Safety Office Veterinary Diagnostic Directorate, Tábornok u. 2, H-1143 Budapest, Hungary
| | - István Kiss
- Ceva-Phylaxia Veterinary Biologicals Co. Ltd., Szállás u. 5, H-1107 Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
| | - Miklós Rusvai
- Department of Pathology, Faculty of Veterinary Science, Szent István University, István u. 2, H-1078 Budapest, Hungary
| | - Tomasz Stadejek
- Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences - SGGW, ul. Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Douglas Marthaler
- Veterinary Diagnostic Laboratory, University of Minnesota, 1333 Gortner Avenue, St. Paul, MN 55108, USA
| | - Michael P Murtaugh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary
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24
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Shen T, Yan XM, Zou YL, Gao JM, Dong H. Virologic characteristics of hepatitis B virus in patients infected via maternal-fetal transmission. World J Gastroenterol 2008; 14:5674-82. [PMID: 18837083 PMCID: PMC2748201 DOI: 10.3748/wjg.14.5674] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To determine whether HBV with the same characteristics causes dissimilar mutations in different hosts.
METHODS: Full-length HBV genome was amplified and linked with pMD T18 vector. Positive clones were selected by double-restriction endonuclease digestion (EcoRI and HindIII) and PCR. Twenty seven clones were randomly selected from an asymptomatic mother [at two time points: 602 (1 d) and 6022 (6 mo)] and her son [602 (S)], and the phylogenetic and mutational analysis was performed using BioEditor, Clustal X and MEGA software. Potential immune epitopes were determined by the Stabilized Matrix Method (SMM), SMM-Align Method and Emini Surface Accessibility Prediction.
RESULTS: All of the 27 sequences were genotype C, the divergence between the mother and son was 0%-0.8%. Compared with another 50 complete sequences of genotype C, the mother and her son each had 13 specific nucleotides that differed from the other genotype C isolates. AA 1-11 deletion in preS1 was the dominant mutation in the mother (14/18). The 1762T/1764A double mutation existed in all clones of the mother, 3 of them were also coupled with G1896A mutation, but none were found in the son. 17 bp deletion starting at nucleotide 2330 was the major mutation (5/9) in the son, which caused seven potential HLA class I epitopes and one B cell epitope deletion, and produced a presumptive new start codon, downstream from the original one of the P gene.
CONCLUSION: The HBV strain in the son came from his mother, and discrepant mutation occurred in the mother and her son during infection.
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