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Xu S, Qi X, Gao S, Zhang Y, Wang H, Shao Y, Yang Y, An Y. Modification of DNA regions with metagenomic DNA fragments (MDRMDF): A convenient strategy for efficient protein engineering. Biochimie 2021; 187:75-81. [PMID: 34051307 DOI: 10.1016/j.biochi.2021.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 10/25/2022]
Abstract
In this study, we have established a convenient and efficient approach named Modification of DNA Regions with Metagenomic DNA Fragments (MDRMDF) for protein engineering. Degenerate primers were designed corresponding to conserved regions of the gene of interest which were used for amplification of fragments with template of the metagenomic DNA. The resulting PCR products were used to replace the corresponding regions of the gene of interest to introduce modified gene for function-based screening. Therefore, this method can make full use of the metagenomic DNA sequences with unknown metagenomic gene information for efficient protein engineering. The β-xylosidase BH3683 was used to construct a MDRMDF library which was screened with a newly designed p-NPX-M9 medium-based strategy. As a result, a mutant protein Xyl-M56 showing high activity, improved pH stability and higher tolerance to organic solvents was obtained which may have potential for industrial application. The MDRMDF method may find wide application in enzyme engineering, metabolic engineering and other fields, especially offering a new methodological option for the directed evolution of proteins.
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Affiliation(s)
- Shumin Xu
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yifeng Zhang
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Hongling Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yilun Shao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yao Yang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yingfeng An
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China.
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2
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Álvarez-Díaz DA, Franco-Muñoz C, Laiton-Donato K, Usme-Ciro JA, Franco-Sierra ND, Flórez-Sánchez AC, Gómez-Rangel S, Rodríguez-Calderon LD, Barbosa-Ramirez J, Ospitia-Baez E, Walteros DM, Ospina-Martinez ML, Mercado-Reyes M. Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 84:104390. [PMID: 32505692 PMCID: PMC7272177 DOI: 10.1016/j.meegid.2020.104390] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/31/2020] [Indexed: 12/11/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3' end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3' end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.
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Affiliation(s)
- Diego A Álvarez-Díaz
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Salud Materna y Perinatal, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Carlos Franco-Muñoz
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Parasitología, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Katherine Laiton-Donato
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - José A Usme-Ciro
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Centro de Investigación en Salud para el Trópico-CIST, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia.
| | - Nicolás D Franco-Sierra
- Programa Ciencias de la Biodiversidad, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá 111311, Colombia.
| | | | - Sergio Gómez-Rangel
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Luz D Rodríguez-Calderon
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Juliana Barbosa-Ramirez
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Erika Ospitia-Baez
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | - Diana M Walteros
- Dirección de Vigilancia en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
| | | | - Marcela Mercado-Reyes
- Unidad de Secuenciación y Genómica, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Grupo de Salud Materna y Perinatal, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia; Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá 111321, Colombia.
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3
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Chouhy D, Kocjan BJ, Staheli JP, Bolatti EM, Hošnjak L, Sagadin M, Giri AA, Rose TM, Poljak M. Detection of novel Betapapillomaviruses and Gammapapillomaviruses in eyebrow hair follicles using a single-tube 'hanging droplet' PCR assay with modified pan-PV CODEHOP primers. J Gen Virol 2017; 99:109-118. [PMID: 29244018 DOI: 10.1099/jgv.0.000988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A modified pan-PV consensus-degenerate hybrid oligonucleotide primer (CODEHOP) PCR was developed for generic and sensitive detection of a broad-spectrum of human papillomaviruses (HPVs) infecting the cutaneous epithelium. To test the analytical sensitivity of the assay we examined 149 eyebrow hair follicle specimens from immunocompetent male patients. HPV DNA was detected in 60 % (89/149) of analysed eyebrow samples with a total of 48 different HPV sequences, representing 21 previously described HPVs and 27 putative novel HPV types. Evidence for ten novel HPV subtypes and seven viral variants, clustering to three out of five genera containing cutaneous HPVs, was also obtained. Thus, we have shown that the modified pan-PV CODEHOP PCR assay is able to identify multiple HPV types, even from different genera, in the same clinical sample. Overall, these results demonstrate that the pan-PV CODEHOP PCR is an excellent tool for screening and identification of novel cutaneous HPVs, even in samples with low viral loads.
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Affiliation(s)
- Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000 Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Boštjan J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1105 Ljubljana, Slovenia
| | - Jeannette P Staheli
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Elisa M Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000 Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1105 Ljubljana, Slovenia
| | - Martin Sagadin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1105 Ljubljana, Slovenia
| | - Adriana A Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000 Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Timothy M Rose
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1105 Ljubljana, Slovenia
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Kocjan BJ, Bzhalava D, Forslund O, Dillner J, Poljak M. Molecular methods for identification and characterization of novel papillomaviruses. Clin Microbiol Infect 2015; 21:808-16. [PMID: 26003284 DOI: 10.1016/j.cmi.2015.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/27/2015] [Accepted: 05/12/2015] [Indexed: 02/02/2023]
Abstract
Papillomaviruses (PV) are a remarkably heterogeneous family of small DNA viruses that infect a wide variety of vertebrate species and are aetiologically linked with the development of various neoplastic changes of the skin and mucosal epithelia. Based on nucleotide similarity, PVs are hierarchically classified into genera, species and types. Novel human PV (HPV) types are given a unique number only after the whole genome has been cloned and deposited with the International HPV Reference Center. As of 9 March 2015, 200 different HPV types, belonging to 49 species, had been recognized by the International HPV Reference Center. In addition, 131 animal PV types identified from 66 different animal species exist. Recent advances in molecular techniques have resulted in an explosive increase in the identification of novel HPV types and novel subgenomic HPV sequences in the last few years. Among PV genera, the γ-PV genus has been growing most rapidly in recent years with 80 completely sequenced HPV types, followed by α-PV and β-PV genera that have 65 and 51 recognized HPV types, respectively. We reviewed in detail the contemporary molecular methods most often used for identification and characterization of novel PV types, including PCR, rolling circle amplification and next-generation sequencing. Furthermore, we present a short overview of 12 and 10 novel HPV types recently identified in Sweden and Slovenia, respectively. Finally, an update on the International Human Papillomavirus Reference Center is provided.
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Affiliation(s)
- B J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - D Bzhalava
- International Human Papillomavirus Reference Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - O Forslund
- Department of Laboratory Medicine, Lund University, Malmö, Sweden
| | - J Dillner
- International Human Papillomavirus Reference Center, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - M Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia.
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5
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Hošnjak L, Kocjan BJ, Pirš B, Seme K, Poljak M. Characterization of two novel gammapapillomaviruses, HPV179 and HPV184, isolated from common warts of a renal-transplant recipient. PLoS One 2015; 10:e0119154. [PMID: 25748516 PMCID: PMC4351898 DOI: 10.1371/journal.pone.0119154] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/09/2015] [Indexed: 11/19/2022] Open
Abstract
Gammapapillomavirus (Gamma-PV) is a diverse and rapidly expanding PV-genus, currently consisting of 76 fully characterized human papillomavirus (HPV) types. In this study, DNA genomes of two novel HPV types, HPV179 and HPV184, obtained from two distinct facial verrucae vulgares specimens of a 64 year-old renal-transplant recipient, were fully cloned, sequenced and characterized. HPV179 and HPV184 genomes comprise 7,228-bp and 7,324-bp, respectively, and contain four early (E1, E2, E6 and E7) and two late genes (L1 and L2); the non-coding region is typically positioned between L1 and E6 genes. Phylogenetic analysis of the L1 nucleotide sequence placed both novel types within the Gamma-PV genus: HPV179 was classified as a novel member of species Gamma-15, additionally containing HPV135 and HPV146, while HPV184 was classified as a single member of a novel species Gamma-25. HPV179 and HPV184 type-specific quantitative real-time PCRs were further developed and used in combination with human beta-globin gene quantitative real-time PCR to determine the prevalence and viral load of the novel types in the patient's facial warts and several follow-up skin specimens, and in a representative collection, a total of 569 samples, of HPV-associated benign and malignant neoplasms, hair follicles and anal and oral mucosa specimens obtained from immunocompetent individuals. HPV179 and HPV184 viral loads in patients' facial warts were estimated to be 2,463 and 3,200 genome copies per single cell, respectively, suggesting their active role in the development of common warts in organ-transplant recipients. In addition, in this particular patient, both novel types had established a persistent infection of the skin for more than four years. Among immunocompetent individuals, HPV179 was further detected in low-copy numbers in a few skin specimens, indicating its cutaneous tissue tropism, while HPV184 was further detected in low-copy numbers in one mucosal and a few skin specimens, suggesting its dual tissue tropism.
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Affiliation(s)
- Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Branko Pirš
- Private Center for Laser and Aesthetic Dermatology, Ljubljana, Slovenia
| | - Katja Seme
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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6
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Song J, Doggett N, Wren M, Burr T, Fenimore PW, Hatcher EL, Bruno WJ, Li PE, Stubben C, Wolinsky M. Development of forensic assay signatures for ebolaviruses. J Forensic Sci 2015; 60:315-25. [PMID: 25677086 DOI: 10.1111/1556-4029.12655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 02/12/2014] [Accepted: 02/26/2014] [Indexed: 11/29/2022]
Abstract
Ebolaviruses are a diverse group of RNA viruses comprising five different species, four of which cause fatal hemorrhagic fever in humans. Because of their high infectivity and lethality, ebolaviruses are considered major biothreat agents. Although detection assays exist, no forensic assays are currently available. Here, we report the development of forensic assays that differentiate ebolaviruses. We performed phylogenetic analyses and identified canonical SNPs for all species, major clades and isolates. TaqMan-MGB allelic discrimination assays based on these SNPs were designed, screened against synthetic RNA templates, and validated against ebolavirus genomic RNAs. A total of 45 assays were validated to provide 100% coverage of the species and variants with additional resolution at the isolate level. These assays enabled accurate forensic analysis on 4 "unknown" ebolaviruses. Unknowns were correctly classified to species and variant. A goal of providing resolution below the isolate level was not successful. These high-resolution forensic assays allow rapid and accurate genotyping of ebolaviruses for forensic investigations.
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Affiliation(s)
- Jian Song
- Bioenergy and Biome Sciences (B-11), Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545
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7
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Stockinger DE, Fong DL, Vogel KW, Durning WM, Torrence AE, Rose TM, Staheli JP, Baldessari A, Murnane RD, Hukkannen RR. Oral squamous cell carcinoma in a pigtailed macaque (Macaca nemestrina). Comp Med 2014; 64:234-239. [PMID: 24956217 PMCID: PMC4067589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/29/2013] [Accepted: 11/12/2013] [Indexed: 06/03/2023]
Abstract
An adult, gravid, female pigtailed macaque (Macaca nemestrina) presented for facial swelling centered on the left mandible that was approximately 5 cm wide. Differential diagnoses included infectious, inflammatory, and neoplastic origins. Definitive antemortem diagnosis was not possible, and the macaque's condition worsened despite supportive care. Necropsy findings included a mandibular mass that was locally invasive and expansile, encompassing approximately 80% of the left mandibular bone. The mass replaced portions of the soft palate, hard palate, sinuses, ear canal, and the caudal-rostral calvarium and masseter muscle. Histologically, the mass was a neoplasm that was poorly circumscribed, unencapsulated, and infiltrative invading regional bone and soft tissue. The mass consisted of polygonal squamous epithelial cells with intercellular bridging that breached the epithelial basement membrane and formed invasive nests, cords, and trabeculae. The mitotic rate averaged 3 per 400× field of view, with occasional bizarre mitotic figures. Epithelial cells often exhibited dyskeratosis, and the nests often contained compact lamellated keratin (keratin pearls). The neoplasm was positive via immunohistochemistry for pancytokeratin, variably positive for S100, and negative for vimentin, smooth muscle actin, and desmin. The gross, histologic, and immunohistochemical findings were consistent with an aggressive oral squamous cell carcinoma. The neoplasm was negative via PCR for papilloma virus. In general, neoplasia in macaques is rare. Although squamous cell carcinomas are one of the most common oral neoplasia in many species, to our knowledge this case represents the first reported oral squamous cell carcinoma in a pigtailed macaque.
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Affiliation(s)
- Diane E Stockinger
- Washington National Primate Research Center, Seattle Children's Research Institute, Seattle, Washington, USA; Valley Biosystems, West Sacramento, California, USA.
| | - Derek L Fong
- Washington National Primate Research Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Keith W Vogel
- Washington National Primate Research Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - W McIntyre Durning
- Washington National Primate Research Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Anne E Torrence
- Washington National Primate Research Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Timothy M Rose
- Department of Pediatrics, Division of Infectious Diseases, Center for Childhood Infections and Prematurity Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jeannette P Staheli
- Center for Childhood Infections and Prematurity Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Audrey Baldessari
- Washington National Primate Research Center, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Robert D Murnane
- Washington National Primate Research Center, Department of Comparative Medicine, University of Washington, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Renee R Hukkannen
- Department of Comparative Medicine, University of Washington, Seattle Children's Research Institute, Seattle, Washington, USA
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8
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Song J, Wolinsky M, Wren M, Burr T, Li PE, Doggett N. Forensic signatures for Marburgviruses. Forensic Sci Int 2013; 233:338-47. [PMID: 24314539 DOI: 10.1016/j.forsciint.2013.09.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/30/2013] [Indexed: 11/30/2022]
Abstract
Marburgvirus is one of the most important hemorrhagic fever viruses with extremely high infectivity and fatality rate (~90%). It is transmitted easily in human populations through a respiratory route and therefore considered as a major biothreat agent. Although detection assays have been developed, no assay is available for forensic analysis. Here we report development of forensic assays for Marburgvirus. We performed detailed phylogenetic analysis of strains and isolates from all known Marburg virus outbreaks as well as from several laboratory strains and identified canonical SNPs for all major clades (outbreaks) and strains. TaqMan-MGB allelic discrimination assays targeting these SNPs were designed and experimentally screened against synthetic RNA templates and genomic RNAs. A total of 45 assays were validated to provide 100% coverage of the clades (outbreaks) and 91% at the strain level (21 out of the 23 targeted Marburgvirus strains) with built-in redundancy for increased robustness. Using these validated assays, we were able to provide accurate forensic analysis on 3 "unknown" Marburgviruses. These high-resolution forensic assays allow rapid and accurate genotyping of Marburgviruses for forensic investigations.
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Affiliation(s)
- Jian Song
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
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9
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Zlateva KT, Coenjaerts FEJ, Crusio KM, Lammens C, Leus F, Viveen M, Ieven M, Spaan WJM, Claas ECJ, Gorbalenya AE. No novel coronaviruses identified in a large collection of human nasopharyngeal specimens using family-wide CODEHOP-based primers. Arch Virol 2013; 158:251-5. [PMID: 23053517 PMCID: PMC7087030 DOI: 10.1007/s00705-012-1487-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/16/2012] [Indexed: 11/26/2022]
Abstract
Novel viruses might be responsible for numerous disease cases with unknown etiology. In this study, we screened 1800 nasopharyngeal samples from adult outpatients with respiratory disease symptoms and healthy individuals. We employed a reverse transcription (RT)-PCR assay and CODEHOP-based primers (CT12-mCODEHOP) previously developed to recognize known and unknown corona- and toroviruses. The CT12-mCODEHOP assay detected 42.0 % (29/69) of samples positive for human coronaviruses (HCoV), including HCoV-229 (1/16), HCoV-NL63 (9/17), and HCoV-OC43 (19/36), and additionally HCoV-HKU1 (3), which was not targeted by the diagnostic real-time PCR assays. No other coronaviruses were identified in the analyzed samples.
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Affiliation(s)
- Kalina T. Zlateva
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Frank E. J. Coenjaerts
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kelly M. Crusio
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Christine Lammens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen, University Hospital Antwerp, Antwerp, Belgium
| | - Frank Leus
- Department of Data Management, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marco Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Margareta Ieven
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen, University Hospital Antwerp, Antwerp, Belgium
| | - Willy J. M. Spaan
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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10
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Novel animal papillomavirus sequences and accurate phylogenetic placement. Mol Phylogenet Evol 2012; 65:883-91. [PMID: 22960206 DOI: 10.1016/j.ympev.2012.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 07/13/2012] [Accepted: 08/14/2012] [Indexed: 01/08/2023]
Abstract
All amniotes are probably infected by specific papillomaviruses (PVs), but knowledge about PV diversity remains sparse. An insufficient taxon sampling, and a focus on humans as hosts, may perturb phylogenetic analyses leading to wrong conclusions about PV evolution. We performed a systematic approach to explore the diversity of PVs combining rolling circle amplification with the use of "universal" primers to search for the presence of novel PV sequences in animal samples. We communicate 12 sequences putatively corresponding to novel PVs gained from 10 host species in eight mammal families: Bovidae, Canidae, Cervidae, Equidae, Hominidae, Phocoenidae, Procyonidae and Pteropodidae. The phylogenetic position of the new sequences was inferred with an evolutionary placement algorithm under a Maximum Likelihood framework using a pre-computed, well-resolved tree constructed with the E1-E2-L1 gene sequences as a backbone. The new sequences were phylogenetically diverse and could be respectively placed with confidence within all four PV crown groups. The prevailing presence of sequences from the crown groups Alpha+Omikron-PVs and Beta+Xi-PVs may correspond to an increased viral diversity in these taxa, or rather reflect a combination of anthropocentric bias and preferential amplification from commonly used "universal" primers. Our results combined with literature data support the view that the number and diversity of animal PVs is overwhelmingly large.
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11
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Zlateva KT, Crusio KM, Leontovich AM, Lauber C, Claas E, Kravchenko AA, Spaan WJM, Gorbalenya AE. Design and validation of consensus-degenerate hybrid oligonucleotide primers for broad and sensitive detection of corona- and toroviruses. J Virol Methods 2011; 177:174-83. [PMID: 21864579 PMCID: PMC7112876 DOI: 10.1016/j.jviromet.2011.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 08/01/2011] [Accepted: 08/04/2011] [Indexed: 02/05/2023]
Abstract
The ssRNA+ family Coronaviridae includes two subfamilies prototyped by coronaviruses and toroviruses that cause respiratory and enteric infections. To facilitate the identification of new distantly related members of the family Coronaviridae, we have developed a molecular assay with broad specificity. The consensus-degenerated hybrid oligonucleotide primer (CODEHOP) strategy was modified to design primers targeting the most conserved motifs in the RNA-dependent RNA polymerase locus. They were evaluated initially on RNA templates from virus-infected cells using a two-step RT-PCR protocol that was further advanced to a one-step assay. The sensitivity of the assay ranged from 102 to 106 and from 105 to 109 RNA copy numbers for individual corona-/torovirus templates when tested, respectively, with and without an excess of RNA from human cells. This primer set compared to that designed according to the original CODEHOP rules showed 10–103 folds greater sensitivity for 5 of the 6 evaluated corona-/torovirus templates. It detected 57% (32 of 56) of the respiratory specimens positive for 4 human coronaviruses, as well as stool specimens positive for a bovine torovirus. The high sensitivity and broad virus range of this assay makes it suitable for screening biological specimens in search for new viruses of the family Coronaviridae.
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Affiliation(s)
- Kalina T Zlateva
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Cheng L, Chen W, Zhai L, Xu D, Huang T, Lin S, Zhou X, Deng Z. Identification of the genecluster involved in muraymycin biosynthesis from Streptomyces sp. NRRL 30471. ACTA ACUST UNITED AC 2011; 7:920-7. [DOI: 10.1039/c0mb00237b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
While PCR primer design for the amplification of known sequences is usually quite straightforward, the design, and successful application of primers aimed at the detection of as yet unknown genes is often not. The search for genes that are presumed to be distantly related to a known gene sequence, such as homologous genes in different species, paralogs in the same genome, or novel pathogens in diverse hosts, often turns into the proverbial search for the needle in the haystack. PCR-based methods commonly used to address this issue involve the use of either consensus primers or degenerate primers, both of which have significant shortcomings regarding sensitivity and specificity. We have developed a novel primer design approach that diminishes these shortcomings and instead takes advantage of the strengths of both consensus and degenerate primer designs, by combining the two concepts into a Consensus-Degenerate Hybrid Oligonucleotide Primer (CODEHOP) approach. CODEHOP PCR primers contain a relatively short degenerate 3' core and a 5' nondegenerate clamp. The 3' degenerate core consists of a pool of primers containing all possible codons for a 3-4 aminoacid motif that is highly conserved in multiply aligned sequences from known members of a protein family. Each primer in the pool also contains a single 5' nondegenerate nucleotide sequence derived from a codon consensus across the aligned aminoacid sequences flanking the conserved motif. During the initial PCR amplification cycles, the degenerate core is responsible for specific binding to sequences encoding the conserved aminoacid motif. The longer consensus clamp region serves to stabilize the primer and allows the participation of all primers in the pool in the efficient amplification of products during later PCR cycles. We have developed an interactive web site and algorithm (iCODEHOP) for designing CODEHOP PCR primers from multiply aligned protein sequences, which is freely available online. Here, we describe the workflow of a typical CODEHOP PCR assay design and optimization and give a specific implementation example along with "best-practice" advice.
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Affiliation(s)
- Jeannette P Staheli
- Center for Childhood Infection and Prematurity Research, Seattle Children's Research Institute, Seattle, WA, USA
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Novel genes retrieved from environmental DNA by polymerase chain reaction: current genome-walking techniques for future metagenome applications. J Biotechnol 2009; 144:75-82. [PMID: 19712711 DOI: 10.1016/j.jbiotec.2009.08.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 08/11/2009] [Accepted: 08/17/2009] [Indexed: 11/24/2022]
Abstract
Environmental DNA is an extremely rich source of genes encoding enzymes with novel biocatalytic activities. To tap this source, function-based and sequence-based strategies have been established to isolate, clone, and express these novel metagenome-derived genes. Sequence-based strategies, which rely on PCR with consensus primers and genome walking, represent an efficient and inexpensive alternative to activity-based screening of recombinant strains harbouring fragments of environmental DNA. This review covers the diverse array of genome-walking techniques, which were originally developed for genomic DNA and currently are also used for PCR-based recovery of entire genes from the metagenome. These sequence-based gene mining methods appear to offer a powerful tool for retrieving from the metagenome novel genes encoding biocatalysts with potential applications in biotechnology.
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