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Cells Mar 2023Despite scientific discoveries in the field of gene and cell therapy, some diseases still have no effective treatment. Advances in genetic engineering methods have... (Review)
Review
Despite scientific discoveries in the field of gene and cell therapy, some diseases still have no effective treatment. Advances in genetic engineering methods have enabled the development of effective gene therapy methods for various diseases based on adeno-associated viruses (AAVs). Today, many AAV-based gene therapy medications are being investigated in preclinical and clinical trials, and new ones are appearing on the market. In this article, we present a review of AAV discovery, properties, different serotypes, and tropism, and a following detailed explanation of their uses in gene therapy for disease of different organs and systems.
Topics: Serogroup; Genetic Vectors; Genetic Therapy; Genetic Engineering; Tropism; Dependovirus
PubMed: 36899921
DOI: 10.3390/cells12050785 -
Nature Reviews. Microbiology Apr 2022The magnitude of immune evasion of Omicron raises the question whether it should be considered as a distinct SARS-CoV-2 serotype. Here, we discuss lines of evidence in...
The magnitude of immune evasion of Omicron raises the question whether it should be considered as a distinct SARS-CoV-2 serotype. Here, we discuss lines of evidence in support or against the concept of SARS-CoV-2 serotypes, and the implications of this classification.
Topics: COVID-19; Humans; SARS-CoV-2; Serogroup; Spike Glycoprotein, Coronavirus
PubMed: 35181769
DOI: 10.1038/s41579-022-00708-x -
Transboundary and Emerging Diseases Sep 2022Rapid and accurate detection and serotyping of foot-and-mouth disease (FMD) virus (FMDV) is essential for implementing control policies against emergent FMD outbreaks....
Rapid and accurate detection and serotyping of foot-and-mouth disease (FMD) virus (FMDV) is essential for implementing control policies against emergent FMD outbreaks. Current serotyping assays, such as VP1 reverse transcription-polymerase chain reaction (RT-PCR)/sequencing (VP1 RT-PCR/sequencing) and antigen detection enzyme-linked immunosorbent assay (ELISA), have problems with increasing serotyping failure of FMDVs from FMD outbreaks. This study was conducted to develop a multiplex real-time RT-PCR for specific detection and differential serotyping of FMDV serotype O, A, and Asia 1 directly from field clinical samples. Primers and probes were designed based on 571 VP1 coding region sequences originated from seven pools. Multiplex real-time RT-PCR using these primers and probes demonstrated serotype-specific detection with enhanced sensitivity compared to VP1 RT-PCR/sequencing for reference FMDV (n = 24). Complete serotyping conformity between the developed multiplex real-time RT-PCR and previous VP1 RT-PCR/sequencing was demonstrated using FMDV field viruses (n = 113) prepared in cell culture. For FMDV field clinical samples (n = 55), the serotyping rates of multiplex real-time RT-PCR and VP1 RT-PCR/sequencing were 92.7% (51/55) and 72.7% (40/55), respectively. Moreover, the developed multiplex real-time RT-PCR demonstrated improved FMDV detection (up to 33.3%) and serotyping (up to 67.7%) capabilities for saliva samples when compared with 3D real-time RT-PCR and VP1 RT-PCR/sequencing, during 10 days of challenge infection with FMDV serotype O, A, and Asia 1. Collectively, this study suggests that the newly developed multiplex real-time RT-PCR assay may be useful for the detection and differential serotyping of FMDV serotype O, A, and Asia 1 in the field.
Topics: Animals; DNA Primers; Foot-and-Mouth Disease; Foot-and-Mouth Disease Virus; Reverse Transcriptase Polymerase Chain Reaction; Sensitivity and Specificity; Serogroup; Serotyping
PubMed: 35614493
DOI: 10.1111/tbed.14603 -
Frontiers in Cellular and Infection... 2021Shiga toxin-producing (STEC) have more than 470 serotypes. The well-known STEC O157:H7 serotype is a leading cause of STEC infections in humans. However, the incidence...
Shiga toxin-producing (STEC) have more than 470 serotypes. The well-known STEC O157:H7 serotype is a leading cause of STEC infections in humans. However, the incidence of non-O157:H7 STEC serotypes associated with foodborne outbreaks and human infections has increased in recent years. Current detection and serotyping assays are focusing on O157 and top six ("Big six") non-O157 STEC serogroups. In this study, we performed phylogenetic analysis of nearly 41,000 publicly available STEC genomes representing 460 different STEC serotypes and identified 19 major and 229 minor STEC clusters. STEC cluster-specific gene markers were then identified through comparative genomic analysis. We further identified serotype-specific gene markers for the top 10 most frequent non-O157:H7 STEC serotypes. The cluster or serotype specific gene markers had 99.54% accuracy and more than 97.25% specificity when tested using 38,534 STEC and 14,216 non-STEC genomes, respectively. In addition, we developed a freely available serotyping pipeline named STECFinder that combined these robust gene markers with established serotype specific O and H antigen genes and genes for accurate identification, cluster determination and serotyping of STEC. STECFinder can assign 99.85% and 99.83% of 38,534 STEC isolates to STEC clusters using assembled genomes and Illumina reads respectively and can simultaneously predict subtypes and STEC serotypes. Using shotgun metagenomic sequencing reads of STEC spiked food samples from a published study, we demonstrated that STECFinder can detect the spiked STEC serotypes, accurately. The cluster/serotype-specific gene markers could also be adapted for culture independent typing, facilitating rapid STEC typing. STECFinder is available as an installable package (https://github.com/LanLab/STECFinder) and will be useful for STEC cluster identification and serotyping using genome data.
Topics: Adhesins, Bacterial; Cluster Analysis; Escherichia coli Infections; Escherichia coli Proteins; Genomics; Humans; Phylogeny; Serogroup; Serotyping; Shiga-Toxigenic Escherichia coli
PubMed: 35083165
DOI: 10.3389/fcimb.2021.772574 -
Viruses Aug 2021Multiple serotypes and topotypes of foot-and-mouth disease virus (FMDV) circulate in endemic areas, posing considerable impacts locally. In addition, introductions into... (Comparative Study)
Comparative Study
Multiple serotypes and topotypes of foot-and-mouth disease virus (FMDV) circulate in endemic areas, posing considerable impacts locally. In addition, introductions into new areas are of great concern. Indeed, in recent years, multiple FMDV outbreaks, caused by topotypes that have escaped from their original areas, have been recorded in various parts of the world. In both cases, rapid and accurate diagnosis, including the identification of the serotype and topotype causing the given outbreaks, plays an important role in the implementation of the most effective and appropriate measures to control the spread of the disease. In the present study, we describe the performance of a range of diagnostic and typing tools for FMDV on a panel of vesicular samples collected in northern Tanzania (East Africa, EA) during 2012-2018. Specifically, we tested these samples with a real-time RT-PCR targeting 3D sequence for pan-FMDV detection; an FMDV monoclonal antibody-based antigen (Ag) detection and serotyping ELISA kit; virus isolation (VI) on LFBKαVβ6 cell line; and a panel of four topotype-specific real-time RT-PCRs, specifically tailored for circulating strains in EA. The 3D real-time RT-PCR showed the highest diagnostic sensitivity, but it lacked typing capacity. Ag-ELISA detected and typed FMDV in 71% of sample homogenates, while VI combined with Ag-ELISA for typing showed an efficiency of 82%. The panel of topotype-specific real-time RT-PCRs identified and typed FMDV in 93% of samples. However, the SAT1 real-time RT-PCR had the highest (20%) failure rate. Briefly, topotype-specific real-time RT-PCRs had the highest serotyping capacity for EA FMDVs, although four assays were required, while the Ag-ELISA, which was less sensitive, was the most user-friendly, hence suitable for any laboratory level. In conclusion, when the four compared tests were used in combination, both the diagnostic and serotyping performances approached 100%.
Topics: Africa, Eastern; Animals; Antibodies, Viral; Clinical Laboratory Techniques; Enzyme-Linked Immunosorbent Assay; Foot-and-Mouth Disease; Foot-and-Mouth Disease Virus; Phylogeny; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Serogroup; Serotyping
PubMed: 34452448
DOI: 10.3390/v13081583 -
Frontiers in Cellular and Infection... 2022There is a growing demand for rapid, sensitive, field-deployable nucleic acid tests for cholera, which usually occurs in rural areas. In this study, we developed a...
There is a growing demand for rapid, sensitive, field-deployable nucleic acid tests for cholera, which usually occurs in rural areas. In this study, we developed a Cas12a-assisted rapid isothermal detection (CARID) system for the detection of toxigenic serogroups O1 and O139 by combining recombinase-aided amplification and CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins). The results can be determined by fluorescence signal and visualized by lateral flow dipstick. We identified 154 V strains and 129 strains of other intestinal diarrheagenic bacteria with a 100% coincidence rate. The limit of detection of CARID was 20 copies/reaction of genomic DNA, which is comparable to that of polymerase chain reaction (PCR) and qPCR. Multiple-CARID was also established for efficiency and economic considerations with an acceptable decrease in sensitivity. Simulated sample tests showed that CARID is suitable for complex samples. In conclusion, CARID is a rapid, sensitive, economically efficient, and portable method for the detection of , which makes it suitable for field responses to cholera.
Topics: Cholera; Cholera Toxin; Humans; Serogroup; Serotyping; Vibrio cholerae O1
PubMed: 35433512
DOI: 10.3389/fcimb.2022.863435 -
International Journal of Food... Nov 2021Cronobacter spp. are foodborne pathogens that can cause severe infections in neonates through contaminated powdered infant formula. Accurate and rapid pathogen...
Cronobacter spp. are foodborne pathogens that can cause severe infections in neonates through contaminated powdered infant formula. Accurate and rapid pathogen identification and serotyping are crucial to limit the detrimental effects of bacterial infections, and to prevent outbreaks and sporadic infections. Conventional serotyping is tedious, laborious, and time-consuming; however, with whole-genome sequencing (WGS) becoming faster and cheaper, WGS has vast potential in routine typing and surveillance. Hence, in this study, we developed a publicly available tool, CroTrait (CronobacterTraits), for in silico species identification and O serotyping of Cronobacter isolates based on WGS data. CroTrait showed excellent performance in species identification and O serotyping when 810 genomes with known species identities and 276 genomes with known O serotype were tested. Moreover, CroTrait allows rapid prediction of new potential O serotypes. We identified 11 novel potential O serotypes of Cronobacter using CroTrait. Therefore, CroTrait is a convenient and promising tool for species identification and O serotyping of Cronobacter isolates.
Topics: Computer Simulation; Cronobacter; Cronobacter sakazakii; Humans; Infant; Infant, Newborn; Serogroup; Serotyping; Whole Genome Sequencing
PubMed: 34563883
DOI: 10.1016/j.ijfoodmicro.2021.109405 -
BMC Infectious Diseases Oct 2015Pneumococcal diseases remain a leading cause of vaccine-preventable death worldwide in children <5 years of age. The seven-valent pneumococcal conjugate vaccine (PCV7)... (Review)
Review
BACKGROUND
Pneumococcal diseases remain a leading cause of vaccine-preventable death worldwide in children <5 years of age. The seven-valent pneumococcal conjugate vaccine (PCV7) was approved in 2001 in Europe and was introduced into the national immunization programmes of many European countries from 2006-2008. In 2009, higher-valent PCVs (PCV10 and PCV13) became available, replacing PCV7 from 2009-2011. This article describes the evolution of vaccine and non-vaccine serotypes causing invasive pneumococcal disease (IPD) following the introduction of PCVs in Western Europe, based on data from publicly-available medical publications and national surveillance systems from January 2010 to May 2015.
DISCUSSION
In countries with high vaccine uptake, 5-7 years after PCV7 introduction IPD caused by vaccine serotypes has almost disappeared in children. Non-PCV7 serotypes have emerged, particularly serotypes 19A, 7 F, 3 and 1. A rapid and significant reduction of the additional serotypes included in higher-valent vaccines has been observed consistently following the introduction of these vaccines. A significant and rapid decline of serotypes 19A, 7 F, 1 and 6A in both vaccine-eligible and older age groups has been observed in countries using PCV13 while serotype 19A and 3 has increased in countries using PCV10. Serotype 3 has become one of the most prevalent serotypes in adults, with some reduction only in the UK and France. Serotype diversity increased and varied by age group, the type of vaccine in use, and the time since the introduction of higher-valent PCVs. Serotypes that are currently more frequent include 24 F, 22 F, 8 and 15A in countries that use PCV13, and serotypes 19A and 3 in countries that use PCV10. Compared with the time before the introduction of higher valent PCVs, to date, there is no single '19A-like' serotype emerging across countries and most of the newly emerging non-PCV13 vaccine types are less invasive with a low case-carrier ratio.
CONCLUSIONS
It is important to closely monitor not only evolving serotypes but also the magnitude of the effect in order to evaluate the overall impact of pneumococcal vaccination programmes and to initiate the appropriate vaccination strategy. Emerging serotypes may also need to be considered for the future development of new vaccines.
Topics: Adolescent; Aged; Child; Child, Preschool; Europe; Heptavalent Pneumococcal Conjugate Vaccine; Humans; Immunization Programs; Infant; Pneumococcal Infections; Pneumococcal Vaccines; Serogroup; Serotyping; Streptococcus pneumoniae; Vaccines, Conjugate
PubMed: 26468008
DOI: 10.1186/s12879-015-1147-x -
The Journal of Molecular Diagnostics :... May 2020Salmonella is a common cause of foodborne disease worldwide, including Australia. More than 85% of outbreaks of human salmonellosis in Australia were caused by five...
Salmonella is a common cause of foodborne disease worldwide, including Australia. More than 85% of outbreaks of human salmonellosis in Australia were caused by five Salmonella serovars. Rapid, accurate, and sensitive identification of Salmonella serovars is vital for diagnosis and public health surveillance. Recently, an isothermal amplification technique, termed multiple cross-displacement amplification (MCDA), has been employed to detect Salmonella at the species level. Herein, seven MCDA assays were developed and evaluated for rapid detection and differentiation of the five most common Salmonella serovars in Australia: Typhimurium, Enteritidis, Virchow, Saintpaul, and Infantis. MCDA primer sets were designed by targeting seven serovar/lineage-specific gene markers identified through genomic comparisons. The sensitivity and specificity of the seven MCDA assays were evaluated using 79 target strains and 32 nontarget strains. The assays were all highly sensitive and specific to target serovars, with the sensitivity ranging from 92.9% to 100% and the specificity from 93.3% to 100%. The limit of detection of the seven MCDA assays was 50 fg per reaction (10 copies) from pure DNA, and positive results were detected in as little as 8 minutes. These seven MCDA assays offer a rapid, accurate, and sensitive serotyping method. With further validation in clinically relevant conditions, these assays could be used for culture-independent serotyping of common Salmonella serovars directly from clinical samples.
Topics: Genes, Bacterial; Humans; Nucleic Acid Amplification Techniques; Phylogeny; Salmonella; Sensitivity and Specificity; Serogroup; Serotyping
PubMed: 32359725
DOI: 10.1016/j.jmoldx.2020.02.006 -
Pediatrics and Neonatology Oct 2016
Topics: Humans; Pneumococcal Infections; Pneumococcal Vaccines; Serogroup; Serotyping; Streptococcus pneumoniae
PubMed: 27641269
DOI: 10.1016/j.pedneo.2015.08.012