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Tripathi P. Medical viruses: diagnostic techniques. Virol J 2023; 20:143. [PMID: 37434239 DOI: 10.1186/s12985-023-02108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
The recent epidemics and pandemics caused by different viruses such as SARS-CoV-2, monkey pox, H1N1, ebola virus etc. have been a cause of mass destruction in the human race, the biggest decline slope in the global economy and mental trauma. A number of viruses have been discovered that may cause serious problems and to overcome this problem, early diagnosis of the viruses and understanding their infection pattern is a must. Early detection of viruses inside the host provides timely management in a strategic manner. Scientists have developed some effective and efficient methods to detect the viruses. In this review, we have explained a few types of diagnostic techniques: Biosensor based, immunological-based, and molecular-based diagnostic techniques that are prominent methodologies to identify and detect the course of infection related to the medical viruses. In biosensor-based diagnostic technique, an analytical device consisting of biological elements and physicochemical component gives a signal upon detection of viral antigen. In immunological-based diagnostic techniques, enzyme-linked antibodies are utilized to find the particular antiviral antibody or viral antigen in human specimens, and nucleic acid-based diagnostic techniques are based on the principle of amplification of the viral genome.
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Affiliation(s)
- Pratima Tripathi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Bijnor-Sisendi Road, Sarojini Nagar, Near CRPF Base Camp, Lucknow, UP, 226002, India.
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Xia YJ, Xu L, Zhao JJ, Li YX, Wu RZ, Song XP, Zhao QZ, Liu YB, Wang Q, Zhang QY. Development of a quadruple PCR-based gene microarray for detection of vaccine and wild-type classical swine fever virus, African swine fever virus and atypical porcine pestivirus. Virol J 2022; 19:201. [PMID: 36447230 PMCID: PMC9708128 DOI: 10.1186/s12985-022-01933-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Classical swine fever (CSF), African swine fever (ASF), and atypical porcine pestivirus (APPV) are acute, virulent, and contagious viral diseases currently hampering the pig industry in China, which result in mummification or stillbirths in piglets and mortality in pigs. Diagnostic assays for the differentiation of infection and vaccination of CSFV, in addition to the detection of ASFV and APPV, are urgently required for better prevention, control, and elimination of these viral diseases in China. METHODS A quadruple PCR-based gene microarray assay was developed in this study to simultaneously detect wild-type and vaccine CSFV strains, ASFV and APPV according to their conserved regions. Forty-two laboratory-confirmed samples, including positive samples of 10 other swine viral diseases, were tested using this assay to confirm its high specificity. RESULTS This assay's limit of detections (LODs) for the wild-type and vaccine CSFV were 6.98 and 6.92 copies/µL. LODs for ASFV and APPV were 2.56 × 10 and 1.80 × 10 copies/µL, respectively. When compared with standard RT-PCR or qPCR for CSFV (GB/T 26875-2018), ASFV (MARR issue No.172), or APPV (CN108611442A) using 219 clinical samples, the coincidence was 100%. The results showed that this assay with high sensitivity could specifically distinguish ASFV, APPV, and CSFV, including CSFV infection and immunization. CONCLUSION This assay provides a practical, simple, economic, and reliable test for the rapid detection and accurate diagnosis of the three viruses and may have good prospects for application in an epidemiological investigation, prevention, and control and elimination of these three diseases.
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Affiliation(s)
- Ying-ju Xia
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Lu Xu
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Jun-jie Zhao
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Yuan-xi Li
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Rui-zhi Wu
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Xiang-peng Song
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Qi-zu Zhao
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Ye-bing Liu
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Qin Wang
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
| | - Qian-yi Zhang
- grid.418540.cChina Institute of Veterinary Drug Control, Beijing, 100081 People’s Republic of China
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High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach. Microbiol Spectr 2022; 10:e0185321. [PMID: 35196791 PMCID: PMC8865552 DOI: 10.1128/spectrum.01853-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We recently carried out a metagenomic study to determine the fecal virome of infants during their first year of life in a semirural community in Mexico. A total of 97 stool samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In this work, we describe the prevalence and incidence of caliciviruses in this birth cohort. We found that 54 (56%) and 24 (25%) of the samples were positive for norovirus and sapovirus sequence reads detected by next-generation sequencing, respectively. Potential infections were arbitrarily considered when at least 20% of the complete virus genome was determined. Considering only these samples, there were 3 cases per child/year for norovirus and 0.33 cases per child/year for sapovirus. All nine children had sequence reads related to norovirus in at least 2 and up to 10 samples, and 8 children excreted sapovirus sequence reads in 1 and up to 5 samples during the study. The virus in 35 samples could be genotyped. The results showed a high diversity of both norovirus (GI.3[P13], GI.5, GII.4, GII.4[P16], GII.7[P7], and GII.17[P17]) and sapovirus (GI.1, GI.7, and GII.4) in the community. Of interest, despite the frequent detection of caliciviruses in the stools, all children remained asymptomatic during the study. Our results clearly show that metagenomic studies in stools may reveal a detailed picture of the prevalence and diversity of gastrointestinal viruses in the human gut during the first year of life. IMPORTANCE Human caliciviruses are important etiological agents of acute gastroenteritis in children under 5 years of age. Several studies have characterized their association with childhood diarrhea and their presence in nondiarrheal stool samples. In this work, we used a next-generation sequencing approach to determine, in a longitudinal study, the fecal virome of infants during their first year of life. Using this method, we found that caliciviruses can be detected significantly more frequently than previously reported, providing a more detailed picture of the prevalence and genetic diversity of these viruses in the human gut during early life.
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Zaczek-Moczydlowska MA, Beizaei A, Dillon M, Campbell K. Current state-of-the-art diagnostics for Norovirus detection: Model approaches for point-of-care analysis. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.06.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Taboada B, Morán P, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximenez C, Arias CF. The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021; 16:e0240958. [PMID: 33852569 PMCID: PMC8046192 DOI: 10.1371/journal.pone.0240958] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant's immune system or on the health of the infants later in life, remains to be investigated.
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Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Cecilia Ximenez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (CFA); (CX); (JT)
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Mohan SV, Hemalatha M, Kopperi H, Ranjith I, Kumar AK. SARS-CoV-2 in environmental perspective: Occurrence, persistence, surveillance, inactivation and challenges. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 405:126893. [PMID: 32901196 PMCID: PMC7471803 DOI: 10.1016/j.cej.2020.126893] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 05/03/2023]
Abstract
The unprecedented global spread of the severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 is depicting the distressing pandemic consequence on human health, economy as well as ecosystem services. So far novel coronavirus (CoV) outbreaks were associated with SARS-CoV-2 (2019), middle east respiratory syndrome coronavirus (MERS-CoV, 2012), and SARS-CoV-1 (2003) events. CoV relates to the enveloped family of Betacoronavirus (βCoV) with positive-sense single-stranded RNA (+ssRNA). Knowing well the persistence, transmission, and spread of SARS-CoV-2 through proximity, the faecal-oral route is now emerging as a major environmental concern to community transmission. The replication and persistence of CoV in the gastrointestinal (GI) tract and shedding through stools is indicating a potential transmission route to the environment settings. Despite of the evidence, based on fewer reports on SARS-CoV-2 occurrence and persistence in wastewater/sewage/water, the transmission of the infective virus to the community is yet to be established. In this realm, this communication attempted to review the possible influx route of the enteric enveloped viral transmission in the environmental settings with reference to its occurrence, persistence, detection, and inactivation based on the published literature so far. The possibilities of airborne transmission through enteric virus-laden aerosols, environmental factors that may influence the viral transmission, and disinfection methods (conventional and emerging) as well as the inactivation mechanism with reference to the enveloped virus were reviewed. The need for wastewater epidemiology (WBE) studies for surveillance as well as for early warning signal was elaborated. This communication will provide a basis to understand the SARS-CoV-2 as well as other viruses in the context of the environmental engineering perspective to design effective strategies to counter the enteric virus transmission and also serves as a working paper for researchers, policy makers and regulators.
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Key Words
- (h+), Photoholes
- +ssRNA, Positive Sense Single-Stranded RNA
- A-WWTS, Algal-WWTS
- ACE2, Angiotensin-converting enzyme 2
- AH, Absolute Humidity
- AOPs, Advanced Oxidation Processes
- ASP, Activate Sludge Process
- Aerosols
- BCoV, Bovine Enteric Coronavirus)
- BSL, Biosafety Level
- BVDV1, Bovine Viral Diarrhea Virus Type 1
- BVDV2, Bovine Viral Diarrhea Virus Type 2
- BoRv, Bovine Rotavirus Group A
- CCA, Carbon Covered Alumina
- CNT, Carbon Nanotubes
- COVID-19
- COVID-19, Coronavirus Disease 2019
- CRFK, Crandell Reese feline kidney cell line (CRFK)
- CVE, Coxsackievirus B5
- ClO2, Chlorine dioxide
- Cl−, Chlorine
- Cys, Cysteine
- DBP, Disinfection by-products
- DBT, L2 and Delayed Brain Tumor Cell Cultures
- DMEM, Dulbecco’s Modified Eagle Medium
- DNA, deoxyribose nucleic acid
- Disinfection
- E gene, Envelope protein gene
- EV, Echovirus 11
- Enteric virus
- Enveloped virus
- FC, Free Chlorine
- FFP3, Filtering Face Piece
- FIPV, Feline infectious peritonitis virus
- GI, Gastrointestinal tract
- H2O2, Hydrogen Peroxide
- H3N2, InfluenzaA
- H6N2, Avian influenza virus
- HAV, Hepatitis A virus (HAV)
- HAdV, Human Adenovirus
- HCoV, Human CoV
- HEV, Hepatitis E virus
- HKU1, Human CoV1
- ICC-PCR, Integrated Cell Culture with PCR
- JCV, JCV polyomavirus
- MALDI-TOF MS, Mass Spectrometry
- MBR, Membrane Bioreactor (MBR)
- MERS-CoV, Middle East Respiratory Syndrome Coronavirus
- MHV, Murine hepatitis virus
- MNV-1, Murine Norovirus
- MWCNTs, Multiwalled Carbon Nanotubes
- Met, Methionine
- N gene, Nucleocapsid protein gene
- NCoV, Novel coronavirus
- NGS, Next generation sequencing
- NTP, Non-Thermal Plasma
- O2, Singlet Oxygen
- O3, Ozone
- ORF, Open Reading Frame
- PAA, Para Acetic Acid
- PCR, Polymerase Chain Reaction
- PEC, Photoelectrocatalytical
- PEG, Polyethylene Glycol
- PFU, Plaque Forming Unit
- PMMoV, Pepper Mild Mottle Virus
- PMR, Photocatalytic Membrane Reactors
- PPE, Personal Protective Equipment
- PTAF, Photocatalytic Titanium Apatite Filter
- PV-1, Polivirus-1
- PV-3, Poliovirus 3
- PVDF, Polyvinylidene Fluoride
- Qβ, bacteriophages
- RH, Relative Humidity
- RNA, Ribose nucleic acid
- RONS, Reactive Oxygen and/or Nitrogen Species
- RT-PCR, Real Time Polymerase Chain Reaction
- RVA, Rotaviruses A
- SARS-CoV-1, Severe Acute Respiratory Syndrome Coronavirus 1
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2
- SBR, Sequential Batch Reactor
- SODIS, Solar water disinfection
- STP, Sewage Treatment Plant
- Sewage
- T90, First order reaction time required for completion of 90%
- T99.9, First order reaction time required for completion of 99.9%
- TGEV, Porcine Coronavirus Transmissible Gastroenteritis Virus
- TGEV, Transmissible Gastroenteritis
- Trp, Tryptophan
- Tyr, Tyrosine
- US-EPA, United States Environmental Protection Agency
- UV, Ultraviolet
- WBE, Wastewater-Based Epidemiology
- WWT, Wastewater Treatment
- WWTPs, Wastewater Treatment Plants
- dPCR, Digital PCR
- ds, Double Stranded
- dsDNA, Double Stranded DNA
- log10, logarithm with base 10
- qRT-PCR, quantitative RT-PCR
- ss, Single Stranded
- ssDNA, Single Stranded DNA
- ssRNA, Single Stranded RNA
- αCoV, Alphacoronavirus
- βCoV, Betacoronavirus
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Affiliation(s)
- S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Campus, Hyderabad 500007, India
| | - Manupati Hemalatha
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Campus, Hyderabad 500007, India
| | - Harishankar Kopperi
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - I Ranjith
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
| | - A Kiran Kumar
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
- CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Dispensary, Hyderabad 500007, India
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Bhatt A, Arora P, Prajapati SK. Occurrence, fates and potential treatment approaches for removal of viruses from wastewater: A review with emphasis on SARS-CoV-2. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2020; 8:104429. [PMID: 32895629 PMCID: PMC7467108 DOI: 10.1016/j.jece.2020.104429] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 05/03/2023]
Abstract
The world is combating the emergence of Coronavirus disease 2019 (COVID-19) caused by novel coronavirus; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Further, due to the presence of SARS-CoV-2 in sewage and stool samples, its transmission through water routes cannot be neglected. Thus, the efficient treatment of wastewater is a matter of utmost importance. The conventional wastewater treatment processes demonstrate a wide variability in absolute removal of viruses from wastewater, thereby posing a severe threat to human health and environment. The fate of SARS-CoV-2 in the wastewater treatment plants and its removal during various treatment stages remains unexplored and demands immediate attention; particularly, where treated effluent is utilised as reclaimed water. Consequently, understanding the prevalence of pathogenic viruses in untreated/treated waters and their removal techniques has become the topical issue of the scientific community. The key objective of the present study is to provide an insight into the distribution of viruses in wastewater, as well as the prevalence of SARS-CoV-2, and its possible transmission by the faecal-oral route. The review also gives a detailed account of the major waterborne and non-waterborne viruses, and environmental factors governing the survival of viruses. Furthermore, a comprehensive description of the potential methods (physical, chemical, and biological) for removal of viruses from wastewater has been presented. The present study also intends to analyse the research trends in microalgae-mediated virus removal and, inactivation. The review also addresses the UN SDG 'Clean Water and Sanitation' as it is aimed at providing pathogenically safe water for recycling purposes.
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Key Words
- ASP, Activated Sludge Process
- COVID-19
- COVID-19, Coronavirus Disease 2019
- DUV-LED, Deep Ultraviolet Light-Emitting Diode
- E.coli, Escherichia coli
- EPS, Exopolysaccharide
- LRV, Log Reduction Value
- MBR, Membrane Bioreactor
- MERS-CoV, Middle East Respiratory Syndrome Coronavirus
- MLSS, Mixed Liquor Suspended Solids
- Microalgaee
- PMR, Photocatalytic Membrane Reactor
- Phycoremediationn
- RH, Relative Humidity
- SARS-CoV, Severe Acute Respiratory Syndrome Coronavirus
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2
- SBBGR, Sequencing Batch Biofilter Granular Reactor
- SEM, Scanning Electron Microscopy
- SSF, Slow Sand Filtration
- UASB, Upflow Anaerobic Sludge Blanket
- UN SDG, United Nations Sustainable Development Goal
- UV, Ultraviolet
- WHO, World Health Organisation
- WWTP, Wastewater Treatment Plant
- Waterbornee
- dsDNA, Double stranded Deoxyribonucleic Acid
- dsRNA, Double stranded Ribonucleic acid
- ssRNA, Single stranded Ribonucleic Acid
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Affiliation(s)
- Ankita Bhatt
- Environment and Biofuel Research Lab (EBRL), Hydro and Renewable Energy Department, Indian Institute of Technology (IIT) Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pratham Arora
- Hydro and Renewable Energy Department, Indian Institute of Technology (IIT) Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Sanjeev Kumar Prajapati
- Environment and Biofuel Research Lab (EBRL), Hydro and Renewable Energy Department, Indian Institute of Technology (IIT) Roorkee, Roorkee, Uttarakhand, 247667, India
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Reta DH, Tessema TS, Ashenef AS, Desta AF, Labisso WL, Gizaw ST, Abay SM, Melka DS, Reta FA. Molecular and Immunological Diagnostic Techniques of Medical Viruses. Int J Microbiol 2020; 2020:8832728. [PMID: 32908530 PMCID: PMC7474384 DOI: 10.1155/2020/8832728] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/24/2020] [Accepted: 08/15/2020] [Indexed: 01/12/2023] Open
Abstract
Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.
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Affiliation(s)
- Daniel Hussien Reta
- School of Veterinary Medicine, Wollo University, Dessie, Ethiopia
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Adey Feleke Desta
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wajana Lako Labisso
- Department of Pathology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Mequanente Abay
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Seifu Melka
- Department of Medical Biochemistry, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fisseha Alemu Reta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Jigjiga University, Jigjiga, Ethiopia
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Aguado-García Y, Taboada B, Morán P, Rivera-Gutiérrez X, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximénez C, Arias CF. Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life. Sci Rep 2020; 10:13595. [PMID: 32788688 PMCID: PMC7423923 DOI: 10.1038/s41598-020-70684-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/29/2020] [Indexed: 11/09/2022] Open
Abstract
Plant viruses have been reported to be common in the gut of human adults, presumably as result of food ingestion. In this work, we report that plant viruses can also be found frequently in the gut and oropharynx of children during their first year of life, even when they are exclusively breast-fed. Fecal and oropharynx samples were collected monthly, from birth to 1 year of age, from three apparently healthy children in a semi-rural community and analyzed by next generation sequencing. In 100% of the fecal samples and 65% of the oropharynx samples at least one plant virus was identified. Tobamoviruses in the Virgaviridae family were by far the most frequently detected, with tropical soda apple mosaic virus, pepper mild mottle virus, and opuntia tobamovirus 2 being the most common species. Seventeen complete virus genomes could be assembled, and phylogenetic analyses showed a large diversity of virus strains circulating in the population. These results suggest that children are continuously exposed to an extensive and highly diverse collection of tobamoviruses. Whether the common presence of plant viruses at an early age influences the infant's immune system, either directly or through interaction with other members of the microbiota, remains to be investigated.
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Affiliation(s)
- Yarenci Aguado-García
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Xaira Rivera-Gutiérrez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06726, Cuauhtémoc, Ciudad de México, Mexico.
| | - Cecilia Ximénez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico.
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico.
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10
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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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11
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Abstract
The immense global burden of infectious disease outbreaks and the need to establish prediction and prevention systems have been recognized by the World Health Organization (WHO), the National Institutes of Health (NIH), the United States Agency of International Development (USAID), the Bill and Melinda Gates Foundation, and the international scientific community. Despite multiple efforts, this infectious burden is still increasing. For example, it has been reported that between 1.5 and 12 million people die each year from waterborne diseases and diarrheal diseases are listed within the top 15 leading causes of death worldwide. Rapid population growth, climate change, natural disasters, immigration, globalization, and the corresponding sanitation and waste management challenges are expected to intensify the problem in the years to come.
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12
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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Guerrero-Latorre L, Romero B, Bonifaz E, Timoneda N, Rusiñol M, Girones R, Rios-Touma B. Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1334-1343. [PMID: 30248857 DOI: 10.1016/j.scitotenv.2018.07.213] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of many enteric pathogens through direct consumption, agricultural and recreational use. Among the different pathogens present in urban discharges, viruses play an important role on disease, being causes of gastroenteritis, hepatitis, meningitis, respiratory infections, among others. This study analyzes the presence of viruses in highly impacted surface waters of urban rivers using next-generation sequencing techniques. Three representative locations of urban rivers, receiving the main discharges from Quito sewerage system, were selected. Water samples of 500 mL were concentrated by skimmed-milk flocculation method and the viral nucleic acid was extracted and processed for high throughput sequencing using Illumina MiSeq. The results yielded very relevant data of circulating viruses in the capital of Ecuador. A total of 29 viral families were obtained, of which 26 species were associated with infections in humans. Among the 26 species identified, several were related to gastroenteritis: Human Mastadenovirus F, Bufavirus, Sapporovirus, Norwalk virus and Mamastrovirus 1. Also detected were: Gammapapillomavirus associated with skin infections, Polyomavirus 1 related to cases of kidney damage, Parechovirus A described as cause of neonatal sepsis with neurological affectations and Hepatovirus A, the etiologic agent of Hepatitis A. Other emergent viruses identified, of which its pathogenicity remains to be fully clarified, were: Bocavirus, Circovirus, Aichi Virus and Cosavirus. The wide diversity of species detected through metagenomics gives us key information about the public health risks present in the urban rivers of Quito. In addition, this study describes for the first time the presence of important infectious agents not previously reported in Ecuador and with very little reports in Latin America.
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Affiliation(s)
- Laura Guerrero-Latorre
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Brigette Romero
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Edison Bonifaz
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Natalia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Blanca Rios-Touma
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería Ambiental, Universidad de las Américas, Quito, Ecuador.
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15
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Nybond S, Réu P, Rhedin S, Svedberg G, Alfvén T, Gantelius J, Svahn HA. Adenoviral detection by recombinase polymerase amplification and vertical flow paper microarray. Anal Bioanal Chem 2018; 411:813-822. [PMID: 30498984 PMCID: PMC6338793 DOI: 10.1007/s00216-018-1503-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/30/2018] [Accepted: 11/16/2018] [Indexed: 12/15/2022]
Abstract
Respiratory viral infections often mimic the symptoms of infections caused by bacteria; however, restricted and targeted administration of antibiotics is needed to combat growing antimicrobial resistance. This is particularly relevant in low-income settings. In this work, we describe the use of isothermal amplification of viral DNA at 37 °C coupled to a paper-based vertical flow microarray (VFM) setup that utilizes a colorimetric detection of amplicons using functionalized gold nanoparticles. Two oligonucleotide probes, one in-house designed and one known adenoviral probe were tested and validated for microarray detection down to 50 nM using a synthetic target template. Furthermore, primers were shown to function in a recombinase polymerase amplification reaction using both synthetic template and viral DNA. As a proof-of-concept, we demonstrate adenoviral detection with four different adenoviral species associated with respiratory infections using the paper-based VFM format. The presented assay was validated with selected adenoviral species using the in-house probe, enabling detection at 1 ng of starting material with intra- and inter-assay %CV of ≤ 9% and ≤ 13%. Finally, we validate our overall method using clinical samples. Based on the results, the combination of recombinase polymerase amplification, paper microarray analysis, and nanoparticle-based colorimetric detection could thus be a useful strategy towards rapid and affordable multiplexed viral diagnostics.
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Affiliation(s)
- Susanna Nybond
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Samuel Rhedin
- Department of Medicine, Solna, Unit of Infectious Diseases, Karolinska Institutet and Karolinska University Hospital, 17176, Stockholm, Sweden
| | - Gustav Svedberg
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Tobias Alfvén
- Sachs' Children & Youth Hospital, South General Hospital, 11883, Stockholm, Sweden.,Department of Public Health Sciences, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Jesper Gantelius
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden.,Department of Public Health Sciences, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Helene Andersson Svahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden.
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16
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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Abstract
Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.
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Du Y, Chen B. Detection approaches for multidrug resistance genes of leukemia. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:1255-1261. [PMID: 28458519 PMCID: PMC5402920 DOI: 10.2147/dddt.s134529] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Leukemia is a clonal malignant hematopoietic stem cell disease. It is the sixth most lethal cancer and accounts for 4% of all cancers. The main form of treatment for leukemia is chemotherapy. While some cancer types with a higher incidence than leukemia, such as lung and gastric cancer, have shown a sharp decline in mortality rates in recent years, leukemia has not followed this trend. Drug resistance is often regarded as the main clinical obstacle to effective chemotherapy in patients diagnosed with leukemia. Many resistance mechanisms have now been identified, and multidrug resistance (MDR) is considered the most important and prevalent mechanism involved in the failure of chemotherapy in leukemia. In order to reverse MDR and improve leukemia prognosis, effective detection methods are needed to identify drug resistance genes at initial diagnosis. This article provides a comprehensive overview of published approaches for the detection of MDR in leukemia. Identification of relevant MDR genes and methods for early detection of these genes will be needed in order to treat leukemia more effectively.
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Affiliation(s)
- Ying Du
- Department of Hematology and Oncology (Key Department of Jiangsu Medicine), School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China
| | - Baoan Chen
- Department of Hematology and Oncology (Key Department of Jiangsu Medicine), School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China
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19
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Pérot P, Lecuit M, Eloit M. Astrovirus Diagnostics. Viruses 2017; 9:v9010010. [PMID: 28085120 PMCID: PMC5294979 DOI: 10.3390/v9010010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 01/25/2023] Open
Abstract
Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
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Affiliation(s)
- Philippe Pérot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Institut Pasteur, Centre d'innovation et de Recherche Technologique (Citech), 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Paris Descartes University, Sorbonne Paris Cité, 75005, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, 75015 Paris, France.
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France.
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Abstract
It was widely believed in the late 1960s that infectious diseases had been conquered by vaccines and antibiotics and humans were no longer under threat by microbial pathogens. Yet, since that time more than 60 pathogens have been discovered that can cause serious emerging infectious diseases. Molecular methods have played critical roles in the discovery, monitoring, and clinical diagnostics of emerging pathogens. In this chapter, we present well-recognized emerging pathogens. We provide examples of the utility of molecular assays in research and clinical care of emerging infectious diseases. We also discuss some theoretical and practical limitations of molecular tests and the future prospects of expanding molecular diagnostics for emerging pathogens based on new advances of knowledge and technologies.
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21
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DNA Microarray Detection of 18 Important Human Blood Protozoan Species. PLoS Negl Trop Dis 2016; 10:e0005160. [PMID: 27911895 PMCID: PMC5135439 DOI: 10.1371/journal.pntd.0005160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/03/2016] [Indexed: 01/22/2023] Open
Abstract
Background Accurate detection of blood protozoa from clinical samples is important for diagnosis, treatment and control of related diseases. In this preliminary study, a novel DNA microarray system was assessed for the detection of Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia in humans, animals, and vectors, in comparison with microscopy and PCR data. Developing a rapid, simple, and convenient detection method for protozoan detection is an urgent need. Methodology/Principal Findings The microarray assay simultaneously identified 18 species of common blood protozoa based on the differences in respective target genes. A total of 20 specific primer pairs and 107 microarray probes were selected according to conserved regions which were designed to identify 18 species in 5 blood protozoan genera. The positive detection rate of the microarray assay was 91.78% (402/438). Sensitivity and specificity for blood protozoan detection ranged from 82.4% (95%CI: 65.9% ~ 98.8%) to 100.0% and 95.1% (95%CI: 93.2% ~ 97.0%) to 100.0%, respectively. Positive predictive value (PPV) and negative predictive value (NPV) ranged from 20.0% (95%CI: 2.5% ~ 37.5%) to 100.0% and 96.8% (95%CI: 95.0% ~ 98.6%) to 100.0%, respectively. Youden index varied from 0.82 to 0.98. The detection limit of the DNA microarrays ranged from 200 to 500 copies/reaction, similar to PCR findings. The concordance rate between microarray data and DNA sequencing results was 100%. Conclusions/Significance Overall, the newly developed microarray platform provides a convenient, highly accurate, and reliable clinical assay for the determination of blood protozoan species. More than 1 billion people are infected with blood protozoan diseases worldwide. The most common blood protozoa in humans, animals, and vectors include Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia. Due to similar morphology among different blood protozoan species, misdiagnosis always occurs. Most molecular techniques are only carried out in laboratories, with a small number of samples detected simultaneously. Meanwhile, common detection methods may not be convenient for field investigation of large amounts of samples. In order to better manage blood protozoan infection, proper tools are required for the monitoring of these pathogens. Here, a comprehensive and sensitive DNA microarray was developed and tested, which allowed the parallel detection of 18 blood protozoan species.
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Narrowing of the Diagnostic Gap of Acute Gastroenteritis in Children 0-6 Years of Age Using a Combination of Classical and Molecular Techniques, Delivers Challenges in Syndromic Approach Diagnostics. Pediatr Infect Dis J 2016; 35:e262-70. [PMID: 27276177 PMCID: PMC4987234 DOI: 10.1097/inf.0000000000001208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Twenty-five percent to 50% of acute gastroenteritis (AGE) cases remain etiologically undiagnosed. Our main aim was to determine the most appropriate list of enteric pathogens to be included in the daily diagnostics scheme of AGE, ensuring the lowest possible diagnostic gap. METHODS Two hundred ninety seven children ≤6 years of age, admitted to hospital in Slovenia, October 2011 to October 2012, with AGE, and 88 ≤6 years old healthy children were included in the study. A broad spectrum of enteric pathogens was targeted with molecular methods, including 8 viruses, 6 bacteria and 2 parasites. RESULTS At least one enteric pathogen was detected in 91.2% of cases with AGE and 27.3% of controls. Viruses were the most prevalent (82.5% and 15.9%), followed by bacteria (27.3% and 10.2%) and parasites (3.0% and 1.1%) in cases and controls, respectively. A high proportion (41.8%) of mixed infections was observed in the cases. For cases with undetermined etiology (8.8%), stool samples were analyzed with next generation sequencing, and a potential viral pathogen was detected in 17 additional samples (5.8%). CONCLUSIONS Our study suggests that tests for rotaviruses, noroviruses genogroup II, adenoviruses 40/41, astroviruses, Campylobacter spp. and Salmonella sp. should be included in the initial diagnostic algorithm, which revealed the etiology in 83.5% of children tested. The use of molecular methods in diagnostics of gastroenteritis is preferable because of their high sensitivity, specificity, fast performance and the possibility of establishing the concentration of the target. The latter may be valuable for assessing the clinical significance of the detected enteric, particularly viral pathogens.
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23
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Chen H, Hu Y. Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses. Open Microbiol J 2016; 10:78-89. [PMID: 27335620 PMCID: PMC4899541 DOI: 10.2174/1874285801610010078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 02/04/2023] Open
Abstract
Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses.
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Affiliation(s)
- Haifeng Chen
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Yuan Hu
- Northeast Region Laboratory, Office of Regulatory Affairs, U.S. Food and Drug Administration, Jamaica, NY, USA
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Yang F, Dong B, Nie K, Shi H, Wu Y, Wang H, Liu Z. Light-Directed Synthesis of High-Density Peptide Nucleic Acid Microarrays. ACS COMBINATORIAL SCIENCE 2015; 17:608-14. [PMID: 26339951 DOI: 10.1021/acscombsci.5b00074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptide nucleic acids (PNAs) are a class of nucleic acid mimics that can bind to the complementary DNA or RNA with high specificity and sensitivity. PNA-based microarrays have distinct characteristics and have improved performance in many aspects compared to DNA microarrays. A new set of PNA monomers has been synthesized and used as the building blocks for the preparation of high density PNA microarrays. These monomers have their backbones protected by the photolabile group 2-(2-nitrophenyl)propyloxy carbonyl (NPPOC), and their exocyclic amino groups protected by amide carbonyl groups. A light-directed synthesis system was designed and applied to the in situ synthesis of a PNA microarray with a density of over 10,000 probes per square centimeter. This PNA microarray was able to detect single and multiple base-mismatches correctly with a high discrimination ratio.
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Affiliation(s)
- Feipeng Yang
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Bo Dong
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Kaixuan Nie
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Huanhuan Shi
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Yanqi Wu
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Hongyin Wang
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
| | - Zhengchun Liu
- Department
of Biomedical
Engineering, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
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