Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring
Abstract
:1. Introduction
2. Enteric Viruses in Water and Their Impact on Public Health
Family | Genus | Virus Name | Genome | Size (Nm) | Types | Disease | Ref. |
---|---|---|---|---|---|---|---|
Picorna-viridae | Hepatovirus | Hepatitis virus | +ssRNA | 27–32 | 3 types | Hepatitis | [22] |
Kobuvirus | Aichivirus | +ssRNA | 30 | 6 types | Gastroenteritis | [23] | |
Enterovirus | Poliovirus | dsDNA | 40 | 14 species | Paralysis, aseptic meningitis | [24] | |
Coxsackievirus | +ssRNA | 30 | Cox A1-23 and B1-6 | Myocarditis, aseptic meningitis, Bornholm disease and epidemic pleurodynia | [25] | ||
Echovirus | +ssRNA | 30 | 28 types | Fever, rash, respiratory and heart disease, aseptic meningitis | [26] | ||
Enterovirus | +ssRNA | 30 | 12 species | Gastroenteritis | [27] | ||
Parechovirus | HPeV | +ssRNA | 28 | 19 genotypes | Gastroenteritis, respiratory and CNS diseases, and sepsis | [28] | |
Cosavirus | HCoSV | +ssRNA | 30 | 5 species | Gastroenteritis non-polio AFP | [29] | |
Aphthovirus | FMDV | +ssRNA | 25 | 7 serotypes | Respiratory diseases | [23] | |
Adeno-viridae | Mastadenovirus | Adenovirus (AdV) | dsDNA | 70 | 60 types |
| [30] |
Parvo-viridae | Erythrovirus | Parvovirus | ssDNA | 22 | 3 genotypes | Gastroenteritis | [31] |
Bocavirus | Bocavirus | ssDNA | 20 | 4 genotypes | Respiratory diseases | [31,32] | |
Reoviridae | Rotavirus | Rotaviruses | dsRNA | 80 | 9 species | Gastroenteritis | [33] |
Hepeviridae | Hepevirus | Hepatitis E virus | +ssRNA | 27–34 | 4 genotypes | Infectious hepatitis | [34] |
Picobirna-viridae | Picobirnavirus | Picobirnavirus | dsRNA | 35 | Human and Rabbit Picobirna-virus | Respiratory diseases and gastroenteritis | [35] |
Astroviridae | Mamastrovirus | Astrovirus | +ssRNA | 35 | 8 serotypes | Gastroenteritis | [36] |
Bunya-viridae | Hantavirus | Hantavirus | −ssRNA | 120 | 4 genera | Hemorrhagic fever and cardiopulmonary syndrome | [37] |
Flavi-viridae | Flavivirus | TBEV | +ssRNA | 50 | 5 subtypes | Fever, meningitis and encephalitis | [38] |
Arena-viridae | Arenavirus | Arenavirus | −ssRNA | 40–200 | 4 genera | Aseptic meningitis and hemorrhagic fever | [39] |
Corona-viridae | Alphacorona-virus | HCoV-229E | +ssRNA | 120–140 | 7 subtypes |
| [11,40] |
HCoV-NL63 | |||||||
Betacoronavirus | HCoV-OC43 | ||||||
HCoV-HKU1 | |||||||
MERS-CoV | |||||||
SARS-CoV | |||||||
SARS-CoV-2 | |||||||
Orthomyxo-viridae | Influenza A virus | AIVs (HSN1 and H9N2) | −ssRNA | 100 | Many subtypes |
| [41] |
Paramyxo-viridae | Henipavirus | Nipah virus | −ssRNA | 40 | 2 genotypes (M and B) |
| [42] |
Calici-viridae | Norovirus | Norovirus | +ssRNA | 27–40 | 9 genotypes | Gastroenteritis | [43,44] |
Sapovirus | Sapovirus | +ssRNA | 27–40 | 18 genotypes | Gastroenteritis |
3. Waterborne Viruses Concentration Methods
3.1. Adsorption/Elution Method
3.2. Ultrafiltration
3.3. Ultracentrifugation
3.4. Hydro-Extraction Method
3.5. Freeze-Drying Technique
3.6. Antibody-Capture Technique
4. Conventional Viral Detection Tools for Aquatic Biomonitoring
4.1. Electron Microscopy
4.2. Cell Culture Systems
4.3. Immunological Methods
4.4. Biosensors
5. Viral Genetic Tools for Aquatic Biomonitoring
5.1. Polymerase Chain Reaction (PCR), Sequencing and Phylogenetic Analysis
5.2. Isothermal Nucleic Acid Amplification-Based Assays
5.3. DNA Microarray Technology
5.4. Next Generation Sequencing (NGS) and Metagenomic Technology
5.5. ChIP-Seq Analysis
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Virus | Cell Line | Origin | Ref. |
---|---|---|---|
Avian influenza viruses | SPF-ECE | Specific pathogen-free embryonated chicken egg | [61] |
MDCK | Madin–Darby Canine Kidney cell | ||
Vero | African green monkey kidney cell | ||
Adenovirus | A549 | Human lung carcinoma cell | [62] |
PK-15 | Porcine kidney epithelial cell | ||
Astrovirus | HEK | Human embryo kidney | [63] |
Caco-2 | Human colorectal adenocarcinoma cell | ||
A549 | Human lung carcinoma cell | ||
Bocavirus | Caco-2 | Human colorectal adenocarcinoma cell | [64] |
HEK293 | Human embryonic kidney cell | [65] | |
HTEpC | Human trachea epithelial primary cell | [66] | |
Coxsackievirus | HeLa | Human cervical cancer cell | [67] |
Coronavirus | MRC-5 | Human fetal lung fibroblast cell | [68] |
Vero-E6 | African green monkey kidney cell | [69] | |
Enterovirus | RD | Human muscle tissue | [70] |
HEV | A549 | Human lung carcinoma cell | [71] |
HAV | Caco-2 | Human colorectal adenocarcinoma cell | Reviewed in [72] |
HepG2-N | Human hepatoma | ||
Huh-7 | Hepatocarcinoma cell | ||
MRC-5 | Human fetal lung fibroblast cell | ||
Vero | African green monkey kidney cell | ||
Norovirus | BJAB | Human B cell lines | [73] |
iPSC–derived IECs | Human induced pluripotent stem cell | [74] | |
Rotavirus | MA-104 | African green monkey epithelial cell | [75] |
HT-29 | Human colon carcinoma cell line | [76] | |
Caco-2 | Human colorectal adenocarcinoma cell | [77] | |
Reovirus | Vero | African green monkey | [78] |
Sapovirus | LLC-PK1 | Porcine kidney cell | [67] |
Technique | Principle | EVs to Detect | Ref. |
---|---|---|---|
Nucleic acid sequence-based amplification (NASBA) |
| Human adenovirus and echovirus | [58,99] |
Loop-mediated isothermal amplification (LAMP) |
| Noroviruses and swine acute diarrhea syndrome-coronavirus | [58,100,101] |
Single primer iso-thermal amplification (SPIA) |
| Human norovirus | [58,102] |
Recombinase polymerase amplification (RPA) |
| Human norovirus, avian influenza virus and bovine viral diarrhea virus (BVDV) | [58,103,104,105] |
Method | Advantages | Disadvantages | Ref. |
---|---|---|---|
Electron microscopy |
|
| [121] |
Cell culture |
|
| [16] |
Immunological methods (e.g., ELISA and latex agglutination technique) |
|
| [122] |
Polymerase chain reaction (PCR) |
|
| [16] |
Nested and semi-nested PCR |
|
| [89] |
Multiplex PCR |
|
| [123] |
Real-time PCR (rt-PCR or qPCR) |
|
| [16] |
ICC-PCR |
|
| [124] |
Digital PCR |
|
| [16,94] |
Isothermal nucleic acid amplification-based assays |
|
| [16] |
Biosensors |
|
| [125] |
Microarrays |
|
| [16] |
Metagenomics or next-generation sequencing (NGS) |
|
| [16] |
ChIP-Seq analysis |
|
| [126] |
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Mostafa-Hedeab, G.; Allayeh, A.K.; Elhady, H.A.; Eledrdery, A.Y.; Mraheil, M.A.; Mostafa, A. Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring. Int. J. Environ. Res. Public Health 2022, 19, 7707. https://doi.org/10.3390/ijerph19137707
Mostafa-Hedeab G, Allayeh AK, Elhady HA, Eledrdery AY, Mraheil MA, Mostafa A. Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring. International Journal of Environmental Research and Public Health. 2022; 19(13):7707. https://doi.org/10.3390/ijerph19137707
Chicago/Turabian StyleMostafa-Hedeab, Gomaa, Abdou Kamal Allayeh, Hany Abdelfattah Elhady, Abozer Y. Eledrdery, Mobarak Abu Mraheil, and Ahmed Mostafa. 2022. "Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring" International Journal of Environmental Research and Public Health 19, no. 13: 7707. https://doi.org/10.3390/ijerph19137707