| Literature DB >> 33235400 |
Nikiforos Alygizakis1, Athina N Markou1, Nikolaos I Rousis1, Aikaterini Galani1, Margaritis Avgeris2, Panagiotis G Adamopoulos3, Andreas Scorilas3, Evi S Lianidou1, Dimitrios Paraskevis4, Soritios Tsiodras5, Athanassios Tsakris6, Meletios-Athanasios Dimopoulos7, Nikolaos S Thomaidis1.
Abstract
In March 2020 the World Health Organization announced a pandemic outbreak. Severe acute respiratory syndrome coronavirus 2 (Entities:
Keywords: COVID-19 pandemic; RT-qPCR; concentration; influent wastewater; isolation; molecular methods detection; sampling; symptomatic and asymptomatic; temperature storage; wastewater-based epidemiology
Year: 2020 PMID: 33235400 PMCID: PMC7677696 DOI: 10.1016/j.trac.2020.116125
Source DB: PubMed Journal: Trends Analyt Chem ISSN: 0165-9936 Impact factor: 12.296
Reviewed studies of the five steps of analysis.
| Sampling | Analysis Volume | Storage conditions | Concentration | Isolation | Detection | External Control | Recovery (%) | Cq | Ref |
|---|---|---|---|---|---|---|---|---|---|
| 100–200 mL | 4°C for 24 h | Adsorption-extraction (pH = 4; neutral pH; 25 mM MgCl2) Centrifugal filter (Amicon ultra-15 (30 K); Centricon Plus-70) Polyethylene glycol (PEG 8000) precipitation Ultracentrifugation | RNeasy PowerMicrobiome Kit (slightly modified) | TaqMan-based RT-qPCR | Oncorhynchus keta (PCR inhibitors) | NA | 19-120 copies/L | [ | |
| Cq: 37.5–39 | |||||||||
| 50 mL | 4°C | Electronegative membranes Ultrafiltration | Combination of two kits (RNeasy PowerWater Kit and RNeasy PowerMicrobiome Kit) | RT-qPCR; Target sequencing (Illumina and Sanger) | Murine hepatitis virus (Recovery) | 26.7–65.7 | NA | [ | |
| Oncorhynchus keta (PCR inhibitors) | |||||||||
| Weekly pooled 24 h and grab | 125 mL (Innovaprep) | Immediately concentrated | InnovaPrep Concentrating Pipette Select Electronegative filtration | Armored RNA Quant (protocol B 2.0.1 with modifications) | Reverse transcription droplet digital PCR (RT-ddPCR) | Bovine coronavirus (BCoV) (Recovery) | 45–73 (no conc, BCoV) 62–88 (no conc, BRSV) 3.1–7.6 (Innovaprep, BCoV) 4.6–10.6 ((Innovaprep, BRSV) 2.0–7.6 (electronegative filtration, BCoV) 2.8–10.4 (electronegative filtration, BRSV) | 102-105 copies/L | [ |
| Bovine respiratory syncytial virus (BRSV) (Recovery) | |||||||||
| Hep G Armored | |||||||||
| RNA (PCR inhibitors) | |||||||||
| 200–5000 mL | Immediately analyzed | Electronegative membrane-vortex Filtration with mixed cellulose-ester membrane | QIAamp Viral RNA Mini Kit and RNeasy PowerWater Kit | RT-qPCR, Nested PCR and Direct nucleotide sequencing using the Sanger method | Coliphage MS2 | 46.4–96.8 (electronegative membrane-vortex) 4.8–12.2 (adsorption direct RNA extraction methods) | EMV method: 1.8 × 105–1.0 × 108 copies/L | [ | |
| Adsorption-direct RNA extraction method: <1.0 × 10–1.3 × 106 copies/L | |||||||||
| 50 mL | 19 days at 4°C and others Immediately analyzed | PEG 9000 | NucleoSpin® RNA Virus | TaqPath™ Covid-19 RT-PCR Kit | Coliphage MS2 | 57 (geometric mean) | 32.45-39.56 | [ | |
| 5.6 × 10 - 3.5 × 102 copies/L | |||||||||
| 250 mL | −20°C | PEG-dextran method | NucliSENS miniMAG semi-automated extraction system | Three different nested RT-PCR assays, one real-time qPCR assay and direct nucleotide sequencing using the Sanger method | Alphacoronavirus HCoV 229E | 1.34-2.74 | 102 -5.6 × 104 copies/L | [ | |
| 250 mL | 4°C for 24 h | Centricon® Plus-70 centrifugal ultrafilters | RNeasy PowerMicrobiome Kit | RT-qPCR | F-specific RNA phages Dengue virus | 8.1–52.7 (Dengue virus internal control) 23–123 (culturable F-specific RNA phages) | 2.6-2.2 × 103 copies/L | [ | |
| Cq: 29.9–39.2 | |||||||||
| 24 h composite (time or flow dependent) | 500 mL | 5 ± 3°C until analysis within 48 h | Direct flocculation | NucliSENS® miniMAG® system | EliGene COVID19 Basic A RT kit | Transmissible gastroenteritis coronavirus (TGEV) | 22.5–48.6 | Cq: 34-40 | [ |
| 200 mL | 4°C for almost two months | Aluminum-driven flocculation | Centrifugation at 1900×g for 30 min | RT-qPCR | Mengovirus vMC0 | 2.56-18.9 | Cq: 33.87–37.84 | [ | |
| 1.6–9.7 × 105 copies/L | |||||||||
| 200 mL | 4°C and concentrated within 24 h | Aluminum hydroxide adsorption-precipitation protocol | Nucleo-Spin RNA virus kit | TaqMan real-time RT-PCR | Mengovirus vMC0 | 8.9–13.1 | 6.3 × 104 -6.3 × 105 copies/L | [ | |
| Cq: 34.68–40 | |||||||||
| 50 mL | Not available | No concentration performed | QIAMP Viral RNA mini kit | RT-qPCR, whole genome sequencing and Ion Torrent PGM | Internal plasmidic control included in the 2019-nCoV real-time RT-PCR kit panel | >90 | Cq: ≤40 | [ | |
| 250 mL | −80°C until analysis and within 6 h | Ultrafiltration Centricon® Plus-70 centrifugal filter Electronegative membrane | ZR Viral RNA Kit | RT-qPCR | Pseudomonas bacteriophage Φ6 | 56 (Centricon Filter) 54 (Electronegative mebrane) | 3.1–7.5 × 103 copies/L | [ | |
| 45 mL | −18°C | Ultrafiltration | NucleoSpin RNA Virus kit | RT-qPCR and Sanger sequencing analysis | NA | NA | 30-200 gene equivalents/L | [ |
Target genes, primers and probes commonly used for analysis of SARS-CoV-2 in wastewater by PCR.
| Target | Primers and probes Sequences (5-3) | References |
|---|---|---|
| N- Sarbeco protein | F-CACATTGGCACCCGCAATC | [ |
| R-GAGGAACGAGAAGAGGCTTG | ||
| P-FAM-ACTTCCTCAAGGAACAACATTGCCA-BHQ1 | ||
| THREE regions of nucleocapsid (N) gene (CDC) | 2019-nCoV_N1–F: GAC CCC AAA ATC AGC GAA AT | [ |
| 2019-nCoV_N1-R: TCT GGT TAC TGC CAG TTG AAT CTG | ||
| 2019-nCoV_N1–P: FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1 | ||
| 2019-nCoV_N2 Forward Primer TTA CAA ACA TTG GCC GCA AA | ||
| 2019-nCoV_N2 Reverse Primer GCG CGA CAT TCC GAA GAA | ||
| 2019-nCoV_N2 Probe FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1 | ||
| 2019-nCoV_Forward Primer: AGA TTT GGA CCT GCG AGC G | ||
| 2019-nCoV_Reverse Primer: GAG CGG CTG TCT CCA CAA GT | ||
| 2019-nCoV_F Probe: FAM – TTC TGA CCT GAA GGC TCT GCG CG – BHQ-1 | ||
| ORF1ab | FW1 GTGCTAAACCACCGCCTG | [ |
| REV1 CAGATCATGGTTGCTTTGTAGGT | ||
| FW2 CGCCTGGAGATCAATTTAAACAC | ||
| REV2 ACCTGTAAAACCCCATTGTTGA | ||
| RdRP | RdRP_SARSr-F2 GTGARATGGTCATGTGTGGCGG | |
| RdRP_SARSr-R2 CARATGTTAAASACACTATTAGCATA | ||
| RdRP_SARSr-P2 FAM-CAGGTGGAACCTCATCAGGAGATGCBHQ1 | ||
| S | WuhanCoV-spk1-F: TTGGCAAAATTCAAGACTCACTTT | |
| WuhanCoV-spk2-R: TGTGGTTCATAAAAATTCCTTTGTG | ||
| Envelope protein (E) gene | E_Sarbeco_F: ACAGGTACGTTAATAGTTAATAGCGT | [ |
| E_Sarbeco_R: ATATTGCAGCAGTACGCACACA | ||
| E_Sarbeco_PROBE: FAM-ACACTAGCCATCCTTACTGCGCTTCG-BBQ |