Table 7.
Enteric virus recoveries from sediment.
| Target virus | Sediment | Elution | Concentration | Quantitation | Mean recovery or range | References |
|---|---|---|---|---|---|---|
| A INDIRECT EXTRACTION: VIRUS ELUTION—CONCENTRATION | ||||||
| Poliovirus 1 | Marine 500 g | 0.25 M glycine, 0.05 M EDTA, pH 11 | 0.06 M AlCl3, pH 3.5 | Culturing | 50% | Gerba et al., 1977b |
| Marine 10 g | 6% beef extract, pH 9 | 8% PEG6000 | Culturing | 6.3–55.8% | Lewis et al., 1985 | |
| Marine 10 g | 4 M urea, 0.05 M lysine, pH 9 | 0.005 M AlCl3, pH 7 | Culturing | 22% | Bitton et al., 1982 | |
| 3% beef extract | pH 3.5–4.5 | 8% | ||||
| 1% purified casein | pH 3.5–4.5 | 14% | ||||
| Estuarine, sewage contaminated 10 g | 0.25 M glycine | None | Culturing | 2.2–3.5% | Tsai et al., 1983 | |
| 0.5% skimmed milk | 0.5–2.7% | |||||
| 0.5% isoelectric casein | 58.8% | |||||
| 3–10% beef extract (paste) | 4.0–9.3% | |||||
| 3–10% beef extract (powder) | 32.7–40.0% | |||||
| 4% nutrient broth | 40–53% | |||||
| Estuarine 10–50 mL | 3% beef extract, 2 M NaNO3, pH 5.5 | 2 M (NH4)2SO4, 0.01 Cat-Floc T pH 3.5 | Culturing | 39–44% | Wait and Sobsey, 1983 | |
| 3% beef extract, 0.25 M glycine, pH 10.50.25 M glycine, 0.05 M EDTA, pH 11 | 0.06 M AlCl3, pH 3.5 | 9.7–18%0–0.1% | ||||
| Freshwater10 g | 6% beef extract, pH 9 | 8% PEG6000 | Culturing | 15.8–76.8% | Lewis et al., 1985 | |
| Freshwater4 types with different sand/silt / clay ratio | 4% nutrient broth, pH 7.5 | None | Culturing | 5.3–10.4% | Johnson et al., 1984 | |
| 4% nutrient broth, pH 9 | 2.0–32.5% | |||||
| 5% beef extract, pH 9 | 0.6–48.9% | |||||
| 0.5% isoelectric casein, pH9 | 0.3–65.3% | |||||
| 0.5% isoelectric casein, 1% crude lecithin, pH9 | 7.0–38.6% | |||||
| 0.5% isoelectric casein, 3% crude lecithin, pH9 | 1.0–25.4% | |||||
| 0.5% isoelectric casein, 1% semi-purified lecithin, pH9 | 0.3–47.9% | |||||
| 0.5% isoelectric casein, 3% semi-purified lecithin, pH9 | 2.6–75.1% | |||||
| 0.5% isoelectric casein, 1% egg lecithin, pH9 | 0.3–56.4% | |||||
| 0.5% isoelectric casein, 3% egg lecithin, pH9 | 0.6–102.6% | |||||
| Silty freshwater 5 g | 0.25 M glycine-NaOH, 0.05 M EDTA | 0.06 M AlCl3, pH 3.5 | qRT-PCR | 1.8% | Miura et al., 2011 | |
| 0.25 M glycine-NaOH, 0.05 M EDTA | 0.1 M MgCl2 | 5.4% | ||||
| 0.1% Laureth-12, 0.01 M Tris, 1 mM EDTA, 0.015% Antifoam Y-30, pH 7.2 | 0.1 M MgCl2 | 0.61% | ||||
| 0.25 M glycine-NaOH, 0.05 M EDTA | 16% PEG6000, 4.7% NaCl | 0% | ||||
| 0.1% Laureth-12, 0.01 M Tris, 1 mM EDTA, 0.015% Antifoam Y-30, pH 7.2 | 16% PEG6000, 4.7% NaCl | 0.18% | ||||
| Sandy freshwater10 g | 4 M urea, 0.05 M lysine, pH 9 | 0.005 M AlCl3, pH 7 | Culturing | 39% | Bitton et al., 1982 | |
| 3% beef extract, pH 9 | pH 3.5–4.5 | 51% | ||||
| 1% purified casein, 0.1% Tween 80 | pH 3.5–4.5 | 59% | ||||
| 1 M trychloroacetate, 1 M glycine | pH 3.5–4.5 | 23% | ||||
| Coxsachievirus B1 | Freshwater4 types with different sand/silt/ clay ratio | 0.5% isoelectric casein, 1% crude lecithin, pH9 | None | Culturing | 12.6–37.8% | Johnson et al., 1984 |
| 0.5% isoelectric casein, 3% crude lecithin, pH9 | 21.8–80.9% | |||||
| 0.5% isoelectric casein, 1% semi-purified lecithin, pH9 | 48.4–61.6% | |||||
| 0.5% isoelectric casein, 3% semi-purified lecithin, pH9 | 54.4–91.5% | |||||
| 0.5% isoelectric casein, 1% egg lecithin, pH9 | 38.6–69.0% | |||||
| 0.5% isoelectric casein, 3% egg lecithin, pH9 | 41.9–73.4% | |||||
| Coxsachievirus B3 | Estuarine, sewage contaminated 10 g | 0.25 M glycine | None | Culturing | 4.3–7.7% | Tsai et al., 1983 |
| 0.5% skim milk | 8.3–9.2% | |||||
| 0.5% isoelectric casein | 18.9% | |||||
| 3–10% beef extract (powder) | 13.0–29.0% | |||||
| 4% nutrient broth | 15.4–25.9% | |||||
| Echovirus 1 | Estuarine 10–50 mL | 3% beef extract, 2 M NaNO3, pH 5.5 | 2 M (NH4)2SO4, 0.01 Cat-Floc T | Culturing | 16–43% | Wait and Sobsey, 1983 |
| 3% beef extract, 0.25 M glycine, pH 10.5 | pH 3.5 | 2.6–4.4% | ||||
| 0.25 M glycine, 0.05 M EDTA, pH 11 | 0.06 M AlCl3, pH 3.5 | 0.1–0.5% | ||||
| Echovirus 11 | Freshwater4 types with different sand/silt/ clay ratio | 0.5% isoelectric casein, 1% crude lecithin, pH9 | None | Culturing | 5.6–42.4% | Johnson et al., 1984 |
| 0.5% isoelectric casein, 3% crude lecithin, pH9 | 33.2–94.7% | |||||
| 0.5% isoelectric casein, 1% semi-purified lecithin, pH9 | 31.6–81.9% | |||||
| 0.5% isoelectric casein, 3% semi-purified lecithin, pH9 | 56.8–78.5% | |||||
| 0.5% isoelectric casein, 1% egg lecithin, pH9 | 66.7–138.4% | |||||
| 0.5% isoelectric casein, 3% egg lecithin, pH9 | 43.3–50.4% | |||||
| Hepatitis A virus | Freshwater | 3% beef extract, 2 M NaNO3, pH 5.5 | 15% PEG6000 | Culturing | 70% | Lewis and Metcalf, 1988 |
| Simian rotavirus 11 | Estuarine10–50 mL | 3% beef extract, 2 M NaNO3, pH 5.5 | 2 M (NH4)2SO4, 0.01 Cat-Floc T | Culturing | 23% | Wait and Sobsey, 1983 |
| 3% beef extract, 0.25 M glycine, pH 10.5 | pH 3.5 | 0% | ||||
| 0.25 M glycine, 0.05 M EDTA, pH 11 | 0.06 M AlCl3, pH 3.5 | 0% | ||||
| Rotavirus WA | Freshwater | 3% beef extract, 2 M NaNO3, pH 5.5 | 15% PEG6000 | Culturing | 70% | Lewis and Metcalf, 1988 |
| Target virus | Sediment | Lysis | Extraction/concentration | Purification | Mean recovery or range | References |
| B DIRECT EXTRACTION OF VIRAL NUCLEIC ACIDS FOLLOWED BY QRT-PCR | ||||||
| Poliovirus 1 | Silty freshwater 5 g | 0.5 N Tris (pH 8), 0.1 M NaCl, 2% SDS, 8 mg skim milk/g sediment | Phenol:chloroform:isoamyl alcohol + isopropanol precipitation | DEAE cellulose column | 0.09% | Miura et al., 2011 |
| 0.5N Tris (pH 8), 0.1 M NaCl, 2% SDS, 8 mg skim milk/g sediment | Phenol:chloroform:isoamyl alcohol + isopropanol precipitation | Oligo(dT) labeled magnetic beads | 0.77% | |||
| 0.1 M EDTA, 0.5 N Tris (pH 8), 0.1 M NaCl, 2% SDS, 8 mg skim milk/g sediment | Phenol:chloroform:isoamyl alcohol + isopropanol precipitation | Oligo(dT) labeled magnetic beads | 11% | |||
| TRIzol reagent | Centrifugation | Oligo(dT) labeled magnetic beads | 0.10% | |||