Table 1.
Summary of virus analyses by approach to pathogen identification (n/a - not available).
| Virus | Sample source | Analytical Method | No. of samples | Reference |
|---|---|---|---|---|
| HBV, HCV | serum | PCR | 730 | [92] |
| Enteric viruses | stool samples | monoplex or multiplex RT-PCR | 227 | [93] |
| HRSV | nasopharyngeal and oropharyngeal swab | real-time RT-PCR | 334 | [94] |
| DENV, ZIKV | serum | RT-qPCR | 46 | [95] |
| Respiratory viruses | throat swabs and sputum samples | RT-qPCR | 408 | [96] |
| Respiratory viruses | nasopharyngeal aspirates, nasopharyngeal and oral pharyngeal swab | rRT-PCR | 8173 | [97] |
| SARS-CoV-2 | sputum, nose and throat swabs | real-time RT-PCR | 297 | [98] |
| LASV | serum, lung and spleen tissue, blood | RT-qPCR | 82 | [99] |
| Respiratory viruses | respiratory tract swabs and aspirates | MALDI-TOF MS | 58 | [89] |
| HR HPV | uterine cervix cytology | MALDI-TOF MS | 356 | [90] |
| Poliovirus | cerebrospinal fluid, throat swab, stool samples | MALDI-TOF MS | 5 | [88] |
| SARS-CoV-2 | nasal swab | MALDI-MS + machine learning analysis | 362 | [39] |
| Enterovirus EV71 | serum | LDI-MS with cellulose acetate membranę and Ag or Au NPs | n/a | [100] |
| HIV, HCV |
serum |
SELDI MS |
151 |
[91] |
| Bacteriophages | ||||
| Triaviruses, Phietaviruses, Biseptimaviruses, Kayviruses, Twortvirus, P68virus | reference and isolates | MALDI-TOF MS | n/a | [101] |
| vB-SdyS-ISF003 | wastewater and sewage | PCR and sequencing DNA | n/a | [102] |
| Kayvirus K1/420 | medicamente isolate | CZE, MALDI-TOF MS | n/a | [85] |
| Staphylococcal phages (K1/420, 11, P68) | physiological saline solution, human serum | MALDI-TOF MS | n/a | [86] |
| Staphylococcal phages (K1/420, 11, P68, 3A, 77) | blood, serum | MALDI-TOF MS | n/a | [56] |