Table 3.
Sample and Laboratory Methods characteristics.
| Authors, Year | sample type | Extractions | Diagnostic assay | Assay platform | Target pathogens |
|---|---|---|---|---|---|
| Kelly et al., 2015 [18] | NP swab | Not mentioned | real-time multiplex PCR and uniplex PCR assay | Not mentioned | Influenza viruses, Influenza A, Influenza B, PIV, PIV1, PIV2, PIV3, Human metapneumovirus, Adenovirus, Rhinovirus/enterovirus, Rhinovirus A, Rhinovirus B, Rhinovirus C, Rhinovirus other |
| Bigogo et al., 2013 [19] | NP/OP swabs | MagMax viral RNA kit and Kingfisher mL instrument (Life Technologies, New York, NY) | AgPath-ID One-step RT-PCR kit | Applied Biosystems, Foster City, CA) | RSV |
| Fuller et al., 2013 [20] | NP/OP swabs | QIAamp Viral RNA Minikit (Qiagen, Valencia, CA) | AgPath-ID One- Step RT-PCR Reagents | Applied Biosystems, Foster City, CA) | Adenovirus, RSV, Human metapneumovirus, Influenza, PIV |
| Bénet et al., 2015 [21] | nasal swabs and pleural effusions | Not mentioned | FTD respiratory pathogens 21 plus | Fast-track Diagnostics, Luxembourg |
S. pneumoniae, S. aureus H. influenza, Mycoplasma spp., Chlamydia spp., Human metapneumovirus, Coronavirus NL63, Coronavirus 229E, Coronavirus OC43, Coronavirus HKU 1, Adenovirus, Enterovirus, Parechovirus, Rhinovirus, RSV, PIV1, PIV2, PIV3, PIV4, Influenza A, Influenza B, Influenza A(H1N1), Bocavirus |
| Bénet et al., 2017 [29] | NP swabs | ||||
| Hammitt et al., 2012 [23] | NP/OP swab and induced sputum (IS) | Not mentioned | multiplex PCR for 16 respiratory pathogens | Not mentioned | RSV, Adenovirus, PIV, Influenza A, Influenza B B. pertussis, M. pneumoniae |
| Zar et al., 2016 [22] | 2 NP swabs | QIAsymphony Virus/Bacteria Mini Kit (Qiagen, Hilden, Germany). | 33-pathogen multiplex quantitative PCR | FTD Resp-33; Fast-track Diagnostics, Sliema, Malta |
B. pertussis, C. pneumoniae H. influenzae type b Non-type b H. influenzae M. catarrhalis, M. pneumoniae S. pneumoniae, Salmonella spp S. aureus, P. jirovecii Adenovirus, Human, cytomegalovirus, Coronavirus 229, Coronavirus 43, Coronavirus 63, Coronavirus HKU, Influenza A, Influenza B, Influenza C, Human bocavirus, Human metapneumovirus A/B, PIV1, PIV2, PIV3, PIV4, Parechovirus/Enterovirus, Human rhinovirus, RSV |
| Mwananyanda et al., 2021 [24] | NP/OP swabs | NucliSENS easyMAG platform (bioMérieux, Marcy l’Etoile, France) | |||
| Tapia et al., 2021 [25] | NP/OP swabs | ||||
| Awori et al., 2021 [26] | NP/OP swabs | ||||
| Howie et al., 2021 [27] | NP/OP swabs | ||||
| Moore et al., 2021 [28] | NP/OP swabs | ||||
| Feikin et al., 2013 [8] | NP/OP swabs | Qiagen's QIAamp viral RNA and MagMAX Viral RNA Isolation Kit (Applied Biosystems) mini kit (Qiagen Inc, Valencia, CA) | TaqMan Universal PCR Master Mix, and AgPath-ID One-Step RT-PCR Reagents | Applied Biosystems | Influenza A Influenza B Influenza A or B RSV Adenovirus PIV1, PIV2, PIV3, Human metapneumovirus Mycoplasma pneumoniae Rhinovirus/enterovirus |
| Breiman et al., 2015 [30] | NP/OP swabs and three mL of blood for culture | MagMAX Viral RNA Isolation Kit (Applied Biosystems) |
qRT-PCR | Not mentioned | Influenza A, Influenza B, Influenza A or B, RSV, Adenovirus, PIV1, PIV2, PIV3, Any parainfluenza, Human, metapneumovirus, Rhinovirus/Enterovirus, Parechovirus |
Respiratory syncytial virus, RSV; Parainfluenza virus 1, PIV 1; Parainfluenza virus 2, PIV 2; Parainfluenza virus 3, PIV 3; Parainfluenza virus 4, PIV 4.