Table 2.

In silico analysis of primers used for amplification compared to common respiratory flora and other respiratory pathogens.

		Number of sequences with % identity 80–100, E value ≤ 10, Query coverage 80–100
	Taxonomy ID	N Fw	N Rv	E Fw	E Rv	S Fw	S Rv
Human coronavirus 229E	11,137	0	0	0	0	0	0
Human coronavirus OC43	31,631	0	0	0	0	0	0
Human coronavirus HKU1	290,028	0	0	0	0	0	0
Human coronavirus NL63	277,944	0	0	0	0	0	0
HCoV-SARS	694,009	3	3	21	3	0	0
MERS-CoV	1,335,626	0	0	0	0	0	0
Human adenovirus	1,907,210	0	0	0	0	0	0
Human metapneumovirus	162,145	0	0	0	0	0	0
parainfluenza virus 1	12,730	0	0	0	0	0	0
Human rubalavirus 2 (Parainfluenza virus 2)	1,979,160	0	0	0	0	0	0
parainfluenza virus 3	11,216	0	0	0	0	0	0
Human rubalavirus 4 (Parainfluenza virus 4)	1,979,161	0	0	0	0	0	0
Influenza A	2,072,034	0	0	0	0	0	0
Influenza B	2,072,149	0	0	0	0	0	0
enterovirus (e.g. EV68)	42,789	0	0	0	0	0	0
respiratory syncytial virus	12,814	0	0	0	0	0	0
rhinovirus (Human rhinovirus A1)	573,824	0	0	0	0	0	0
Chlamydia pneumoniae TW-183	182,082	0	0	0	0	0	0
Haemophilus influenzae	727	0	0	0	0	0	0
Legionella pneumophila	446	0	0	0	0	0	0
Mycobacterium tuberculosis	1773	0	0	0	0	0	0
Streptococcus pneumoniae	1313	0	0	0	0	0	0
Streptococcus pyogenes	1314	0	0	0	0	0	0
Bordetella pertussis	520	0	0	0	0	0	0
Mycoplasma pneumoniae	2104	0	0	0	0	0	0
Pneumocystis jirovecii (PJP)	42,068	0	0	0	0	0	0
Candida albicans	5476	0	0	0	0	0	0
Pseudomonas aeruginosa	287	0	0	0	0	0	0
Staphylococcus epidermis	1282	0	0	0	0	0	0
Staphylococcus salivarius	1304	0	0	0	0	0	0

Per FDA definition, cross-reactivity occurs when homology is greater than 80% between the primer and the template sequence in the targeted microorganism. Fw: forward; RV: reverse. Sequences were retrieved from the National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/taxonomy/.

Bold entries in table aim at highlighting the result.