Table 2.

Findings of three types of genetic test assays of nasopharyngeal specimen upon admission

	Real-time RT-PCRa (Cq value)	BIOFIRE FILMARRAY Respiratory Panelb	Metagenomic analysis using NGS; number of reads (Total, 17,937,281 reads obtained as RNA-Seq metagenomics)
Nasopharyngeal specimen Upon admission	Human coronavirus HKU1 (21.5) Influenza C virus (19.7) Human parainfluenza virus 2 (36.4) (16 viruses undetectable)	Human coronavirus HKU1 + Human parainfluenza virus 2 + (12 viruses and 3 bacteria undetectable)	Human coronavirus HKU1 714 reads (0.004%) Influenza C virus 4698 reads (0.026%) Human 16,716,897 reads (93.1%) (No other viruses read)
Nasopharyngeal specimen Hospital day 2	Human coronavirus HKU1 (30.0) Influenza C virus (25.9) (17 viruses undetectable)	NE	NE
Serum on admission	NE	NE	No viruses read
Cerebrospinal fluid upon admission	NE	NE	No viruses read

^a Targeting nineteen respiratory viruses: influenza A (subtype H1pdm and H3), influenza B and C, human metapneumovirus, human respiratory syncytial viruses A and B, human bocavirus, rhinovirus, human respirovirus 1 and 3, human parainfluenza viruses 2 and 4, human adenoviruses 2 and 4, human coronaviruses NL63, OC43, HKU1 and 229E

^b Targeting fourteen respiratory viruses: influenza A and B, human metapneumovirus, human respiratory syncytial virus, rhinovirus/enterovirus, human parainfluenza viruses 2 and 4, human adenoviruses 2 and 4, human adenovirus, human coronaviruses NL63, OC43, HKU1 and 229E. Targeted bacteria: Bordetella pertussis, Chlamydophila pneumoniae, Mycoplasma pneumoniae. Influenza C virus was not included in the targeted panel and was thus undetectable

NE not examined. +, positive