This analysis was implemented under the following existing study: “The low carriage prevalence of pneumococcus among community-dwelling older people: A cross-sectional study in Japan” [
13]. All methods were conducted in accordance with the Declaration of Helsinki and the study was approved by the Ethical Review Board of the Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan, and the institutional review boards of each study facility. Written informed consent was obtained from all participants or their families. The study was conducted from February 2018 to December 2018 in Nagasaki city, Japan. We included community-dwelling older people aged ≥ 65 years who were ambulatory and attended regular clinic visits or outpatient rehabilitation visits at 4 hospitals in Nagasaki city, Japan. We excluded people with fever or any symptoms of upper respiratory tract infection, people who received antibiotic treatment in the previous 30 days, and people who were admitted to a hospital or a long-term care facility for ≥ 7 days in the previous 30 days. The detailed demographic and clinical information of the 504 participants was described previously [
13]. NP and oropharyngeal (OP) samples were obtained using two swabs: one sample from the nasopharynx using a sterilized swab with an aluminum shaft (TE2201) (Eiken Chemical Co., Tokyo, Japan) and another sample from the oropharynx using a sterilized swab with a wooden shaft (TE8201) (Eiken Chemical Co., Tokyo, Japan). These swabs were immediately individually placed in 1 ml of skim milk-tryptone-glucose-glycerol (STGG) media [
14]. Participants were asked to spit onto the inside of a sterilized sputum container (DE2000) (Eiken Chemical Co., Tokyo, Japan) to collect pure saliva without sputum. The details of use of these sterilized swabs and sputum containers are available online from the manufacturer [
15]. Samples were collected by researchers or trained research nurses. Viral nucleic acids were extracted using a QIAamp viral RNA Mini Kit (QIAGEN Inc., Valencia, CA, USA) and QIAamp DNA Mini Kit (QIAGEN Inc., Valencia, CA, USA), and the following fourteen respiratory viruses were screened with multiplex PCR assays using a One Step RT-PCR Kit (QIAGEN Inc., Valencia, CA, USA) for RNA viruses and GoTaq Flexi DNA Polymerase (Promega, San Luis Obispo, CA, USA) and PCR Nucleotide Mix (Promega, San Luis Obispo, CA, USA) for DNA viruses, as described previously [
16]: influenza A, influenza B, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza virus types 1–4 (PIV-1, PIV-2, PIV-3 and PIV-4), rhinovirus, coronavirus 229E, OC43 (common human coronavirus [HCoV]), adenovirus, bocavirus, and enterovirus. An Additional file
1 shows the sensitivity (detection limit) of the multiplex PCR [see Additional file
1]. The prevalence of PCR positivity for respiratory viruses was defined as the total prevalence detected in at least one NP, OP and/or saliva sample. The calculation of the prevalence of PCR positivity is shown in Additional file
2: Fig. S1. Cohen’s kappa coefficient (
κ) was computed to measure the agreement between each pair of sampling sites.