Abstract
INTRO: It is hypothesized that metagenomics could contribute to the effective sentinel surveillance of emerging infections to identify plausible cause of respiratory symptoms in the population. METHODS: This study forms part of a longitudinal household cohort study involving the collection of respiratory symptoms and vaccination history in Hong Kong. As a pilot, selected households were provided with swab collection kit for collecting nasopharyngeal and throat samples when there was an influenza-like illness (ILI) during a 4-month presumptive period of the year's winter influenza season. Sequence-Independent Single Primer Amplification (SISPA) and nanopore metagenomic sequencing were performed. After basecalling, demultiplexing, and quality filtering, taxonomic classification was done. Unclassified and host reads were removed and only taxon with over 0.1% abundance were included in the analysis. FINDINGS: Between December 2021 and April 2022, of 101 collection kits delivered, 36 (36%) participants returned the samples. Two (6%) had previous COVID-19 diagnosis and almost all (97%) received at least one dose of COVID-19 vaccination. Metagenomics sequencing was performed on 13 samples collected from participants when ILI was present. Of the 1,592,219 reads obtained, 5308 taxa were identified and 136 had over 0.1% abundance, including 128 bacteria, 6 fungi, and 1 virus, which was a bacteriophage. The five most abundant genera of bacteria included Neisseria (19%), Streptococcus (10%), Haemophilus (9%), Veillonella (3%), and Rothia (3%). Haemophilus parainfluenzae was the most abundant species with 97,542 (6%) reads, followed by Neisseria meningitides (5%). Other bacteria identified included Rothia mucilaginosa, Acinetobacter baumannii, Lautropia mirabilis, Veillonella atypica, Streptococcus salivarius, and Streptococcus pneumonia. Inter-participant abundance profile was significantly different (p<0.001). CONCLUSION: The absence of viral infections identified echoed the extremely low proportion (3/21986, or 0.01%) of respiratory specimens testing positive for influenza virus by the government laboratory during the same period. The metagenomic profile could be useful for identifying the likely ILI-causing pathogen.