First Complete Genome Sequence of Human Coronavirus HKU1 from a Nonill Bat Guano Miner in Thailand

The first complete genome sequence of HCoV-HKU1 from Thailand was obtained from a nonill person who worked in a bat cave. Phylogenetic tree analysis revealed that this strain belongs to group B HCoV-HKU1. There are four species of endemic human coronavirus (HCoV) currently recognized by the International Committee for the Taxonomy of Viruses. These include HCoV-OC63, -229E, -NL63, and -HKU1, as well as two endemic CoVs, including SARS-CoV and MERS-CoV. Bats are believed to be the evolutionary source of alpha- and beta-CoV, including SARS-CoV and MERS-CoV. A group C betacoronavirus was detected from dry bat guano collected from a cave in Thailand where bat guano is sold for use as fertilizer. A nasopharyngeal swab from a bat guano miner in Ratchaburi Province, Thailand, was positive for the coronavirus HKU1 strain. The whole genome of this strain was sequenced using next-generation sequencing (NGS) on the Illumina MiSeq platform. A total of 59,704,490 sequencing reads were used for data analysis. Host DNA removal was performed using the SNAP alignment tool, and assembly was performed using the Burrows-Wheeler Aligner (BWA) with the HCoV-HKU1 reference strain. The complete genome of HCoV-HKU1 from Thailand consists of 29,811 bp. Phylogenetic analysis using the maximum likelihood algorithm showed that this strain belongs to the same clade as sequences from China and the United States. It is closely related to HCoV-HKU1 from Hong Kong, isolated in 2006, with 99% nucleotide identity. This strain was detected from a person with high exposure to bat feces, suggesting a high risk of zoonotic virus spillover. The characterization of this strain provides insight into the circulation of endemic infectious diseases in Thailand and increases the country's preparedness for other novel infectious diseases. The human coronavirus HKU1 strain reported here was deposited in GenBank under the accession number MH940245 and SRA accession number PRJNA509533. The sequence was generated using SAMtools mpileup, and the phylogenetic analysis was performed using the MEGA6 program. The results of this study provide new information on the genetic diversity of HCoV-HKU1 and its evolutionary relationships with other coronaviruses.