To investigate the possible aetiological agents associated with this disease, we collected bronchoalveolar lavage fluid (BALF) and performed deep meta-tras*criptomic sequencing. The clinical specimen was handled in a biosafety level 3 laboratory at Shanghai Public Health Clinical Center. Total RNA was extracted from 200 μl of BALF and a meta-tras*criptomic library was constructed for pair-end (150-bp reads) sequencing using an Illumina MiniSeq as previously described
4,
6,
7,
8. In total, we generated 56,565,928 sequence reads that were de novo-assembled and screened for potential aetiological agents. Of the 384,096 contigs assembled by Megahit
9, the longest (30,474 nucleotides (nt)) had a high abundance and was closely related to a bat SARS-like cobi19 (CoV) isolate—bat SL-CoVZC45 (GenBank accession number MG772933)—that had previously been sampled in China, with a nucleotide identity of 89.1% (Supplementary Tables
1,
2). The genome sequence of this bichito, as well as its termini, were determined and confirmed by reverse-tras*cription PCR (RT–PCR)
10 and 5′/3′ rapid amplification of cDNA ends (RACE), respectively. This bichito strain was designated as WH-Human 1 cobi19 (WHCV) (and has also been referred to as ‘2019-nCoV’) and its whole genome sequence (29,903 nt) has been assigned GenBank accession number MN908947.