https://www.nature.com/articles/s41586-020-2012-7
The virus genome consists of six major open-reading frames (ORFs)
that are common to coronaviruses and a number of other accessory genes
(Fig. 1b).
Further analysis indicates that some of the 2019-nCoV genes shared less
than 80% nucleotide sequence identity to SARS-CoV. However, the amino
acid sequences of the seven conserved replicase domains in ORF1ab that
were used for CoV species classification were 94.4% identical between
2019-nCoV and SARS-CoV, suggesting that the two viruses belong to the
same species, SARSr-CoV.
We then found that a short region of
RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV
RaTG13)—which was previously detected in Rhinolophus affinis from
Yunnan province—showed high sequence identity to 2019-nCoV. We carried
out full-length sequencing on this RNA sample (GISAID accession number
EPI_ISL_402131). Simplot analysis showed that 2019-nCoV was highly
similar throughout the genome to RaTG13 (Fig. 1c),
with an overall genome sequence identity of 96.2%. Using the aligned
genome sequences of 2019-nCoV, RaTG13, SARS-CoV and previously reported
bat SARSr-CoVs, no evidence for recombination events was detected in the
genome of 2019-nCoV. Phylogenetic analysis of the full-length genome
and the gene sequences of RdRp and spike (S) showed
that—for all sequences—RaTG13 is the closest relative of 2019-nCoV and
they form a distinct lineage from other SARSr-CoVs (Fig. 1d and Extended Data Fig. 2). The receptor-binding spike protein encoded by the S gene was highly divergent from other CoVs (Extended Data Fig. 2),
with less than 75% nucleotide sequence identity to all previously
described SARSr-CoVs, except for a 93.1% nucleotide identity to RaTG13
(Extended Data Table 3). The S genes of 2019-nCoV and RaTG13 are longer than other SARSr-CoVs. The major differences in the sequence of the S
gene of 2019-nCoV are the three short insertions in the N-terminal
domain as well as changes in four out of five of the key residues in the
receptor-binding motif compared with the sequence of SARS-CoV (Extended
Data Fig. 3).
Whether the insertions in the N-terminal domain of the S protein of
2019-nCoV confer sialic-acid-binding activity as it does in MERS-CoV
needs to be further studied. The close phylogenetic relationship to
RaTG13 provides evidence that 2019-nCoV may have originated in bats.
We rapidly developed a qPCR-based detection method on the basis of the sequence of the receptor-binding domain of the S gene, which was the most variable region of the genome (Fig. 1c).
Our data show that the primers could differentiate 2019-nCoV from all
other human coronaviruses including bat SARSr-CoV WIV1, which shares 95%
identity with SARS-CoV (Extended Data Fig. 4a, b).
Of the samples obtained from the seven patients, we found that six BALF
and five oral swab samples were positive for 2019-nCoV during the first
sampling, as assessed by qPCR and conventional PCR. However, we could
no longer detect virus-positive samples in oral swabs, anal swabs and
blood samples taken from these patients during the second sampling (Fig.
2a). However, we recommend that other qPCR targets, including the RdRp or envelope (E)
genes are used for the routine detection of 2019-nCoV. On the basis of
these findings, we propose that the disease could be transmitted by
airborne transmission, although we cannot rule out other possible routes
of transmission, as further investigation, including more patients, is
required.
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