Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019

Matthew C. Wong; Sara J. Javornik Cregeen; Nadim J. Ajami; Joseph F. Petrosino

An outbreak of respiratory illness caused by a novel coronavirus (nCoV-2019) 1 , first identified in Wuhan China, has resulted in over twenty thousand confirmed cases worldwide (WHO Situation Report, February 5 2020). Data available to date has led to the hypothesis that the outbreak strain originated from bats. The nCoV-2019 has been reported to share 96% sequence identity to the RaTG13 genome, a coronavirus isolated from an intermediate horseshoe bat (Rhinolophus affinis) 2 . RaTG13 is the most closely related coronavirus genome to nCoV-2019, however other viral strains may have contributed to its genomic content. To explore this hypothesis, we examined several viral metagenomic datasets for potential coronaviruses that could harbor RBMs closer to nCoV-2019. We report evidence of a coronavirus recovered from a Malayan pangolin (Manis javanica) viral metagenomic dataset 3 that shares a higher sequence identity at a crucial segment of the genome involved in host infection ( Figure 1 ). This result indicates a potential recombination event and a more complex origin for the nCoV-2019 strain.