Cross-species transmission of the newly identified coronavirus 2019-nCoV
Authors: Xiaofang Zhao
Wei Ji
Junjie Zai
Xingguang Li
Wei Wang
Journal: Journal of medical virology (2020)
Discipline: MICROBIOLOGY
Keywords: 2019-nCoV; codon usage bias; cross-species transmission; phylogenetic analysis; recombination.
Affiliations: Department of MicrobiologyPeking University Health Science Center School of Basic Medical SciencesBeijing China, Department of Spleen and Stomach DiseasesThe First affiliated Hospital of Guangxi University of Chinese MedicineNanning China, Department of Science and TechnologyRuikang Hospital Affiliated to Guangxi University of Chinese MedicineNanning China, Immunology Innovation Team, School of MedicineNingbo UniversityNingbo China, Hubei Engineering Research Center of Viral VectorWuhan University of BioengineeringWuhan China

Abstract:  The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence. Results obtained from our analyses suggest that the 2019-nCoV may appear to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019-nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019-nCoV cross-species transmission. 

Retracted: No

PubPeer comments:
 Figs 1B, 1E. With contrast-enhanced versions at right to emphasise the curious phenomenon in which the background of every band has an identical texture. This texture continues into every other Figure in the paper. ![file] Curiously, the same texture has also been seen in Fig 1E from [Liu et al (2020)] - below, bottom left -- and Fig 2E of [Liu et al (2019)] -- below, bottom right. ![file] Author lists do not overlap. , 
 This paper belongs to a set of over 400 papers (as per February 2020) that share very similar Western blots with tadpole-like shaped bands, the same background pattern, and striking similarities in title structures, paper layout, bar graph design, and - in a subset - flow cytometry panels. Despite these similarities, these papers are authored by researchers from different departments and institutes, with almost no overlap in authors. The list of these papers is available here: https: docs.google.com spreadsheets d 1KXqTAyl4j-jVorFPMD2XRpr76LcIKJ0CVyIvRj0exYQ edit?usp=sharing A more detailed description of this set of papers, suspected to all be generated by a common source, a paper mill , can be found here: * https: forbetterscience.com 2020 01 24 the-full-service-paper-mill-and-its-chinese-customers (January 2020) * https: scienceintegritydigest.com 2020 02 21 the-tadpole-paper-mill (February 2020) The same paper mill has been described in these papers: * Jana Christopher - Systematic fabrication of scientific images revealed - FEBS Letters (2018) - https: febs.onlinelibrary.wiley.com doi full 10.1002 1873-3468.13201 * Jennifer A Byrne and Jana Christopher - Digital magic, or the dark arts of the 21st centuryu2014how can journals and peer reviewers detect manuscripts and publications from paper mills? - FEBS Letters (2020) - https: febs.onlinelibrary.wiley.com doi full 10.1002 1873-3468.13747 , 
 Retracted - no date or separate Retraction Note. ------------------ This article has been retracted at the request of the Editor-in-Chief. Concerns were raised about the background pattern of the Western Blots from Figures 1B and 1E. Given the comments of Dr Elisabeth Bik regarding this article u201cThis paper belongs to a set of over 400 papers (as per February 2020) that share very similar Western blots with tadpole-like shaped bands, the same background pattern, and striking similarities in title structures, paper layout, bar graph design, and - in a subset - flow cytometry panelsu201d, the journal requested the authors to provide the raw data. However, the authors were not able to provide raw data of sufficient quality and detail for the journal to independently audit the provenance and validity of the data, and therefore the Editor-in-Chief decided to retract the article. ,