h年 9/10.10e0/2221751.2020,172299 ®EMi©tbr&n COMMENT 3OPEN ACCESS HIV-1 did not contribute to the 2019-nCoV genome Chuan Xiao,Xiaojun Li,Shuying Liu,Yongming Sang,Shou-Jiang Gao and Feng Gao .TX.USA: MA.USA ARTICLE HISTORY Received Febru When a new pathogen that causes a global epidemic in of use as a bioweapon.This notion has been fully humans,one key question is where it comes from.This debunked in the media.A recent informally pre is especially important for a zoonotic infectious diseas report,however sho d that 2019-nCo and to develop vaccines hen co iruses [8).It wa Discovery of the origin of a newly human pathogen is a sophisticated process that requires extensive and similar to the motifs in the highly variable (V) vigorous scientih validations and generally regions (V1.V4 and V5)in the envelope glyco- case or IV-1 protein or in the tein of some unique Hil natur strains tries(Tha es that t d on ellin the lated that thee often surface as the source.However.in all cases. such theories have been debunked in history. teins could provide an enhanced affinity towards Infection from an emerging pathogenic coronavirus host cell receptors and increase the range of host 6cr20 China.It cells of 201 nCoV.Thi study implies that 2019 22 peopl a e generated by gaining gene fragments 201 conducted careful examination of this new virus was quickly sequenced and made r the sequences of 219-CoV.other Cov and on January 12,only about 2 weeks after the disease HIV-1 as well as GenBank database.Our results was first observed [4].It was named as 2019-nCov demonstrated no evidence that the sequences of these the Wo orld H alth Org our inserts are HIV.I specific or anal sis Firs humans.It is but disti tica mo from cor hits are all from host enes of mammalian.insects.bac [5.6].However,it shares a high level of genetic simi erial and others.There are only a few hits on corona larity(96.3%)with a bat coronavirus RaTGl3 whicl viruses,but none of them are HIV-1 related. Blast was obtained from bat in Yunnan in 2013,suggesting gainst viral sequence database e also showed these that RaTG13- ely the rese virus the m most sources ol current 2019 za,to t Lack of the definite origin of 2019-nCoV has led iruses and a few also hit on HIV.Is to speculation that 2019-nCov might be derived the search against the entire database(Table 1).How. from genetic manipulation or even for the purpose ever.while the 100%match between the insertion 1 and CONTACT Chuan artment of Che and Biochemistry,The Un 130012,COMMENT HIV-1 did not contribute to the 2019-nCoV genome Chuan Xiaoa , Xiaojun Li b , Shuying Liuc , Yongming Sangd , Shou-Jiang Gaoe and Feng Gao b,f a Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, USA; b Department of Medicine, Duke University Medical Center, Durham, NC, USA; c NA BioTech Corp, M2D2 Incubator, University of Massachusetts Medical School, Worcester, MA, USA; d Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, USA; e UPMC Hillman Cancer Center, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA; f National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, People’s Republic of China ARTICLE HISTORY Received 4 February 2020; Accepted 4 February 2020 When a new pathogen that causes a global epidemic in humans, one key question is where it comes from. This is especially important for a zoonotic infectious disease that jumps from animals to humans. Knowing the ori￾gin of such a pathogen is critical to develop means to block further transmission and to develop vaccines. Discovery of the origin of a newly human pathogen is a sophisticated process that requires extensive and vigorous scientific validations and generally takes many years, such as the cases for HIV-1 [1], SARS [2] and MERS [3]. Unfortunately, before the natural sources of new pathogens are clearly defined, conspi￾racy theories that the new pathogens are man-made often surface as the source. However, in all cases, such theories have been debunked in history. Infection from an emerging pathogenic coronavirus was first reported in December 2019 in China. It has now affected over 42,000 people and caused over 1,000 deaths in 25 countries (https://2019ncov. Chinacdc.Cn/2019-Ncov). The complete genome of this new virus was quickly sequenced and made public on January 12, only about 2 weeks after the disease was first observed [4]. It was named as 2019-nCoV the following day by the World Health Organization (WHO). Phylogenetic analysis shows that 2019- nCoV is a new member of coronaviruses that infect humans. It is genetically homogenous but distinct from coronaviruses that cause SARS and MERS [5,6]. However, it shares a high level of genetic simi￾larity (96.3%) with a bat coronavirus RaTG13 which was obtained from bat in Yunnan in 2013, suggesting that RaTG13-like viruses are most likely the reservoir, but not the immediate sources of the current 2019- nCoV viruses [7]. Lack of the definite origin of 2019-nCoV has led to speculation that 2019-nCoV might be derived from genetic manipulation or even for the purpose of use as a bioweapon. This notion has been fully debunked in the media. A recent informally pre￾sented report, however, showed that 2019-nCoV had four insertions in the spike glycoprotein gene that is critical for the virus to enter the target cells when compared to other coronaviruses [8]. It was claimed that these inserts were either identical or similar to the motifs in the highly variable (V) regions (V1, V4 and V5) in the envelope glyco￾protein or in the Gag protein of some unique HIV- 1 strains from three different countries (Thailand, Kenya and India). Together with the structure mod￾elling analysis, the authors speculated that these motif insertions sharing similarity with HIV-1 pro￾teins could provide an enhanced affinity towards host cell receptors and increase the range of host cells of 2019-nCoV. This study implies that 2019- nCoV might be generated by gaining gene fragments from the HIV-1 genome. Current report conducted careful examination of the sequences of 2019-nCoV, other CoV viruses and HIV-1 as well as GenBank database. Our results demonstrated no evidence that the sequences of these four inserts are HIV-1 specific or the 2019-nCoV viruses obtain these insertions from HIV-1. First, the results of blast search of these motifs against GenBank shows that the top 100 identical or highly homologous hits are all from host genes of mammalian, insects, bac￾terial and others. There are only a few hits on corona￾viruses, but none of them are HIV-1 related. Blast against viral sequence database also showed these insertion sequences widely exist in all kinds of viruses from bacteriophage, influenza, to giant eukaryotic viruses (Table 1). More hits were found for corona￾viruses and a few also hit on HIV-1 sequences than the search against the entire database (Table 1). How￾ever, while the 100% match between the insertion 1 and © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. CONTACT Chuan Xiao cxiao@utep.edu Department of Chemistry and Biochemistry, The University of Texas at El Paso, 500 W. University Ave, El Paso, TX 79968, USA; Feng Gao fgao@duke.edu Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, People’s Republic of China Emerging Microbes & Infections 2020, VOL. 9 https://doi.org/10.1080/22221751.2020.1727299