Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction.

Abstract:

:The emergence of SARS-CoV-2 has led to the current global coronavirus pandemic and more than one million infections since December 2019. The exact origin of SARS-CoV-2 remains elusive, but the presence of a distinct motif in the S1/S2 junction region suggests the possible acquisition of cleavage site(s) in the spike protein that promoted cross-species transmission. Through plaque purification of Vero-E6 cultured SARS-CoV-2, we found a series of variants which contain 15-30-bp deletions (Del-mut) or point mutations respectively at the S1/S2 junction. Examination of the original clinical specimen from which the isolate was derived, and 26 additional SARS-CoV-2 positive clinical specimens, failed to detect these variants. Infection of hamsters shows that one of the variants (Del-mut-1) which carries deletion of 10 amino acids (30bp) does not cause the body weight loss or more severe pathological changes in the lungs that is associated with wild type virus infection. We suggest that the unique cleavage motif promoting SARS-CoV-2 infection in humans may be under strong selective pressure, given that replication in permissive Vero-E6 cells leads to the loss of this adaptive function. It would be important to screen the prevalence of these variants in asymptomatic infected cases. The potential of the Del-mut variants as an attenuated vaccine or laboratory tool should be evaluated.

journal_name

Emerg Microbes Infect

authors

Lau SY,Wang P,Mok BW,Zhang AJ,Chu H,Lee AC,Deng S,Chen P,Chan KH,Song W,Chen Z,To KK,Chan JF,Yuen KY,Chen H

doi

10.1080/22221751.2020.1756700

subject

Has Abstract

pub_date

2020-12-01 00:00:00

pages

837-842

issue

1

issn

2222-1751

journal_volume

9

pub_type

杂志文章
  • mRNA and miRNA profiling of Zika virus-infected human umbilical cord mesenchymal stem cells identifies miR-142-5p as an antiviral factor.

    abstract::Zika virus (ZIKV) infection during pregnancy is associated with congenital brain abnormalities, a finding that highlights the urgent need to understand mother-to-fetus transmission mechanisms. Human umbilical cord mesenchymal stem cells (hUCMSCs) are susceptible to ZIKV infection but the underlying mechanisms of viral...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1821581

    authors: Seong RK,Lee JK,Cho GJ,Kumar M,Shin OS

    更新日期:2020-12-01 00:00:00

  • Cross-reactive antibodies binding to H4 hemagglutinin protect against a lethal H4N6 influenza virus challenge in the mouse model.

    abstract::Influenza viruses of the H4 subtype are widespread in wild birds, circulate in domestic poultry, readily infect mammals, and tolerate the insertion of a polybasic cleavage site. In addition, serological evidence suggests that humans working with poultry are exposed to these viruses. While H4 viruses are not of immedia...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2018.1564369

    authors: Amanat F,Meade P,Strohmeier S,Krammer F

    更新日期:2019-01-01 00:00:00

  • Predominance and high antibiotic resistance of the emerging Clostridium difficile genotypes NAPCR1 and NAP9 in a Costa Rican hospital over a 2-year period without outbreaks.

    abstract::Clostridium difficile is the major causative agent of nosocomial antibiotic-associated diarrhea. In a 2009 outbreak of C. difficile-associated diarrhea that was recorded in a major Costa Rican hospital, the hypervirulent NAP1 strain (45%) predominated together with a local genotype variant (NAPCR1, 31%). Both strains ...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2016.38

    authors: López-Ureña D,Quesada-Gómez C,Montoya-Ramírez M,del Mar Gamboa-Coronado M,Somogyi T,Rodríguez C,Rodríguez-Cavallini E

    更新日期:2016-05-11 00:00:00

  • Evidence of H10N8 influenza virus infection among swine in southern China and its infectivity and transmissibility in swine.

    abstract::Infection with a novel H10N8 influenza virus in humans was first described in China in December 2013, which raised concerns related to public health. This novel virus was subsequently confirmed to have originated from a live poultry market. However, whether this virus can infect other mammals remains unclear. In the p...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1708811

    authors: Fu X,Huang Y,Fang B,Liu Y,Cai M,Zhong R,Huang J,Wenbao Q,Tian Y,Zhang G

    更新日期:2020-01-03 00:00:00

  • The expanding spectrum of human infections caused by Kocuria species: a case report and literature review.

    abstract::Although not previously known to cause human infections, Kocuria species have now emerged as human pathogens, mostly in compromised hosts with severe underlying disease. Recently, there has been an increasing incidence of different types of Kocuria infections reported, most likely due to the adoption of better identif...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2013.71

    authors: Purty S,Saranathan R,Prashanth K,Narayanan K,Asir J,Sheela Devi C,Kumar Amarnath S

    更新日期:2013-10-01 00:00:00

  • An H5N1-based matrix protein 2 ectodomain tetrameric peptide vaccine provides cross-protection against lethal infection with H7N9 influenza virus.

    abstract::In March 2013, a patient infected with a novel avian influenza A H7N9 virus was reported in China. Since then, there have been 458 confirmed infection cases and 177 deaths. The virus contains several human-adapted markers, indicating that H7N9 has pandemic potential. The outbreak of this new influenza virus highlighte...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2015.22

    authors: Leung HC,Chan CC,Poon VK,Zhao HJ,Cheung CY,Ng F,Huang JD,Zheng BJ

    更新日期:2015-04-01 00:00:00

  • Novel FKS1 and FKS2 modifications in a high-level echinocandin resistant clinical isolate of Candida glabrata.

    abstract::Echinocandin resistance in Candida glabrata poses a serious clinical challenge. The underlying resistance mechanism of a pan-echinocandin-resistant C. glabrata isolate (strain L74) was investigated in this study. FKS mutants carrying specific mutations found in L74 were reconstructed by the Alt-R CRISPR-Cas9 system (F...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1684209

    authors: Hou X,Healey KR,Shor E,Kordalewska M,Ortigosa CJ,Paderu P,Xiao M,Wang H,Zhao Y,Lin LY,Zhang YH,Li YZ,Xu YC,Perlin DS,Zhao Y

    更新日期:2019-01-01 00:00:00

  • Enterovirus 71 induces dsRNA/PKR-dependent cytoplasmic redistribution of GRP78/BiP to promote viral replication.

    abstract::GRP78/BiP is an endoplasmic reticulum (ER) chaperone protein with the important function of maintaining ER homeostasis, and the overexpression of GRP78/BiP alleviates ER stress. Our previous studies showed that infection with enterovirus 71 (EV71), a (+)RNA picornavirus, induced GRP78/BiP upregulation; however, ectopi...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2016.20

    authors: Jheng JR,Wang SC,Jheng CR,Horng JT

    更新日期:2016-03-23 00:00:00

  • COVID-19 pandemic - an African perspective.

    abstract::The recently emerged novel coronavirus, "severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)", caused a highly contagious disease called coronavirus disease 2019 (COVID-19). The virus was first reported from Wuhan city in China in December, 2019, which in less than three months spread throughout the globe and...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章,评审

    doi:10.1080/22221751.2020.1775132

    authors: Lone SA,Ahmad A

    更新日期:2020-12-01 00:00:00

  • Dengue virus and the host innate immune response.

    abstract::Dengue virus (DENV) is a mosquito-borne Flavivirus that is endemic in many tropical and sub-tropical countries where the transmission vectors Aedes spp. mosquitoes resides. There are four serotypes of the virus. Each serotype is antigenically different, meaning they elicit heterologous antibodies. Infection with one s...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章,评审

    doi:10.1038/s41426-018-0168-0

    authors: Uno N,Ross TM

    更新日期:2018-10-10 00:00:00

  • Accurate serology for SARS-CoV-2 and common human coronaviruses using a multiplex approach.

    abstract::Serology is a crucial part of the public health response to the ongoing SARS-CoV-2 pandemic. Here, we describe the development, validation and clinical evaluation of a protein micro-array as a quantitative multiplex immunoassay that can identify S and N-directed SARS-CoV-2 IgG antibodies with high specificity and sens...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1813636

    authors: van Tol S,Mögling R,Li W,Godeke GJ,Swart A,Bergmans B,Brandenburg A,Kremer K,Murk JL,van Beek J,Wintermans B,Reimerink J,Bosch BJ,Reusken C

    更新日期:2020-12-01 00:00:00

  • Molecular characteristics of eae-positive clinical Shiga toxin-producing Escherichia coli in Sweden.

    abstract::Shiga toxin (Stx)-producing Escherichia coli (STEC) can cause a wide range of symptoms from asymptomatic carriage, mild diarrhea to bloody diarrhea (BD) and hemolytic uremic syndrome (HUS). Intimin, encoded by the eae gene, also plays a critical role in STEC pathogenesis. Herein, we investigated the prevalence and gen...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1850182

    authors: Hua Y,Bai X,Zhang J,Jernberg C,Chromek M,Hansson S,Frykman A,Yang X,Xiong Y,Wan C,Matussek A

    更新日期:2020-12-01 00:00:00

  • Human pathogenic Mycobacterium kansasii (former subtype Ⅰ) with zoonotic potential isolated from a diseased indoor pet cat, Japan.

    abstract::Nontuberculous mycobacterial (NTM) infections in humans have increased in prevalence in recent decades. Mycobacterium kansasii is one of the most prevalent human pathogenic NTM species worldwide. Herein, we report the first isolation of M. kansasii from an indoor domestic cat in Japan. Comparative genome sequence anal...

    journal_title:Emerging microbes & infections

    pub_type: 信件

    doi:10.1080/22221751.2021.1878935

    authors: Fukano H,Terazono T,Hirabayashi A,Yoshida M,Suzuki M,Wada S,Ishii N,Hoshino Y

    更新日期:2021-01-19 00:00:00

  • A novel norovirus GII.17 lineage contributed to adult gastroenteritis in Shanghai, China, during the winter of 2014–2015.

    abstract::Norovirus (NoV) is now recognized as a leading cause of nonbacterial acute gastroenteritis; however, the NoV GII.17 genotype has rarely been reported as the predominant genotype in clinical diarrhea cases. During the winter of 2014–2015, the GII.17 genotype, together with the NoV GII.4 genotype, dominated in sporadic ...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2015.67

    authors: Chen H,Qian F,Xu J,Chan M,Shen Z,Zai S,Shan M,Cai J,Zhang W,He J,Liu Y,Zhang J,Yuan Z,Zhu Z,Hu Y

    更新日期:2015-11-01 00:00:00

  • Papillomavirus can be transmitted through the blood and produce infections in blood recipients: Evidence from two animal models.

    abstract::Human papillomaviruses (HPV) contribute to most cervical cancers and are considered to be sexually transmitted. However, papillomaviruses are often found in cancers of internal organs, including the stomach, raising the question as to how the viruses gain access to these sites. A possible connection between blood tran...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1637072

    authors: Cladel NM,Jiang P,Li JJ,Peng X,Cooper TK,Majerciak V,Balogh KK,Meyer TJ,Brendle SA,Budgeon LR,Shearer DA,Munden R,Cam M,Vallur R,Christensen ND,Zheng ZM,Hu J

    更新日期:2019-01-01 00:00:00

  • The role of biomedical research in global tuberculosis control: gaps and challenges: A perspective from the US National Institute of Allergy and Infectious Diseases, National Institutes of Health.

    abstract::Tuberculosis (TB) has been a persistent public health concern for hundreds of years. Despite advances in medicine and science, eliminating this disease has been beyond our reach. Several organizations, including the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Healt...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章,评审

    doi:10.1038/emi.2012.21

    authors: Sizemore CF,Schleif AC,Bernstein JB,Heilman CA

    更新日期:2012-07-01 00:00:00

  • Identification and genetic characterization of a novel parvovirus associated with serum hepatitis in horses in China.

    abstract::A novel equine parvovirus, equine parvovirus-hepatitis (EqPV-H), was first discovered in a horse that died of equine serum hepatitis in the USA in 2018. EqPV-H was shown to be a novel etiological agent associated with equine serum hepatitis. Following this initial report, no additional studies on EqPV-H have been publ...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-018-0174-2

    authors: Lu G,Sun L,Ou J,Xu H,Wu L,Li S

    更新日期:2018-10-23 00:00:00

  • miR-1303 regulates BBB permeability and promotes CNS lesions following CA16 infections by directly targeting MMP9.

    abstract::Coxsackievirus A16 (CA16) is a member of the Picornaviridae family and causes mild and self-limiting hand, foot, and mouth disease (HFMD) in infants and young children. CA16 infection can also progress to central nervous system (CNS) complications; however, the underlying mechanism by which CA16 penetrates the blood-b...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-018-0157-3

    authors: Song J,Hu Y,Li H,Huang X,Zheng H,Hu Y,Wang J,Jiang X,Li J,Yang Z,Fan H,Guo L,Shi H,He Z,Yang F,Wang X,Dong S,Li Q,Liu L

    更新日期:2018-09-19 00:00:00

  • Cumulative acquisition of pathogenicity islands has shaped virulence potential and contributed to the emergence of LEE-negative Shiga toxin-producing Escherichia coli strains.

    abstract::Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens causing severe gastroenteritis, which may lead to hemolytic uremic syndrome. The Locus of Enterocyte Effacement (LEE), a Pathogenicity Island (PAI), is a major determinant of intestinal epithelium attachment of a group of STEC strains; however, the ...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1595985

    authors: Montero DA,Canto FD,Velasco J,Colello R,Padola NL,Salazar JC,Martin CS,Oñate A,Blanco J,Rasko DA,Contreras C,Puente JL,Scheutz F,Franz E,Vidal RM

    更新日期:2019-01-01 00:00:00

  • Comparison of the genotypic and phenotypic properties of HIV-1 standard subtype B and subtype B/B' env molecular clones derived from infections in China.

    abstract::Although a number of standardized human immunodeficiency virus 1 (HIV-1) pseudoviruses have been generated to assess neutralizing antibodies, subtype B/B' has not been comprehensively characterized either genotypically or phenotypically. Full-length env genes were isolated from plasma samples derived from B/B'-infecte...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-018-0087-0

    authors: Xie H,Nie J,Chen Q,Huang W,Wang Y

    更新日期:2018-05-16 00:00:00

  • Prevalence and characteristics of hypoxic hepatitis in the largest single-centre cohort of avian influenza A(H7N9) virus-infected patients with severe liver impairment in the intensive care unit.

    abstract::Avian influenza A(H7N9) virus (A(H7N9)) emerged in February 2013. Liver impairment of unknown cause is present in 29% of patients with A(H7N9) infection, some of whom experience severe liver injury. Hypoxic hepatitis (HH) is a type of acute severe liver injury characterized by an abrupt, massive increase in serum amin...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2016.1

    authors: Zhang Y,Liu J,Yu L,Zhou N,Ding W,Zheng S,Shi D,Li L

    更新日期:2016-01-06 00:00:00

  • Identification of a novel broadly HIV-1-neutralizing antibody from a CRF01_AE-infected Chinese donor.

    abstract::The isolation and characterization of monoclonal broadly neutralizing antibodies (nAbs) from natural HIV-1-infected individuals play very important roles in understanding nAb responses to HIV-1 infection and designing vaccines and therapeutics. Many broadly nAbs have been isolated from individuals infected with HIV-1 ...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-018-0175-1

    authors: Ju B,Li D,Ren L,Hou J,Hao Y,Liang H,Wang S,Zhu J,Wei M,Shao Y

    更新日期:2018-11-01 00:00:00

  • Comparison of the virulence and transmissibility of canine H3N2 influenza viruses and characterization of their canine adaptation factors.

    abstract::Recent canine influenza outbreaks have raised concerns about the generation of pathogenic variants that may pose a threat to public health. Here, we examine avian-like H3N2 canine influenza viruses (CIVs) isolated from 2009 to 2013 in South Korea from dogs. Phylogenetic analysis revealed that these viruses are closely...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-017-0013-x

    authors: Lee IW,Kim YI,Lim GJ,Kwon HI,Si YJ,Park SJ,Kim EH,Kim SM,Nguyen HD,Song MS,Choi YK

    更新日期:2018-03-07 00:00:00

  • Hypothesis for potential pathogenesis of SARS-CoV-2 infection-a review of immune changes in patients with viral pneumonia.

    abstract::Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with droplets and contact as the main means of transmission. Since the first case appeared in Wuhan, China, in December 2019, the outbreak has gradually spread nationwide. Up to now, acco...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1746199

    authors: Lin L,Lu L,Cao W,Li T

    更新日期:2020-12-01 00:00:00

  • Laboratory diagnosis of emerging human coronavirus infections - the state of the art.

    abstract::The three unprecedented outbreaks of emerging human coronavirus (HCoV) infections at the beginning of the twenty-first century have highlighted the necessity for readily available, accurate and fast diagnostic testing methods. The laboratory diagnostic methods for human coronavirus infections have evolved substantiall...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章,评审

    doi:10.1080/22221751.2020.1745095

    authors: Loeffelholz MJ,Tang YW

    更新日期:2020-12-01 00:00:00

  • Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates.

    abstract::We report the discovery and confirmation of 23 novel mutations with previously undocumented role in isoniazid (INH) drug resistance, in catalase-peroxidase (katG) gene of Mycobacterium tuberculosis (Mtb) isolates. With these mutations, a synonymous mutation in fabG1 (g609a), and two canonical mutations, we were able t...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2015.42

    authors: Torres JN,Paul LV,Rodwell TC,Victor TC,Amallraja AM,Elghraoui A,Goodmanson AP,Ramirez-Busby SM,Chawla A,Zadorozhny V,Streicher EM,Sirgel FA,Catanzaro D,Rodrigues C,Gler MT,Crudu V,Catanzaro A,Valafar F

    更新日期:2015-07-01 00:00:00

  • Penaeidins restrict white spot syndrome virus infection by antagonizing the envelope proteins to block viral entry.

    abstract::Emerging studies have indicated that some penaeidins restrict virus infection; however, the mechanism(s) involved are poorly understood. In the present study, we uncovered that penaeidins are a novel family of antiviral effectors against white spot syndrome virus (WSSV), which antagonize the envelope proteins to block...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1729068

    authors: Xiao B,Fu Q,Niu S,Zhu P,He J,Li C

    更新日期:2020-12-01 00:00:00

  • Detection and characterization of tigecycline heteroresistance in E. cloacae: clinical and microbiological findings.

    abstract::Tigecycline is regarded as a last-resort treatment for carbapenem-resistant Enterobacteriaceae (CRE), however, the emergence of tigecycline heteroresistance has posted the therapeutic challenge to combat this "nightmare bacteria". The primary purpose of this study was to demonstrate the existence of tigecycline hetero...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1601031

    authors: Liu H,Jia X,Zou H,Sun S,Li S,Wang Y,Xia Y

    更新日期:2019-01-01 00:00:00

  • Avian influenza A H5N1 virus: a continuous threat to humans.

    abstract::We report the first case of severe pneumonia due to co-infection with the emerging avian influenza A (H5N1) virus subclade 2.3.2.1 and Mycoplasma pneumoniae. The patient was a returning traveller who had visited a poultry market in South China. We then review the epidemiology, virology, interspecies barrier limiting p...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章,评审

    doi:10.1038/emi.2012.24

    authors: To KK,Ng KH,Que TL,Chan JM,Tsang KY,Tsang AK,Chen H,Yuen KY

    更新日期:2012-09-01 00:00:00

  • Converting monoclonal antibody-based immunotherapies from passive to active: bringing immune complexes into play.

    abstract::Monoclonal antibodies (mAbs), which currently constitute the main class of biotherapeutics, are now recognized as major medical tools that are increasingly being considered to fight severe viral infections. Indeed, the number of antiviral mAbs developed in recent years has grown exponentially. Although their direct ef...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章,评审

    doi:10.1038/emi.2016.97

    authors: Lambour J,Naranjo-Gomez M,Piechaczyk M,Pelegrin M

    更新日期:2016-08-17 00:00:00