A host-based whole genome sequencing study reveals novel risk loci associated with severity of influenza A(H1N1)pdm09 infection.

Abstract:

:Influenza A(H1N1)pdm09 virus has remained in a seasonal circulation since being recognized in 2009. Although it followed a mild course in most patients, in others it caused a series of severe clinical illnesses. Epidemiologic studies have implicated that host factors have a major influence on the disease severity of influenza A(H1N1)pdm09 infection. However, an understanding of relevant genetic variations and the underlying mechanisms is still limited. In this present study, we used a host-based whole genome sequencing (WGS) method to comprehensively explore the genetic risk loci associated with severity of influenza A(H1N1)pdm09 infection. From the common single-nucleotide variants (SNVs) analysis, we identified the abnormal nominally significant (P < 1 × 10-4) common SNVs enriched in PTBP3 gene. The results of rare functional SNVs analysis supported that there were several novel candidate genes might confer risk of severe influenza A(H1N1)pdm09 diseases, such as FTSJ3, CPVL, BST2, NOD2 and MAVS. Moreover, our results of gene set based analysis indicated that the HIF-1 transcription factor and IFN-γ pathway might play an important role in the underlying mechanism of severe influenza A(H1N1)pdm09. These findings will increase our knowledge about biological mechanism underlying the severe influenza A(H1N1)pdm09 and facilitate to design novel personalized treatments.

journal_name

Emerg Microbes Infect

authors

Li M,Chen Y,Chen T,Hu S,Chen L,Shen L,Li F,Yang J,Sun Y,Wang D,He L,Qin S,Shu Y

doi

10.1080/22221751.2020.1870412

subject

Has Abstract

pub_date

2021-12-01 00:00:00

pages

123-131

issue

1

issn

2222-1751

journal_volume

10

pub_type

杂志文章
  • Profiling serum cytokines in COVID-19 patients reveals IL-6 and IL-10 are disease severity predictors.

    abstract::Since the outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China, it has rapidly spread across many other countries. While the majority of patients were considered mild, critically ill patients involving respiratory failure and multiple organ dysfunction syndrome are not uncommon, which could result death. We...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1770129

    authors: Han H,Ma Q,Li C,Liu R,Zhao L,Wang W,Zhang P,Liu X,Gao G,Liu F,Jiang Y,Cheng X,Zhu C,Xia Y

    更新日期:2020-12-01 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

  • Detection and characterization of an emerging type of Babesia sp. similar to Babesia motasi for the first case of human babesiosis and ticks in Korea.

    abstract::Babesiosis is a tick-transmitted intraerythrocytic zoonosis. In Korea, the first mortalities were reported in 2005 due to Babesia sp. detection in sheep; herein we report epidemiological and genetic characteristics of a second case of babesiosis. Microscopic analysis of patient blood revealed polymorphic merozoites. T...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1622997

    authors: Hong SH,Kim SY,Song BG,Rho JR,Cho CR,Kim CN,Um TH,Kwak YG,Cho SH,Lee SE

    更新日期:2019-01-01 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 live attenuated vaccine prevents replication and transmission of H7N9 highly pathogenic influenza viruses in mammals.

    abstract::H7N9 influenza viruses emerged in 2013 and have caused severe disease and deaths in humans in China. Some H7N9 viruses circulating in chickens have mutated to highly pathogenic viruses that have caused several disease outbreaks in chickens. Studies have shown that when the H7N9 highly pathogenic viruses replicate in f...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-018-0154-6

    authors: Yang W,Yin X,Guan L,Li M,Ma S,Shi J,Deng G,Suzuki Y,Chen H

    更新日期:2018-09-12 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

  • 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

  • The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj.

    abstract::We conducted this study to describe the dynamics of the acquisition of respiratory pathogens, their potential interactions and risk factors for possible lower respiratory tract infection symptoms (LRTI) among French pilgrims during the 2018 Hajj. Each participant underwent four successive systematic nasopharyngeal swa...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1693247

    authors: Hoang VT,Dao TL,Ly TDA,Belhouchat K,Chaht KL,Gaudart J,Mrenda BM,Drali T,Yezli S,Alotaibi B,Fournier PE,Raoult D,Parola P,de Santi VP,Gautret P

    更新日期:2019-01-01 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

  • Clinical observation and management of COVID-19 patients.

    abstract::Three leading infectious disease experts in China were invited to share their bedside observations in the management of COVID-19 patients. Professor Taisheng Li was sent to Wuhan to provide frontline medical care. He depicts the clinical course of SARS-CoV-2 infection. Furthermore, he observes the significant abnormal...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1741327

    authors: Li T,Lu H,Zhang W

    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

  • Characterization of swine-origin H1N1 canine influenza viruses.

    abstract::Host switch events of influenza A viruses (IAVs) continuously pose a zoonotic threat to humans. In 2013, swine-origin H1N1 IAVs emerged in dogs soon after they were detected in swine in the Guangxi province of China. This host switch was followed by multiple reassortment events between these H1N1 and previously circul...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1637284

    authors: Wang G,Dos Anjos Borges LG,Stadlbauer D,Ramos I,Bermúdez González MC,He J,Ding Y,Wei Z,Ouyang K,Huang W,Simon V,Fernandez-Sesma A,Krammer F,Nelson MI,Chen Y,García-Sastre A

    更新日期:2019-01-01 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

  • Genetic regulation of the development of mating projections in Candida albicans.

    abstract::Candida albicans is a major human fungal pathogen, capable of switching among a range of morphological types, such as the yeast form, including white and opaque cell types and the GUT (gastrointestinally induced transition) cell type, the filamentous form, including hyphal and pseudohyphal cell types, and chlamydospor...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1729067

    authors: Liang W,Guan G,Li C,Nobile CJ,Tao L,Huang G

    更新日期:2020-02-21 00:00:00

  • Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection.

    abstract::Outbreaks of avian influenza virus continue to pose threats to human health. Animal models such as the mouse, ferret, and macaque are used to understand the pathogenesis of avian influenza virus infection in humans. We previously reported that the tree shrew (Tupaia belangeri, family Tupaiidae), which is regarded as a...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-018-0167-1

    authors: Li R,Yuan B,Xia X,Zhang S,Du Q,Yang C,Li N,Zhao J,Zhang Y,Zhang R,Feng Y,Jiao J,Peiris M,Zhong N,Mok CKP,Yang Z

    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

  • Culex pipiens quinquefasciatus: a potential vector to transmit Zika virus.

    abstract::Zika virus (ZIKV) has become a threat to global health since the outbreak in Brazil in 2015. Although ZIKV is generally considered an Aedes-transmitted pathogen, new evidence has shown that parts of the virus closely resemble Culex-transmitted viruses. Therefore, it is important to evaluate the competence of Culex spe...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2016.102

    authors: Guo XX,Li CX,Deng YQ,Xing D,Liu QM,Wu Q,Sun AJ,Dong YD,Cao WC,Qin CF,Zhao TY

    更新日期:2016-09-07 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

  • Characterization of anti-MERS-CoV antibodies against various recombinant structural antigens of MERS-CoV in an imported case in China.

    abstract::The first imported case of Middle East respiratory syndrome (MERS) in China recently occurred, allowing for the characterization of antibody titers in a series of the patient's sera using the following methods based on recombinant viral structural antigens: inactivated MERS coronavirus (MERS-CoV) enzyme-linked immunos...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2016.114

    authors: Wang W,Wang H,Deng Y,Song T,Lan J,Wu G,Ke C,Tan W

    更新日期:2016-11-09 00:00:00

  • Aetiology of acute meningoencephalitis in Cambodian children, 2010-2013.

    abstract::Acute meningoencephalitis (AME) is associated with considerable morbidity and mortality in children in developing countries. Clinical specimens were collected from children presenting with AME at two Cambodian paediatric hospitals to determine the major aetiologies associated with AME in the country. Cerebrospinal flu...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2017.15

    authors: Horwood PF,Duong V,Laurent D,Mey C,Sothy H,Santy K,Richner B,Heng S,Hem S,Cheval J,Gorman C,Dussart P,de Jong MD,Kerleguer A,Guillard B,Murgue B,Lecuit M,de Lamballerie X,Farrar JJ,Tarantola A,Eloit M,Buchy P

    更新日期:2017-05-24 00:00:00

  • 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

  • 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

  • Role of domestic ducks in the emergence of a new genotype of highly pathogenic H5N1 avian influenza A viruses in Bangladesh.

    abstract::Highly pathogenic avian influenza H5N1 viruses were first isolated in Bangladesh in February 2007. Subsequently, clades 2.2.2, 2.3.4.2 and 2.3.2.1a were identified in Bangladesh, and our previous surveillance data revealed that by the end of 2014, the circulating viruses exclusively comprised clade 2.3.2.1a. We recent...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2017.60

    authors: Barman S,Marinova-Petkova A,Hasan MK,Akhtar S,El-Shesheny R,Turner JC,Franks J,Walker D,Seiler J,Friedman K,Kercher L,Jeevan T,Darnell D,Kayali G,Jones-Engel L,McKenzie P,Krauss S,Webby RJ,Webster RG,Feeroz MM

    更新日期:2017-08-09 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

  • Adaptive mutation F772S-enhanced p7-NS4A cooperation facilitates the assembly and release of hepatitis C virus and is associated with lipid droplet enlargement.

    abstract::Hepatitis C virus (HCV) infection is a major cause of chronic hepatitis and liver cancer worldwide. Adaptive mutations play important roles in the development of the HCV replicon and its infectious clones. We and others have previously identified the p7 mutation F772S and the co-presence of NS4A mutations in infectiou...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/s41426-018-0140-z

    authors: Duan X,Anwar MI,Xu Z,Ma L,Yuan G,Chen Y,Liu X,Xia J,Zhou Y,Li YP

    更新日期:2018-08-08 00:00:00

  • Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing.

    abstract::The Beijing genotype comprises a highly disseminated strain type that is frequently associated with multidrug resistant (MDR) tuberculosis (TB) and increased transmissibility but, countries such as Portugal and Guinea-Bissau fall outside the regions phylogeographically associated with this specific genotype. Neverthel...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1774425

    authors: Perdigão J,Silva C,Maltez F,Machado D,Miranda A,Couto I,Rabna P,Florez de Sessions P,Phelan J,Pain A,McNerney R,Hibberd ML,Mokrousov I,Clark TG,Viveiros M,Portugal I

    更新日期:2020-12-01 00:00:00

  • Silent geographical spread of the H7N9 virus by online knowledge analysis of the live bird trade with a distributed focused crawler.

    abstract::Unlike those infected by H5N1, birds infected by the newly discovered H7N9 virus have no observable clinical symptoms. Public health workers in China do not know where the public health threat lies. In this study, we used a distributed focused crawler to analyze online knowledge of the live bird trade in first-wave pr...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1038/emi.2013.91

    authors: Chen C,Lu S,Du P,Wang H,Yu W,Song H,Xu J

    更新日期:2013-12-01 00:00:00

  • Genomic epidemiology of erythromycin-resistant Bordetella pertussis in China.

    abstract::Macrolides such as erythromycin are the empirical treatment of Bordetella pertussis infections. China has experienced an increase in erythromycin-resistant B. pertussis isolates since they were first reported in 2013. Here, we undertook a genomic study on Chinese B. pertussis isolates from 2012 to 2015 to elucidate th...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1587315

    authors: Xu Z,Wang Z,Luan Y,Li Y,Liu X,Peng X,Octavia S,Payne M,Lan R

    更新日期:2019-01-01 00:00:00

  • Characterization of highly virulent community-associated methicillin-resistant Staphylococcus aureus ST9-SCCmec XII causing bloodstream infection in China.

    abstract::Previous studies have shown that livestock (LA)-MRSA ST398 evolved from a human-adapted methicillin-susceptible S. aureus (MSSA) clone. However, detailed information regarding ST9 is still unclear. Here, we characterized a community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) ST9-SCCmec XII isolat...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2020.1848354

    authors: Jin Y,Yu X,Chen Y,Chen W,Shen P,Luo Q,Zhang S,Kong X,Zheng B,Xiao Y

    更新日期:2020-12-01 00:00:00

  • Successful treatment of a Candida auris intra-articular infection.

    abstract::A 78-year-old woman with a long-term ankle spacer with antibacterials developed an intra-articular Candida auris infection. Treatment with systemic antifungal therapy plus an amphotericin B moulded cement spacer was successful. ...

    journal_title:Emerging microbes & infections

    pub_type: 杂志文章

    doi:10.1080/22221751.2019.1625287

    authors: Roberts SC,Zembower TR,Bolon MK,Kadakia AR,Gilley JH,Ko JH,Clark J,Ward-Fore S,Taiwo BO

    更新日期:2019-01-01 00:00:00