Microbiology

  • Article
    | Open Access

    In metabolic engineering, mechanistic models require prior metabolism knowledge of the chassis strain, whereas machine learning models need ample training data. Here, the authors combine the mechanistic and machine learning models to improve prediction performance of tryptophan metabolism in baker’s yeast.

    • Jie Zhang
    • , Søren D. Petersen
    • , Tijana Radivojevic
    • , Andrés Ramirez
    • , Andrés Pérez-Manríquez
    • , Eduardo Abeliuk
    • , Benjamín J. Sánchez
    • , Zak Costello
    • , Yu Chen
    • , Michael J. Fero
    • , Hector Garcia Martin
    • , Jens Nielsen
    • , Jay D. Keasling
    •  & Michael K. Jensen
  • Article
    | Open Access

    Here, Colangeli et al. use a human household contact cohort to measure the rate of mutation and evolution of Mycobacterium tuberculosis strains and find that long term latency is characterized by reduced mutation rates compared to latency in the first year, coinciding with clinical risk of developing active TB.

    • Roberto Colangeli
    • , Aditi Gupta
    • , Solange Alves Vinhas
    • , Uma Deepthi Chippada Venkata
    • , Soyeon Kim
    • , Courtney Grady
    • , Edward C. Jones-López
    • , Patricia Soteropoulos
    • , Moisés Palaci
    • , Patrícia Marques-Rodrigues
    • , Padmini Salgame
    • , Jerrold J. Ellner
    • , Reynaldo Dietze
    •  & David Alland
  • Article
    | Open Access

    Abiraterone acetate (AA) is indicated for the treatment of patients with metastatic castrate-resistant prostate cancer. Here, the authors show that, in prostate cancer patients, orally administered AA remodels the gut microbiome and promotes the enrichment of the commensal bacterium Akkermansia muciniphila at the expense of androgen-utilizing Corynebacterium species.

    • Brendan A. Daisley
    • , Ryan M. Chanyi
    • , Kamilah Abdur-Rashid
    • , Kait F. Al
    • , Shaeley Gibbons
    • , John A. Chmiel
    • , Hannah Wilcox
    • , Gregor Reid
    • , Amanda Anderson
    • , Malcolm Dewar
    • , Shiva M. Nair
    • , Joseph Chin
    •  & Jeremy P. Burton
  • Article
    | Open Access

    Herpesviruses code for conserved protein kinases (CHPKs) that exert several regulatory functions by interacting with cellular factors. Here, the authors use affinity purification mass spectrometry (AP–MS) to identify differential interaction partners of CHPKs from seven different human herpesviruses, finding Cyclin A and associated factors as a specific signature of β-herpesvirus kinases.

    • Boris Bogdanow
    • , Max Schmidt
    • , Henry Weisbach
    • , Iris Gruska
    • , Barbara Vetter
    • , Koshi Imami
    • , Eleonore Ostermann
    • , Wolfram Brune
    • , Matthias Selbach
    • , Christian Hagemeier
    •  & Lüder Wiebusch
  • Article
    | Open Access

    OgpA is an O-glycopeptidase from Akkermansia muciniphila, a mucin-degrading bacterium commonly found in the human gut. A thorough characterization of OgpA, including crystal structures in complex with substrate or product, reveals molecular basis of O-glycan recognition and enzyme specificity.

    • Beatriz Trastoy
    • , Andreas Naegeli
    • , Itxaso Anso
    • , Jonathan Sjögren
    •  & Marcelo E. Guerin
  • Article
    | Open Access

    Artemisinin (ART) resistance poses a problem for malaria elimination. Here, the authors perform genome-wide CRISPR screens in Toxoplasma gondii and identify that the putative transporter Tmem14c and mitochondrial heme metabolism, through mitochondrial protease DegP2, affect ART susceptibility.

    • Clare R. Harding
    • , Saima M. Sidik
    • , Boryana Petrova
    • , Nina F. Gnädig
    • , John Okombo
    • , Alice L. Herneisen
    • , Kurt E. Ward
    • , Benedikt M. Markus
    • , Elizabeth A. Boydston
    • , David A. Fidock
    •  & Sebastian Lourido
  • Article
    | Open Access

    The bacterial periplasmic predator Bdellovibrio bacteriovorus deacetylates the peptidoglycan of the prey bacterium early upon invasion. Here, the authors identify and characterize a Bdellovibrio lysozyme that acts specifically on deacetylated peptidoglycan and is important for periplasmic exit.

    • Christopher J. Harding
    • , Simona G. Huwiler
    • , Hannah Somers
    • , Carey Lambert
    • , Luke J. Ray
    • , Rob Till
    • , Georgina Taylor
    • , Patrick J. Moynihan
    • , R. Elizabeth Sockett
    •  & Andrew L. Lovering
  • Article
    | Open Access

    SARS-CoV-2 infection is widely diagnosed by RT-PCR, but RNA extraction is a bottleneck for fast and cheap diagnosis. Here, the authors develop protocols to perform RT-PCR directly on heat-inactivated subject samples or samples lysed with readily available detergents and benchmark performance against 597 clinically diagnosed patient samples.

    • Ioanna Smyrlaki
    • , Martin Ekman
    • , Antonio Lentini
    • , Nuno Rufino de Sousa
    • , Natali Papanicolaou
    • , Martin Vondracek
    • , Johan Aarum
    • , Hamzah Safari
    • , Shaman Muradrasoli
    • , Antonio Gigliotti Rothfuchs
    • , Jan Albert
    • , Björn Högberg
    •  & Björn Reinius
  • Article
    | Open Access

    Varicella-zoster virus (VZV) is the causative agent of chickenpox and herpes zoster (shingles). Cryo-EM structure of VZV capsid provides insights into the capsid assembly and reveals a pocket that could potentially be targeted by antiviral drugs.

    • Junqing Sun
    • , Congcong Liu
    • , Ruchao Peng
    • , Fu-Kun Zhang
    • , Zhou Tong
    • , Sheng Liu
    • , Yi Shi
    • , Zhennan Zhao
    • , Wen-Bo Zeng
    • , George Fu Gao
    • , Hong-Jie Shen
    • , Xiaoming Yang
    • , Minhua Luo
    • , Jianxun Qi
    •  & Peiyi Wang
  • Article
    | Open Access

    Here, the authors perform a temporal multi-omic analysis of a minimalistic cellulose-degrading and methane-producing consortium at the strain level and estimate protein-to-RNA ratios and RNA-protein dynamics of the community simultaneously over time.

    • F. Delogu
    • , B. J. Kunath
    • , P. N. Evans
    • , M. Ø. Arntzen
    • , T. R. Hvidsten
    •  & P. B. Pope
  • Article
    | Open Access

    Studies of microbial community assembly mechanisms typically use metrics for turnover within the whole community. Here, the authors develop an alternative approach based on turnover within lineages and dissect mechanistic change in grassland bacterial assembly under experimental warming.

    • Daliang Ning
    • , Mengting Yuan
    • , Linwei Wu
    • , Ya Zhang
    • , Xue Guo
    • , Xishu Zhou
    • , Yunfeng Yang
    • , Adam P. Arkin
    • , Mary K. Firestone
    •  & Jizhong Zhou
  • Article
    | Open Access

    Neisseria meningitidis capsular polysaccharide (CPS) is a major virulence factor and vaccine formulations against Neisseria meningitidis serogroup A (NmA) contain O-acetylated CPS. Here, the authors provide mechanistic insights into CPS O-acetylation in NmA by determining the crystal structure of the O-acetyltransferase CsaC and NMR measurements further reveal that the CsaC-mediated reaction is regioselective for O3 and that the O4 modification results from spontaneous O-acetyl migration.

    • Timm Fiebig
    • , Johannes T. Cramer
    • , Andrea Bethe
    • , Petra Baruch
    • , Ute Curth
    • , Jana I. Führing
    • , Falk F. R. Buettner
    • , Ulrich Vogel
    • , Mario Schubert
    • , Roman Fedorov
    •  & Martina Mühlenhoff
  • Article
    | Open Access

    Pathogenic agents can spread from an initial to a secondary site via the lymphatics. Here, using a mouse model of infection, the authors show that S. pyogenes readily transit through sequential lymph nodes within efferent lymphatics to reach the bloodstream and drive systemic infection, while remaining extracellular.

    • Matthew K. Siggins
    • , Nicola N. Lynskey
    • , Lucy E. Lamb
    • , Louise A. Johnson
    • , Kristin K. Huse
    • , Max Pearson
    • , Suneale Banerji
    • , Claire E. Turner
    • , Kevin Woollard
    • , David G. Jackson
    •  & Shiranee Sriskandan
  • Article
    | Open Access

    Antibody mediated immunity to SARS-CoV-2 will affect future transmission and disease severity. This systematic review on antibody response to coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and endemic coronaviruses provides insights into kinetics, correlates of protection, and association with disease severity.

    • Angkana T. Huang
    • , Bernardo Garcia-Carreras
    • , Matt D. T. Hitchings
    • , Bingyi Yang
    • , Leah C. Katzelnick
    • , Susan M. Rattigan
    • , Brooke A. Borgert
    • , Carlos A. Moreno
    • , Benjamin D. Solomon
    • , Luke Trimmer-Smith
    • , Veronique Etienne
    • , Isabel Rodriguez-Barraquer
    • , Justin Lessler
    • , Henrik Salje
    • , Donald S. Burke
    • , Amy Wesolowski
    •  & Derek A. T. Cummings
  • Article
    | Open Access

    Alphaviruses need to selectively package genomic viral RNA for transmission, but the packaging mechanism remains unclear. Here, Brown et al. combine PAR-CLIP with biotinylated capsid protein (Cp) retrieval and identify multiple Cp binding sites on genomic viral RNA that promote virion formation.

    • Rebecca S. Brown
    • , Dimitrios G. Anastasakis
    • , Markus Hafner
    •  & Margaret Kielian
  • Article
    | Open Access

    Favipiravir (T-705) is an inhibitor of viral RNA-dependent-RNA-polymerases (RdRp) and clinical trials for the treatment of COVID-19 are ongoing. Here, the authors show that SARS-CoV nsp12 is the fastest known viral RdRp and they provide insights into the mechanism of action of Favipiravir, demonstrating that its antiviral effect on SARS-CoV-2 is primarily mediated through lethal mutagenesis.

    • Ashleigh Shannon
    • , Barbara Selisko
    • , Nhung-Thi-Tuyet Le
    • , Johanna Huchting
    • , Franck Touret
    • , Géraldine Piorkowski
    • , Véronique Fattorini
    • , François Ferron
    • , Etienne Decroly
    • , Chris Meier
    • , Bruno Coutard
    • , Olve Peersen
    •  & Bruno Canard
  • Article
    | Open Access

    Highly accurate antibody tests for SARS-CoV-2 are needed for surveillance in low-prevalence populations. Here, the authors find seroprevalence of less than 1% in two San Francisco Bay Area populations at the beginning of April, and that seroreactivity is generally predictive of in vitro neutralising activity.

    • Dianna L. Ng
    • , Gregory M. Goldgof
    • , Brian R. Shy
    • , Andrew G. Levine
    • , Joanna Balcerek
    • , Sagar P. Bapat
    • , John Prostko
    • , Mary Rodgers
    • , Kelly Coller
    • , Sandra Pearce
    • , Sergej Franz
    • , Li Du
    • , Mars Stone
    • , Satish K. Pillai
    • , Alicia Sotomayor-Gonzalez
    • , Venice Servellita
    • , Claudia Sanchez San Martin
    • , Andrea Granados
    • , Dustin R. Glasner
    • , Lucy M. Han
    • , Kent Truong
    • , Naomi Akagi
    • , David N. Nguyen
    • , Neil M. Neumann
    • , Daniel Qazi
    • , Elaine Hsu
    • , Wei Gu
    • , Yale A. Santos
    • , Brian Custer
    • , Valerie Green
    • , Phillip Williamson
    • , Nancy K. Hills
    • , Chuanyi M. Lu
    • , Jeffrey D. Whitman
    • , Susan L. Stramer
    • , Candace Wang
    • , Kevin Reyes
    • , Jill M. C. Hakim
    • , Kirk Sujishi
    • , Fariba Alazzeh
    • , Lori Pham
    • , Edward Thornborrow
    • , Ching-Ying Oon
    • , Steve Miller
    • , Theodore Kurtz
    • , Graham Simmons
    • , John Hackett Jr.
    • , Michael P. Busch
    •  & Charles Y. Chiu
  • Article
    | Open Access

    Human coronavirus-HKU1 contains two surface projections called spike and haemagglutinin-esterase (HE), with the latter acting as a receptor-destroying enzyme. Here, the authors use cryo-EM and mass spectrometry to characterise the small, heavily glycosylated HKU1 HE, revealing a vestigial lectin domain covered with a putative glycan shield; and they discuss these features in the context of host adaptation.

    • Daniel L. Hurdiss
    • , Ieva Drulyte
    • , Yifei Lang
    • , Tatiana M. Shamorkina
    • , Matti F. Pronker
    • , Frank J. M. van Kuppeveld
    • , Joost Snijder
    •  & Raoul J. de Groot
  • Article
    | Open Access

    New York City is one of the areas most affected by the SARS-CoV-2 pandemic in the United States, and there has been large variation in rates of hospitalisation and death by city borough. Here, the authors show that boroughs with the largest reduction in daily commutes also had the lowest SARS-CoV-2 prevalence.

    • Stephen M. Kissler
    • , Nishant Kishore
    • , Malavika Prabhu
    • , Dena Goffman
    • , Yaakov Beilin
    • , Ruth Landau
    • , Cynthia Gyamfi-Bannerman
    • , Brian T. Bateman
    • , Jon Snyder
    • , Armin S. Razavi
    • , Daniel Katz
    • , Jonathan Gal
    • , Angela Bianco
    • , Joanne Stone
    • , Daniel Larremore
    • , Caroline O. Buckee
    •  & Yonatan H. Grad
  • Article
    | Open Access

    Dimethylsulfoniopropionate (DMSP) is an osmolyte produced by marine microbes that plays an important role in nutrient cycling and atmospheric chemistry. Here the authors go to the Mariana Trench—the deepest point in the ocean—and find bacteria are key DMSP producers, and that DMSP has a role in protection against high pressure.

    • Yanfen Zheng
    • , Jinyan Wang
    • , Shun Zhou
    • , Yunhui Zhang
    • , Ji Liu
    • , Chun-Xu Xue
    • , Beth T. Williams
    • , Xiuxiu Zhao
    • , Li Zhao
    • , Xiao-Yu Zhu
    • , Chuang Sun
    • , Hong-Hai Zhang
    • , Tian Xiao
    • , Gui-Peng Yang
    • , Jonathan D. Todd
    •  & Xiao-Hua Zhang
  • Article
    | Open Access

    Emergence of tigecycline-resistance tet(X) genes is of concern. Here, the authors determine tet(X) prevalence in more than 6,000 clinical Gram-negative bacterial isolates collected between 1994 to 2019 in hospitals in China and suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance genes.

    • Rong Zhang
    • , Ning Dong
    • , Zhangqi Shen
    • , Yu Zeng
    • , Jiauyue Lu
    • , Congcong Liu
    • , Hongwei Zhou
    • , Yanyan Hu
    • , Qiaoling Sun
    • , Qipeng Cheng
    • , Lingbing Shu
    • , Jiachang Cai
    • , Edward Wai-Chi Chan
    • , Gongxiang Chen
    •  & Sheng Chen
  • Article
    | Open Access

    Metagenomics allows virus genome discovery, but the viral hosts are often not identified. Here, Kinsella et al. use recombination events between virus genomes, statistical association of viruses to hosts in clinical samples, and analysis of endogenous viral elements in host genomes to identify probable hosts of three CRESS virus families.

    • Cormac M. Kinsella
    • , Aldert Bart
    • , Martin Deijs
    • , Patricia Broekhuizen
    • , Joanna Kaczorowska
    • , Maarten F. Jebbink
    • , Tom van Gool
    • , Matthew Cotten
    •  & Lia van der Hoek
  • Article
    | Open Access

    The blooming alga Emiliania huxleyi and its viruses are a model for density-dependent virulent dynamics. However, Knowles et al. show that this host–virus system exhibits temperate dynamics at natural host densities, in a manner dependent on host physiology.

    • Ben Knowles
    • , Juan A. Bonachela
    • , Michael J. Behrenfeld
    • , Karen G. Bondoc
    • , B. B. Cael
    • , Craig A. Carlson
    • , Nick Cieslik
    • , Ben Diaz
    • , Heidi L. Fuchs
    • , Jason R. Graff
    • , Juris A. Grasis
    • , Kimberly H. Halsey
    • , Liti Haramaty
    • , Christopher T. Johns
    • , Frank Natale
    • , Jozef I. Nissimov
    • , Brittany Schieler
    • , Kimberlee Thamatrakoln
    • , T. Frede Thingstad
    • , Selina Våge
    • , Cliff Watkins
    • , Toby K. Westberry
    •  & Kay D. Bidle
  • Article
    | Open Access

    A biologically-interpretable and robust metric that provides insight into one’s health status from a gut microbiome sample is an important clinical goal in current human microbiome research. Herein, the authors introduce a species-level index that predicts the likelihood of having a disease.

    • Vinod K. Gupta
    • , Minsuk Kim
    • , Utpal Bakshi
    • , Kevin Y. Cunningham
    • , John M. Davis III
    • , Konstantinos N. Lazaridis
    • , Heidi Nelson
    • , Nicholas Chia
    •  & Jaeyun Sung
  • Article
    | Open Access

    Inflammasome activation plays a role in malaria pathogenesis, but details aren’t well understood. Here, the authors show that caspase-8 is a central mediator of systemic inflammation in rodent malaria and that monocytes from malaria patients express active caspases-1, -4 and -8.

    • Larissa M. N. Pereira
    • , Patrícia A. Assis
    • , Natalia M. de Araújo
    • , Danielle F. Durso
    • , Caroline Junqueira
    • , Marco Antônio Ataíde
    • , Dhelio B. Pereira
    • , Egil Lien
    • , Katherine A. Fitzgerald
    • , Dario S. Zamboni
    • , Douglas T. Golenbock
    •  & Ricardo T. Gazzinelli
  • Article
    | Open Access

    SARS-CoV-2 spike protein binds host ACE2 for virus entry. Here, the authors determine kinetic and thermodynamic properties of this interaction using atomic force microscopy, develop peptides that inhibit binding and suggest existence of additional attachment factors.

    • Jinsung Yang
    • , Simon J. L. Petitjean
    • , Melanie Koehler
    • , Qingrong Zhang
    • , Andra C. Dumitru
    • , Wenzhang Chen
    • , Sylvie Derclaye
    • , Stéphane P. Vincent
    • , Patrice Soumillion
    •  & David Alsteens
  • Article
    | Open Access

    Here, using a humanized phage display library with recombinant SARS- CoV-2 receptor binding domain (RBD) proteins, the authors identify a number of single domain antibodies (sdAbs) that neutralize SARS-CoV-2 in vitro by inhibiting the interaction of the RDB with the host entry receptor ACE2.

    • Xiaojing Chi
    • , Xiuying Liu
    • , Conghui Wang
    • , Xinhui Zhang
    • , Xiang Li
    • , Jianhua Hou
    • , Lili Ren
    • , Qi Jin
    • , Jianwei Wang
    •  & Wei Yang
  • Article
    | Open Access

    A unique cell envelope contributes to the antibiotic resistance of the pathogen Acinetobacter baumannii. Here, Geisinger et al. identify A. baumannii mutants with altered antibiotic susceptibility, infer the function of uncharacterized proteins involved in envelope synthesis, and predict antibiotic synergies.

    • Edward Geisinger
    • , Nadav J. Mortman
    • , Yunfei Dai
    • , Murat Cokol
    • , Sapna Syal
    • , Andrew Farinha
    • , Delaney G. Fisher
    • , Amy Y. Tang
    • , David W. Lazinski
    • , Stephen Wood
    • , Jon Anthony
    • , Tim van Opijnen
    •  & Ralph R. Isberg
  • Article
    | Open Access

    Estimating the extent of SARS-CoV-2 infection in a population is challenging due to the limitations of testing. Here, the authors estimate that the true number of infections in the United States in mid-April was up to 20 times higher than the number of confirmed cases.

    • Sean L. Wu
    • , Andrew N. Mertens
    • , Yoshika S. Crider
    • , Anna Nguyen
    • , Nolan N. Pokpongkiat
    • , Stephanie Djajadi
    • , Anmol Seth
    • , Michelle S. Hsiang
    • , John M. Colford Jr.
    • , Art Reingold
    • , Benjamin F. Arnold
    • , Alan Hubbard
    •  & Jade Benjamin-Chung
  • Article
    | Open Access

    Tissue resident CD8 + T cells present at mucosal surfaces are poised to elicit function in situ, however approaches to boost their number in the gastrointestinal mucosa has been limited. Here the authors combine the use of Listeria monocytogenese and transient depletion of the intestinal microbiome to boost the resident CD8 + T cell response.

    • Simone Becattini
    • , Eric R. Littmann
    • , Ruth Seok
    • , Luigi Amoretti
    • , Emily Fontana
    • , Roberta Wright
    • , Mergim Gjonbalaj
    • , Ingrid M. Leiner
    • , George Plitas
    • , Tobias M. Hohl
    •  & Eric G. Pamer
  • Article
    | Open Access

    Infection is a growing issue in artificial implants and has become an area of significant interest. Here, the authors report on graphdiyne titanium dioxide composite nanofibres with enhanced photocatalytic reactive oxygen species generation and osteoinductive properties, demonstrated in infected implant models.

    • Rui Wang
    • , Miusi Shi
    • , Feiyan Xu
    • , Yun Qiu
    • , Peng Zhang
    • , Kailun Shen
    • , Qin Zhao
    • , Jiaguo Yu
    •  & Yufeng Zhang
  • Article
    | Open Access

    Identification of individuals at risk of severe COVID-19 disease could inform treatment and public health planning. Here, the authors develop and validate a risk prediction model for COVID-19 mortality in Israel by building a model for severe respiratory infection and recalibrating it using COVID-19 case fatality rates.

    • Noam Barda
    • , Dan Riesel
    • , Amichay Akriv
    • , Joseph Levy
    • , Uriah Finkel
    • , Gal Yona
    • , Daniel Greenfeld
    • , Shimon Sheiba
    • , Jonathan Somer
    • , Eitan Bachmat
    • , Guy N. Rothblum
    • , Uri Shalit
    • , Doron Netzer
    • , Ran Balicer
    •  & Noa Dagan
  • Article
    | Open Access

    Reoviridae undergo a complex assembly pathway in the host cell. Here the authors use cryo-electron tomography to visualize the assembly stages of mammalian orthoreovirus revealing a single shelled intermediate with gross similarity to an early assembly stage of a family of prokaryotic dsRNA viruses.

    • Geoff Sutton
    • , Dapeng Sun
    • , Xiaofeng Fu
    • , Abhay Kotecha
    • , Corey W. Hecksel
    • , Daniel K. Clare
    • , Peijun Zhang
    • , David I. Stuart
    •  & Mark Boyce
  • Article
    | Open Access

    The Neisseria meningitidis serogroup A capsular polysaccharide (MenA CPS) is a component of commercial vaccines, but is unstable. Here, the authors generate glycomimetic oligomers that demonstrate higher stability than their natural counterparts and induce protective antibodies in mice.

    • Jacopo Enotarpi
    • , Marta Tontini
    • , Cristiana Balocchi
    • , Daan van der Es
    • , Ludovic Auberger
    • , Evita Balducci
    • , Filippo Carboni
    • , Daniela Proietti
    • , Daniele Casini
    • , Dmitri V. Filippov
    • , Hermen S. Overkleeft
    • , Gijsbert A. van der Marel
    • , Cinzia Colombo
    • , Maria Rosaria Romano
    • , Francesco Berti
    • , Paolo Costantino
    • , Jeroen D. C. Codeé
    • , Luigi Lay
    •  & Roberto Adamo
  • Article
    | Open Access

    So far no vaccine or antiviral therapy is available for Echovirus 30 (E30) that causes aseptic meningitis. Here, the authors generate and characterise two E30-specific monoclonal antibodies that block binding of the virus to its attachment receptor CD55 and uncoating receptor FcRn, and determine the cryo-EM structures of E30 with the bound neutralizing antibodies.

    • Kang Wang
    • , Binyang Zheng
    • , Li Zhang
    • , Lunbiao Cui
    • , Xuan Su
    • , Qian Zhang
    • , Zhenxi Guo
    • , Yu Guo
    • , Wei Zhang
    • , Ling Zhu
    • , Fengcai Zhu
    • , Zihe Rao
    •  & Xiangxi Wang
  • Article
    | Open Access

    Echovirus 30 (E30) belongs to the Enterovirus-B group and causes aseptic meningitis in humans. Here, the authors present the cryo-EM structures of the E30 E-particle, A-particle and the mature virion, as well as structures of E30 in complex with its receptor FcRn and CD55, and furthermore they describe a structure-based algorithm that allows the prediction of EV receptor usage.

    • Kang Wang
    • , Ling Zhu
    • , Yao Sun
    • , Minhao Li
    • , Xin Zhao
    • , Lunbiao Cui
    • , Li Zhang
    • , George F. Gao
    • , Weiwei Zhai
    • , Fengcai Zhu
    • , Zihe Rao
    •  & Xiangxi Wang
  • Article
    | Open Access

    Here, Hanke et al. immunize an alpaca with SARS-CoV-2 spike protein domains and identify a nanobody that binds the receptor binding domain of spike in both the up and down conformations and sterically hinders ACE2 engagement.

    • Leo Hanke
    • , Laura Vidakovics Perez
    • , Daniel J. Sheward
    • , Hrishikesh Das
    • , Tim Schulte
    • , Ainhoa Moliner-Morro
    • , Martin Corcoran
    • , Adnane Achour
    • , Gunilla B. Karlsson Hedestam
    • , B. Martin Hällberg
    • , Ben Murrell
    •  & Gerald M. McInerney
  • Article
    | Open Access

    Coronavirus main protease is essential for viral polyprotein processing and maturation. Here Fu et al. report efficient inhibition of SARS-CoV-2 replication using two inhibitors - Boceprevir and GC376 - targeting the active site of the main viral protease.

    • Lifeng Fu
    • , Fei Ye
    • , Yong Feng
    • , Feng Yu
    • , Qisheng Wang
    • , Yan Wu
    • , Cheng Zhao
    • , Huan Sun
    • , Baoying Huang
    • , Peihua Niu
    • , Hao Song
    • , Yi Shi
    • , Xuebing Li
    • , Wenjie Tan
    • , Jianxun Qi
    •  & George Fu Gao
  • Article
    | Open Access

    Bacteriophages and their hosts are involved in a constant evolutionary arms race that should lead to divergence between phage genes over time. Here, the authors recruit metagenomic reads to virus reference genomes and genome fragments in samples from cryoconite holes and show that phages with near-identical core genomes maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants.

    • Christopher M. Bellas
    • , Declan C. Schroeder
    • , Arwyn Edwards
    • , Gary Barker
    •  & Alexandre M. Anesio
  • Article
    | Open Access

    SARS-CoV-2 mainly transmits via respiratory droplets. Here Deng et al. show that SARS-CoV-2 can infect rhesus macaques via ocular conjunctival inoculation.

    • Wei Deng
    • , Linlin Bao
    • , Hong Gao
    • , Zhiguang Xiang
    • , Yajin Qu
    • , Zhiqi Song
    • , Shuran Gong
    • , Jiayi Liu
    • , Jiangning Liu
    • , Pin Yu
    • , Feifei Qi
    • , Yanfeng Xu
    • , Fengli Li
    • , Chong Xiao
    • , Qi Lv
    • , Jing Xue
    • , Qiang Wei
    • , Mingya Liu
    • , Guanpeng Wang
    • , Shunyi Wang
    • , Haisheng Yu
    • , Ting Chen
    • , Xing Liu
    • , Wenjie Zhao
    • , Yunlin Han
    •  & Chuan Qin
  • Article
    | Open Access

    Some infants develop broadly neutralizing antibodies (bnAbs) to HIV in a shorter time frame than adults, but the reasons aren’t well understood. Here, the authors study a cohort of 51 HIV-1 clade C perinatally infected infants of Indian origin and find that multivariant infection is associated with bnAbs in elite neutralizers.

    • Nitesh Mishra
    • , Shaifali Sharma
    • , Ayushman Dobhal
    • , Sanjeev Kumar
    • , Himanshi Chawla
    • , Ravinder Singh
    • , Muzamil Ashraf Makhdoomi
    • , Bimal Kumar Das
    • , Rakesh Lodha
    • , Sushil Kumar Kabra
    •  & Kalpana Luthra
  • Article
    | Open Access

    Fusarium graminearum is a major fungal pathogen of cereals. Here the authors show that F. graminearum secretes an effector, Osp24, that induces degradation of the wheat TaSnRK1α kinase to promote disease while an orphan wheat protein, TaFROG1, can compete with Osp24 for binding to TaSnRK1α and protect it from degradation

    • Cong Jiang
    • , Ruonan Hei
    • , Yang Yang
    • , Shijie Zhang
    • , Qinhu Wang
    • , Wei Wang
    • , Qiang Zhang
    • , Min Yan
    • , Gengrui Zhu
    • , Panpan Huang
    • , Huiquan Liu
    •  & Jin-Rong Xu
  • Article
    | Open Access

    Linking antibiotic resistance (AR) in the gut microbiome with their bacterial hosts remains challenging. Here, the authors apply bacterial Hi-C to map mobile genetic elements in metagenomes, and illustrate that genes are present in more diverse taxa in neutropenic patients than healthy subjects.

    • Alyssa G. Kent
    • , Albert C. Vill
    • , Qiaojuan Shi
    • , Michael J. Satlin
    •  & Ilana Lauren Brito
  • Article
    | Open Access

    Genome sequencing can be used to infer pathogen transmission dynamics and inform public health responses. Here, the authors sequence >1,200 SARS-CoV-2 samples from Victoria, Australia and find genomic support for the effectiveness of social restrictions in reducing transmission.

    • Torsten Seemann
    • , Courtney R. Lane
    • , Norelle L. Sherry
    • , Sebastian Duchene
    • , Anders Gonçalves da Silva
    • , Leon Caly
    • , Michelle Sait
    • , Susan A. Ballard
    • , Kristy Horan
    • , Mark B. Schultz
    • , Tuyet Hoang
    • , Marion Easton
    • , Sally Dougall
    • , Timothy P. Stinear
    • , Julian Druce
    • , Mike Catton
    • , Brett Sutton
    • , Annaliese van Diemen
    • , Charles Alpren
    • , Deborah A. Williamson
    •  & Benjamin P. Howden
  • Article
    | Open Access

    COVID-19 disease is less common in children than adults, but the extent to which SARS-CoV-2 infections are missed through symptom-driven testing is not well understood. In this study, the authors show that approximately 1% of children seeking care for reasons other than COVID-19 at a Seattle hospital in March/April 2020 were seropositive for SARS-CoV-2.

    • Adam S. Dingens
    • , Katharine H. D. Crawford
    • , Amanda Adler
    • , Sarah L. Steele
    • , Kirsten Lacombe
    • , Rachel Eguia
    • , Fatima Amanat
    • , Alexandra C. Walls
    • , Caitlin R. Wolf
    • , Michael Murphy
    • , Deleah Pettie
    • , Lauren Carter
    • , Xuan Qin
    • , Neil P. King
    • , David Veesler
    • , Florian Krammer
    • , Jane A. Dickerson
    • , Helen Y. Chu
    • , Janet A. Englund
    •  & Jesse D. Bloom
  • Article
    | Open Access

    Bacterial transcriptomic data have been used to predict antibiotic susceptibility in a species- or antibiotic-specific manner. Here, the authors show that global transcriptional disorder is a common stress response in bacteria with low fitness, and present a general approach that can predict bacterial fitness independently of species or type of stress.

    • Zeyu Zhu
    • , Defne Surujon
    • , Juan C. Ortiz-Marquez
    • , Wenwen Huo
    • , Ralph R. Isberg
    • , José Bento
    •  & Tim van Opijnen
  • Article
    | Open Access

    Gut microbial and metabolite alterations are linked to inflammatory bowel diseases pathogenesis. Here the authors identify functional microbiota signatures that correlate with disease activity by comparing patients with Crohn’s disease undergoing autologous hematopoietic stem cell transplantation who either did not respond to therapy, experienced relapse after remission or maintained remission, and show that these microbial signatures recapitulate disease activity when transferred to mice.

    • Amira Metwaly
    • , Andreas Dunkel
    • , Nadine Waldschmitt
    • , Abilash Chakravarthy Durai Raj
    • , Ilias Lagkouvardos
    • , Ana Maria Corraliza
    • , Aida Mayorgas
    • , Margarita Martinez-Medina
    • , Sinah Reiter
    • , Michael Schloter
    • , Thomas Hofmann
    • , Matthieu Allez
    • , Julian Panes
    • , Azucena Salas
    •  & Dirk Haller
  • Article
    | Open Access

    The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes during the packaging process.

    • Ivan Haralampiev
    • , Simon Prisner
    • , Mor Nitzan
    • , Matthias Schade
    • , Fabian Jolmes
    • , Max Schreiber
    • , Maria Loidolt-Krüger
    • , Kalle Jongen
    • , Jasmine Chamiolo
    • , Niklaas Nilson
    • , Franziska Winter
    • , Nir Friedman
    • , Oliver Seitz
    • , Thorsten Wolff
    •  & Andreas Herrmann
  • Article
    | Open Access

    Here, Giansanti et al. perform a system-wide and time-resolved characterization of the changes in the host cell proteome and phosphoproteome of cells infected with the enterovirus coxsackievirus B3 during a full round of replication and identify mTORC1 signalling as a major regulation network during virus infection.

    • Piero Giansanti
    • , Jeroen R. P. M. Strating
    • , Kyra A. Y. Defourny
    • , Ieva Cesonyte
    • , Alexia M. S. Bottino
    • , Harm Post
    • , Ekaterina G. Viktorova
    • , Vien Quang Tri Ho
    • , Martijn A. Langereis
    • , George A. Belov
    • , Esther N. M. Nolte-‘t Hoen
    • , Albert J. R. Heck
    •  & Frank J. M. van Kuppeveld