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1.
Int J Stem Cells ; 15(1): 3-13, 2022 Feb 28.
Article in English | MEDLINE | ID: covidwho-1716191

ABSTRACT

The current COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has completely changed human life for more than two years. Upon the emergence of this new lethal virus, multiple approaches were utilized to gain basic knowledge about its biology. Moreover, modern technologies, such as the organoid model system and next-generation sequencing, enabled us to rapidly establish strategies to tackle the disease, including vaccines and therapeutics. The recently developed organoid technology reflects human physiology more closely than other model systems. Coupled with its rapidness, high efficiency, and outstanding reliability, it has provided an opportunity to develop new drugs and understand the impact of the viral pathogen on the host. Recent findings using organoids have successfully revealed the cellular tropism of the virus in different organs and identified potential drug candidates that impact the disease. This review will summarize current achievements made with organoids in the fight against COVID-19.

2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-325339

ABSTRACT

SARS-CoV-2 is more infectious and transmissible in humans than SARS-CoV, despite the genetic relatedness and sharing the same cellular receptor. We sought to assess whether human airway organoids can model SARS-CoV-2 infection in the human airway and elucidate the cellular basis underlying its higher transmissibility. We demonstrate that SARS-CoV-2 can establish a productive infection in human airway organoids, in which ciliated cell and basal cell are infected. Wildtype SARS-CoV-2 carrying a furin cleavage motif exhibits comparable replication kinetics to a mutant virus without the motif. Human airway organoids sustain higher replication of SARS-CoV-2 than SARS-CoV, whereas interferon response is more potently induced in the latter than the former. Overall, human airway organoids can model SARS-CoV-2 infection and recapitulate the disposable role of furin cleavage motif for virus transmission in humans. SARS-CoV-2 stealth growth and evasion of interferon response may underlie pre-symptomatic virus shedding in COVID-19 patients, leading to its high infectiousness and transmissibility.

3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-314838

ABSTRACT

A new phase of the COVID-19 pandemic has started as SARS-CoV-2 variants are emerging globally, raising concerns for increased transmissibility. Early 2021 the B.1.1.7 (or Alpha) variant, became the dominant variant globally and epidemiological data suggests this variant spreads faster than its ancestors. However, this does not prove that a variant is intrinsically phenotypically different, let alone more transmissible or fit. Therefore, rapid phenotyping of SARS-CoV-2 variants of concern is urgently needed. We found that airway, intestinal and alveolar organoids infected with the B.1.1.7 variant produced higher levels of infectious virus late in infection compared to its 614G-containing ancestor. The B.1.1.7 variant also had a clear fitness advantage in human airway organoids. In alveolar organoids, the B.1.1.7 variant induced lower levels of innate immunity. These findings suggest that the B.1.1.7 variant is phenotypically different from its ancestor and may explain why this clade has spread rapidly across the globe.Funding Information: This work was supported by Netherlands Organization for Health Research and Development (10150062010008;B.L.H.), PPP allowance (LSHM19136;B.L.H.). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 874735. Declaration of Interests: H.C. is inventor on patents held by the Royal Netherlands Academy of Arts and Sciences that cover organoid technology. H.C.’s full disclosure is given at https://www.uu.nl/staff/JCClevers. All other authors have nothing to declare. Ethics Approval Statement: The Medical Ethical Committee of the Erasmus MC Rotterdam granted permission for this study (METC 2012-512). The study was approved by the UMC Utrecht (Utrecht, The Netherlands) ethical committee and was in accordance with the Declaration of Helsinki and according to Dutch law. This study is compliant with all relevant ethical regulations regarding research involving human participants.

4.
Nat Commun ; 12(1): 6610, 2021 11 16.
Article in English | MEDLINE | ID: covidwho-1521737

ABSTRACT

COVID-19 typically manifests as a respiratory illness, but several clinical reports have described gastrointestinal symptoms. This is particularly true in children in whom gastrointestinal symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. These observations raise the question of whether the virus can replicate within the stomach. Here we generate gastric organoids from fetal, pediatric, and adult biopsies as in vitro models of SARS-CoV-2 infection. To facilitate infection, we induce reverse polarity in the gastric organoids. We find that the pediatric and late fetal gastric organoids are susceptible to infection with SARS-CoV-2, while viral replication is significantly lower in undifferentiated organoids of early fetal and adult origin. We demonstrate that adult gastric organoids are more susceptible to infection following differentiation. We perform transcriptomic analysis to reveal a moderate innate antiviral response and a lack of differentially expressed genes belonging to the interferon family. Collectively, we show that the virus can efficiently infect the gastric epithelium, suggesting that the stomach might have an active role in fecal-oral SARS-CoV-2 transmission.


Subject(s)
COVID-19/pathology , Intestinal Mucosa/virology , Organoids/virology , SARS-CoV-2/physiology , Stomach/virology , Virus Replication/physiology , Aborted Fetus , Aged , Animals , COVID-19/virology , Cell Line , Child , Child, Preschool , Chlorocebus aethiops , Humans , Infant , Intestinal Mucosa/pathology , Middle Aged , Organoids/pathology , SARS-CoV-2/isolation & purification , Stomach/pathology
5.
Nat Commun ; 12(1): 5498, 2021 09 17.
Article in English | MEDLINE | ID: covidwho-1428814

ABSTRACT

Rapid identification of host genes essential for virus replication may expedite the generation of therapeutic interventions. Genetic screens are often performed in transformed cell lines that poorly represent viral target cells in vivo, leading to discoveries that may not be translated to the clinic. Intestinal organoids are increasingly used to model human disease and are amenable to genetic engineering. To discern which host factors are reliable anti-coronavirus therapeutic targets, we generate mutant clonal IOs for 19 host genes previously implicated in coronavirus biology. We verify ACE2 and DPP4 as entry receptors for SARS-CoV/SARS-CoV-2 and MERS-CoV respectively. SARS-CoV-2 replication in IOs does not require the endosomal Cathepsin B/L proteases, but specifically depends on the cell surface protease TMPRSS2. Other TMPRSS family members were not essential. The newly emerging coronavirus variant B.1.1.7, as well as SARS-CoV and MERS-CoV similarly depended on TMPRSS2. These findings underscore the relevance of non-transformed human models for coronavirus research, identify TMPRSS2 as an attractive pan-coronavirus therapeutic target, and demonstrate that an organoid knockout biobank is a valuable tool to investigate the biology of current and future emerging coronaviruses.


Subject(s)
Angiotensin-Converting Enzyme 2/genetics , Biological Specimen Banks , CRISPR-Cas Systems , Coronavirus , Dipeptidyl Peptidase 4/genetics , Organoids/metabolism , Serine Endopeptidases/genetics , COVID-19 , Cell Line , Humans , Middle East Respiratory Syndrome Coronavirus , SARS-CoV-2 , Transcriptome , Virus Replication
6.
Dis Model Mech ; 14(6)2021 06 01.
Article in English | MEDLINE | ID: covidwho-1295507

ABSTRACT

The COVID-19 pandemic has emphasised the need to develop effective treatments to combat emerging viruses. Model systems that poorly represent a virus' cellular environment, however, may impede research and waste resources. Collaborations between cell biologists and virologists have led to the rapid development of representative organoid model systems to study severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We believe that lung organoids, in particular, have advanced our understanding of SARS-CoV-2 pathogenesis, and have laid a foundation to study future pandemic viruses and develop effective treatments.


Subject(s)
COVID-19/virology , Lung/virology , Models, Biological , Organoids/virology , SARS-CoV-2 , Animals , COVID-19/epidemiology , Humans , Pandemics , Pulmonary Alveoli/virology , Research Design/trends , SARS-CoV-2/pathogenicity
7.
Stem Cell Reports ; 16(3): 412-418, 2021 03 09.
Article in English | MEDLINE | ID: covidwho-1125251

ABSTRACT

Many pathogenic viruses that affect man display species specificity, limiting the use of animal models. Studying viral biology and identifying potential treatments therefore benefits from the development of in vitro cell systems that closely mimic human physiology. In the current COVID-19 pandemic, rapid scientific insights are of the utmost importance to limit its impact on public health and society. Organoids are emerging as versatile tools to progress the understanding of SARS-CoV-2 biology and to aid in the quest for novel treatments.


Subject(s)
COVID-19/virology , Organoids/virology , Animals , Humans , Pandemics/prevention & control , SARS-CoV-2/pathogenicity
8.
EMBO J ; 40(5): e105912, 2021 03 01.
Article in English | MEDLINE | ID: covidwho-962496

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which may result in acute respiratory distress syndrome (ARDS), multiorgan failure, and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. Here, we describe a human 2D air-liquid interface culture system which was characterized by confocal and electron microscopy and single-cell mRNA expression analysis. In this model, alveolar cells, but also basal cells and rare neuroendocrine cells, are grown from 3D self-renewing fetal lung bud tip organoids. These cultures were readily infected by SARS-CoV-2 with mainly surfactant protein C-positive alveolar type II-like cells being targeted. Consequently, significant viral titers were detected and mRNA expression analysis revealed induction of type I/III interferon response program. Treatment of these cultures with a low dose of interferon lambda 1 reduced viral replication. Hence, these cultures represent an experimental model for SARS-CoV-2 infection and can be applied for drug screens.


Subject(s)
Alveolar Epithelial Cells/metabolism , COVID-19/metabolism , Models, Biological , Organoids/metabolism , SARS-CoV-2/physiology , Virus Replication , Alveolar Epithelial Cells/pathology , Alveolar Epithelial Cells/virology , Animals , COVID-19/virology , Chlorocebus aethiops , Gene Expression Regulation , Humans , Interferon Type I/biosynthesis , Interferons/biosynthesis , Organoids/pathology , Organoids/virology , Vero Cells
9.
Cell ; 183(7): 1930-1945.e23, 2020 12 23.
Article in English | MEDLINE | ID: covidwho-921845

ABSTRACT

RNA viruses are among the most prevalent pathogens and are a major burden on society. Although RNA viruses have been studied extensively, little is known about the processes that occur during the first several hours of infection because of a lack of sensitive assays. Here we develop a single-molecule imaging assay, virus infection real-time imaging (VIRIM), to study translation and replication of individual RNA viruses in live cells. VIRIM uncovered a striking heterogeneity in replication dynamics between cells and revealed extensive coordination between translation and replication of single viral RNAs. Furthermore, using VIRIM, we identify the replication step of the incoming viral RNA as a major bottleneck of successful infection and identify host genes that are responsible for inhibition of early virus replication. Single-molecule imaging of virus infection is a powerful tool to study virus replication and virus-host interactions that may be broadly applicable to RNA viruses.


Subject(s)
Protein Biosynthesis , RNA Viruses/physiology , Virus Replication/physiology , Cell Line, Tumor , Cell Survival , HEK293 Cells , Host-Pathogen Interactions , Humans , Interferons/metabolism , RNA Transport , RNA, Viral/genetics , Reproducibility of Results , Single Molecule Imaging , Time Factors
11.
Curr Biol ; 30(18): R1014-R1018, 2020 09 21.
Article in English | MEDLINE | ID: covidwho-703973

ABSTRACT

Recently, a petition was offered to the European Commission calling for an immediate ban on animal testing. Although a Europe-wide moratorium on the use of animals in science is not yet possible, there has been a push by the non-scientific community and politicians for a rapid transition to animal-free innovations. Although there are benefits for both animal welfare and researchers, advances on alternative methods have not progressed enough to be able to replace animal research in the foreseeable future. This trend has led first and foremost to a substantial increase in the administrative burden and hurdles required to make timely advances in research and treatments for human and animal diseases. The current COVID-19 pandemic clearly highlights how much we actually rely on animal research. COVID-19 affects several organs and systems, and the various animal-free alternatives currently available do not come close to this complexity. In this Essay, we therefore argue that the use of animals is essential for the advancement of human and veterinary health.


Subject(s)
Animal Experimentation , Biomedical Research , Coronavirus Infections , Disease Models, Animal , Pandemics , Pneumonia, Viral , Animals , Betacoronavirus , COVID-19 , Humans , SARS-CoV-2
12.
Nat Rev Mol Cell Biol ; 21(7): 355-356, 2020 07.
Article in English | MEDLINE | ID: covidwho-459241
13.
Science ; 369(6499): 50-54, 2020 07 03.
Article in English | MEDLINE | ID: covidwho-154670

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause coronavirus disease 2019 (COVID-19), an influenza-like disease that is primarily thought to infect the lungs with transmission through the respiratory route. However, clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) is highly expressed on differentiated enterocytes. In human small intestinal organoids (hSIOs), enterocytes were readily infected by SARS-CoV and SARS-CoV-2, as demonstrated by confocal and electron microscopy. Enterocytes produced infectious viral particles, whereas messenger RNA expression analysis of hSIOs revealed induction of a generic viral response program. Therefore, the intestinal epithelium supports SARS-CoV-2 replication, and hSIOs serve as an experimental model for coronavirus infection and biology.


Subject(s)
Betacoronavirus/physiology , Enterocytes/virology , Ileum/virology , Virus Replication , Angiotensin-Converting Enzyme 2 , Betacoronavirus/ultrastructure , Cell Culture Techniques , Cell Differentiation , Cell Lineage , Cell Proliferation , Culture Media , Enterocytes/metabolism , Enterocytes/ultrastructure , Gene Expression , Humans , Ileum/metabolism , Ileum/ultrastructure , Lung/virology , Male , Organoids , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , Receptors, Virus/genetics , Receptors, Virus/metabolism , Respiratory Mucosa/virology , SARS Virus/physiology , SARS-CoV-2
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