Manger au temps du coronavirus. Enquête sur les systèmes alimentaires
Yuna ChiffoleauCatherine DarrotGilles MaréchalLuc BodiguelGrégori AkermannBlaise BergerFélix LallemandBrit Anne-CécileFlorence EgalDoriane Guennoc
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Abstract:
Le 15 mars 2020, a la veille du confinement, un appel a retours d'experiences a ete lance pour saisir les impacts du la crise du coronavirus sur les systemes alimentaires : quelle mise a l'epreuve ? Quelles adaptations ? Quelles innovations ?
Avec l'appui du Reseau Mixte Technologique Alimentation Locale, 780 temoignages ont ete recueillis, en provenance de toute la France, et analyses pas une equipe associant chercheurs et acteurs du developpement. Cinq bulletins de partage ont ete diffuses, a chaque etape de la pandemie en France, compilant les experiences autour de plusieurs themes : des foyers jusqu'aux exploitations agricoles, en passant par les chaines de solidarite et d'approvisionnement.
Cet ouvrage reprend ces themes en deroulant les fil des evenements jusqu'au mois de juin 2020. Il donne une place preponderante a l'expression brute des acteurs, mais il propose aussi des lectures transversales et des recommandations pour les acteurs publics et prives.Keywords:
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The coronavirus COVID19 pandemic is an emerging biosafety threat to the nation and the world (1). There are no treatments approved for coronavirus infection in humans (2) and there is a lack of information available regarding the basic transcriptional behavior of human cells and mammalian tissues following coronavirus infection. We mined multiple independent public (3) or published datasets (4-7) containing transcriptome data from infection models of human coronavirus 229E, the severe acute respiratory syndrome (SARS) coronavirus and Middle East respiratory syndrome (MERS) coronavirus to discover genes whose differential expression was conserved across the coronavirus family. We identified the GTP binding protein overexpressed in skeletal muscle, GEM (8), also known as Kir, as a differentially expressed gene following infection of human cells with two types of MERS coronavirus, after infection of human cells with human coronavirus 229E, and in the lungs of mice and ferrets infected with SARS coronavirus. GEM induction after viral infection appears to be conserved across the coronavirus family and may be found in patients infected with the novel coronavirus SARS-CoV-2.
Coronavirus
Pandemic
Bovine coronavirus
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The sequences of spike glycoprotein genes of six human coronavirus strains,five avian infectious bronchitis virus strains,four murine hepatitis virus strains,seven bovine coronavirus strains,two feline coronavirus strains,nine porcine coronavirus strains (epidemic diarrhea virus,transmissible gastroenteritis virus),four canine coronavirus strains and five SARS coronavirus strains were compared by software DNAstar.It is shown that the sequence consensus of human coronavirus spike glycoprotein genes is 27.2%～99.5%;that of avian infectious bronchitis viruses is 81.5%～100%;of feline coronavirus strains is 79.5%～89.6%;of bovine coronavirus strains is 97.7%～100%;of canine coronavirus strains is 64.9%～98.8%;of SARS-related coronavirus is 99.9%～100%.The sequence consensus of spike glycoprotein genes of SARS coronavirus strains compared with forty-two other coronavirus strains is lower than 30.8%,which indicates that SARS-related coronavirus might not evolve from the other kind of viruses,but it is a new kind of virus that humankind has never touched before.
Coronavirus
Bovine coronavirus
Coronaviridae
Mouse hepatitis virus
Nidovirales
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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reignited global interest in animal coronaviruses and their potential for human transmission. While bats are thought to be the wildlife reservoir of SARS-CoV and SARS-CoV-2, the widespread human coronavirus OC43 is thought to have originated in rodents. Here, we sampled 297 rodents and shrews, representing eight species, from three municipalities of southern China. We report coronavirus prevalences of 23.3% and 0.7% in Guangzhou and Guilin, respectively, with samples from urban areas having significantly higher coronavirus prevalences than those from rural areas. We obtained three coronavirus genome sequences from Rattus norvegicus, including a Betacoronavirus (rat coronavirus [RCoV] GCCDC3), an Alphacoronavirus (RCoV-GCCDC5), and a novel Betacoronavirus (RCoV-GCCDC4). Recombination analysis suggests that there was a potential recombination event involving RCoV-GCCDC4, murine hepatitis virus (MHV), and Longquan Rl rat coronavirus (LRLV). Furthermore, we uncovered a polybasic cleavage site, RARR, in the spike (S) protein of RCoV-GCCDC4, which is dominant in RCoV. These findings provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the value of a One Health approach to virus discovery. IMPORTANCE Surveillance of viruses among rodents in rural and urban areas of South China identified three rodent coronaviruses, RCoV-GCCDC3, RCoV-GCCDC4, and RCoV-GCCDC5, one of which was identified as a novel potentially recombinant coronavirus with a polybasic cleavage site in the spike (S) protein. Through reverse transcription-PCR (RT-PCR) screening of coronaviruses, we found that coronavirus prevalence in urban areas is much higher than that in rural areas. Subsequently, we obtained three coronavirus genome sequences by deep sequencing. After different method-based analyses, we found that RCoV-GCCDC4 was a novel potentially recombinant coronavirus with a polybasic cleavage site in the S protein, dominant in RCoV. This newly identified coronavirus RCoV-GCCDC4 with its potentially recombinant genome and polybasic cleavage site provides a new insight into the evolution of coronaviruses. Furthermore, our results provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the necessity of a One Health approach for zoonotic disease surveillance.
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Betacoronavirus
Mouse hepatitis virus
Coronaviridae
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COVID-19 is caused by the virus SARS-CoV-2 that belongs to the Coronaviridae groups. The subgroups of the coronavirus families are α , β , γ , and δ coronavirus (the four general human coronaviruses). Representative coronaviruses consist of NL63 coronavirus (human) and porcine transmissible gastroenteritis from the Alphacoronavirus genus; mouse hepatitis coronavirus (MHV), bovine coronavirus (BCoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and Middle East respiratory syndrome coronavirus (MERS-CoV); avian infectious bronchitis virus (IBV); and porcine δ -coronavirus (PdCoV). This work exhibits, δ -coronavirus spikes are fundamentally and evolutionally more similar related to α -coronavirus spikes than to β -coronavirus or γ -coronavirus spikes due to the receptor recognition, membrane fusion phenomenon, and immune evasion behavior.
Coronavirus
Coronaviridae
Bovine coronavirus
Mouse hepatitis virus
Betacoronavirus
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Antisera prepared against each of three single and one pair of major structural proteins of the bovine coronavirus (Mebus strain) were used in immunoblotting studies to measure cross-reactivity with the structural proteins of the human coronavirus OC43 and the mouse hepatitis coronavirus A59. We conclude that the bovine coronavirus is comprised of four major structural proteins, gp190 (normally present as 120- and 100-kilodalton subunits), gp140, pp52, and gp26. The human coronavirus OC43 has an antigenically homologous counterpart of similar molecular mass to each of these proteins. The mouse hepatitis coronavirus A59 has an antigenically homologous counterpart to only three of these proteins: gp190, pp52 and gp26. There is no counterpart in the mouse virus to the 140-kilodalton glycoprotein, the apparent hemagglutinin of the bovine coronavirus.
Coronavirus
Bovine coronavirus
Mouse hepatitis virus
Coronaviridae
Betacoronavirus
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Coronavirus tropism is predominantly determined by the interaction between coronavirus spikes and the host receptors. In this regard, coronaviruses have evolved a complicated receptor-recognition system through their spike proteins. Spikes from highly related coronaviruses can recognize distinct receptors, whereas spikes of distant coronaviruses can employ the same cell-surface molecule for entry. Moreover, coronavirus spikes can recognize a broad range of cell-surface molecules in addition to the receptors and thereby can augment coronavirus attachment or entry. The receptor of Middle East respiratory syndrome coronavirus (MERS-CoV) is dipeptidyl peptidase 4 (DPP4). In this study, we identified membrane-associated 78-kDa glucose-regulated protein (GRP78) as an additional binding target of the MERS-CoV spike. Further analyses indicated that GRP78 could not independently render nonpermissive cells susceptible to MERS-CoV infection but could facilitate MERS-CoV entry into permissive cells by augmenting virus attachment. More importantly, by exploring potential interactions between GRP78 and spikes of other coronaviruses, we discovered that the highly conserved human GRP78 could interact with the spike protein of bat coronavirus HKU9 (bCoV-HKU9) and facilitate its attachment to the host cell surface. Taken together, our study has identified GRP78 as a host factor that can interact with the spike proteins of two Betacoronaviruses, the lineage C MERS-CoV and the lineage D bCoV-HKU9. The capacity of GRP78 to facilitate surface attachment of both a human coronavirus and a phylogenetically related bat coronavirus exemplifies the need for continuous surveillance of the evolution of animal coronaviruses to monitor their potential for human adaptations.
Coronavirus
Bovine coronavirus
Tissue tropism
Lineage (genetic)
Betacoronavirus
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Coronavirus
Mouse hepatitis virus
Coronaviridae
Betacoronavirus
spike protein
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The SARS epidemic has boosted interest in research on coronavirus biodiversity and genomics. Before 2003, there were only 10 coronaviruses with complete genomes available. After the SARS epidemic, up to December 2008, there was an addition of 16 coronaviruses with complete genomes sequenced. These include two human coronaviruses (human coronavirus NL63 and human coronavirus HKU1), 10 other mammalian coronaviruses [bat SARS coronavirus, bat coronavirus (bat-CoV) HKU2, bat-CoV HKU4, bat-CoV HKU5, bat-CoV HKU8, bat-CoV HKU9, bat-CoV 512/2005, bat-CoV 1A, equine coronavirus, and beluga whale coronavirus] and four avian coronaviruses (turkey coronavirus, bulbul coronavirus HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13). Two novel subgroups in group 2 coronavirus (groups 2c and 2d) and two novel subgroups in group 3 coronavirus (groups 3b and 3c) have been proposed. The diversity of coronaviruses is a result of the infidelity of RNA-dependent RNA polymerase, high frequency of homologous RNA recombination, and the large genomes of coronaviruses. Among all hosts, the diversity of coronaviruses is most evidenced in bats and birds, which may be a result of their species diversity, ability to fly, environmental pressures, and habits of roosting and flocking. The present evidence supports that bat coronaviruses are the gene pools of group 1 and 2 coronaviruses, whereas bird coronaviruses are the gene pools of group 3 coronaviruses. With the increasing number of coronaviruses, more and more closely related coronaviruses from distantly related animals have been observed, which were results of recent interspecies jumping and may be the cause of disastrous outbreaks of zoonotic diseases.
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Betacoronavirus
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[Objective] To further compare Bat SARS coronavirus with coronaviruses of human and civets, in order to explore their similarities. [Methods] A system anagenesis relation among Bat SARS coronavirus, Human SARS coronavirus, and Civet SARS coronavirus was explored in present study, and a genetic sequence map was drawn. Additionally, a 3D model of S protein and N protein was predicted. [Results] The sequence analysis showed that Bat SARS coronavirus was with highly similarity as SARS coronaviruses of human and palm civets. The system anagenesis analysis demonstrated that Bat-SARS-CoV and SARS-CoV formed a group called Group 2b CoV, which was distant to Group 2 CoV. [Conclusion] It is not very possible that Bat SARS coronavirus HKU3-1 was not transmitted from Human SARS coronavirus, but Bat SARS coronavirus and Civet SARS coronavirus may share the same origin, which implies Bat SARS coronavirus might still be infectious to human.
Coronavirus
Betacoronavirus
Coronaviridae
2019-20 coronavirus outbreak
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Coronavirus
Betacoronavirus
Lineage (genetic)
Bovine coronavirus
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