SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant

Konno, Yoriyuki; Kimura, Izumi; Uriu, Keiya; Fukushi, Masaya; Irie, Takashi; Koyanagi, Yoshio; Nakagawa, So; Sato, Kei

doi:10.1101/2020.05.11.088179

Cited by 63 publications

(68 citation statements)

References 42 publications

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“…Interestingly, a large overlap of DEGs with previous transcriptomic studies of SARS-CoV infection was found, including the peculiar feature of a limited/absent type I IFN induction and the recruitment of a subset of cytoplasmic PRRs. Similarly to SARS-CoV, in which ORF3B and ORF6 are the main antagonists of IFN, a recent study currently under peerrevision 36 indicates the SARS-CoV-2 ORF3B protein as a potent IFN inhibitor, supporting ours and the published transcriptomic data herein discussed.…”

Section: Discussionsupporting

confidence: 83%

SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids

Giobbe

Bonfante

Zambaiti

et al. 2020

Preprint

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Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global public health emergency. COVID-19 typically manifests as a respiratory illness but an increasing number of clinical reports describe gastrointestinal (GI) symptoms. This is particularly true in children in whom GI symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. By contrast, fetuses seem to be rarely affected by COVID-19, although the virus has been detected in placentas of affected women. These observations raise the question of whether the virus can infect and replicate within the stomach once ingested. Moreover, it is not yet clear whether active replication of SARS-CoV-2 is possible in the stomach of children or in fetuses at different developmental stages. Here we show the novel derivation of fetal gastric organoids from 8-21 post-conception week (PCW) fetuses, and from pediatric biopsies, to be used as an in vitro model for SARS-CoV-2 gastric infection. Gastric organoids recapitulate human stomach with linear increase of gastric mucin 5AC along developmental stages, and expression of gastric markers pepsinogen, somatostatin, gastrin and chromogranin A. In order to investigate SARS-CoV-2 infection with minimal perturbation and under steady-state conditions, we induced a reversed polarity in the gastric organoids (RP-GOs) in suspension. In this condition of exposed apical polarity, the virus can easily access viral receptor angiotensin-converting enzyme 2 (ACE2). The pediatric RP-GOs are fully susceptible to infection with SARS-CoV-2, where viral nucleoprotein is expressed in cells undergoing programmed cell death, while the efficiency of infection is significantly lower in fetal organoids. The RP-GOs derived from pediatric patients show sustained robust viral replication of SARS-CoV-2, compared with organoids derived from fetal stomachs. Transcriptomic analysis shows a moderate innate antiviral response and the lack of differentially expressed genes belonging to the interferon family. Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. However, the virus can efficiently infect gastric epithelium in pediatric patients, suggesting that the stomach might have an active role in fecal-oral transmission of SARS-CoV-2.

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Section: Discussionsupporting

confidence: 83%

SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids

Giobbe

Bonfante

Zambaiti

et al. 2020

Preprint

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“…At least five ORFs encoding accessory genes have been reported for SARS-CoV-2: ORF3a, ORF6, ORF7a, ORF7b and ORF8 (GenBank entry NC_045512.2) as well as potentially ORF3b 99 and ORF9b 100 , the latter of which is probably expressed as a result of leaky scanning of the sgRNA of the nucleocapsid protein 80 , 99 , 101 . In addition, ORF10 has been postulated to be located downstream of the N gene.…”

Section: Viral Gene Expression and Rna Synthesismentioning

confidence: 99%

Coronavirus biology and replication: implications for SARS-CoV-2

et al. 2020

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The SARS-CoV-2 pandemic and its unprecedented global societal and economic disruptive impact has marked the third zoonotic introduction of a highly pathogenic coronavirus into the human population. Although the previous coronavirus SARS-CoV and MERS-CoV epidemics raised awareness of the need for clinically available therapeutic or preventive interventions, to date, no treatments with proven efficacy are available. The development of effective intervention strategies relies on the knowledge of molecular and cellular mechanisms of coronavirus infections, which highlights the significance of studying virus–host interactions at the molecular level to identify targets for antiviral intervention and to elucidate critical viral and host determinants that are decisive for the development of severe disease. In this Review, we summarize the first discoveries that shape our current understanding of SARS-CoV-2 infection throughout the intracellular viral life cycle and relate that to our knowledge of coronavirus biology. The elucidation of similarities and differences between SARS-CoV-2 and other coronaviruses will support future preparedness and strategies to combat coronavirus infections.

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“…Previous studies proposed four ORFs overlapping 3a 6,[8][9][10][11][12][13] : 3c (41 codons), 3d (57 codons), 3b (22 codons, a truncated ortholog of SARS-CoV ORF3b), and a subset of 3d (33 codons). ORF3c was proposed using synonymous constraint across 6 closely-related strains 8 and a broader set of Sarbecoviruses 9 , although on its own such evidence could also stem from other overlapping functional elements (and is abundant in SARS-CoV-2 even outside dual-coding regions), and using ribosome…”

Section: Orf3c Is a Novel Functional Proteinmentioning

confidence: 99%

“…The paper introducing SARS-CoV-2 also shows 3b (which overlaps 3a in SARS-CoV but is truncated in SARS-CoV-2, with several in-frame stop codons) 1 . Other publications [5][6][7][8][9][10][11][12][13] include different subsets, use different names, or propose additional ORFs (including 3c and 3d overlapping 3a). NCBI annotates SARS-CoV (NC_004718.3) orthologs of 3a, 6, 7a, 7b, and 9b, but 8 is split into 8a and 8b, 3b is included, and neither 9c nor 10 are included.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

Jungreis

Sealfon

Kellis

2020

Preprint

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Despite its overwhelming clinical importance for understanding and mitigating the COVID-19 pandemic, the protein-coding gene content of the SARS-CoV-2 genome remains unresolved, with the function and even protein-coding status of many hypothetical proteins unknown and often conflicting among different annotations, thus hindering efforts for systematic dissection of its biology and the impact of recent mutations. Comparative genomics is a powerful approach for distinguishing protein-coding versus non-coding functional elements, based on their characteristic patterns of change, which we previously used to annotate protein-coding genes in human, fly, and other species. Here, we use comparative genomics to provide a high-confidence set of SARS-CoV-2 protein-coding genes, to characterize their protein-level and nucleotide-level evolutionary constraint, and to interpret the functional implications for SARS-CoV-2 mutations acquired during the current pandemic. We select 44 complete Sarbecovirus genomes at evolutionary distances well-suited for protein-coding and non-coding element identification, create whole-genome alignments spanning all named and putative genes, and quantify their protein-coding evolutionary signatures using PhyloCSF and their overlapping constraint using FRESCo. We find strong protein-coding signatures for all named genes and for hypothetical ORFs 3a, 6, 7a, 7b, and 8, indicating protein-coding roles, and provide strong evidence of protein-coding status for a recently-proposed alternate-frame novel ORF within 3a. By contrast, ORF10 shows no protein-coding signatures but shows unusually-high nucleotide-level constraint, indicating it has important but non-coding functions, and ORF14 and SARS-CoV-1 ORF3b, which overlap other genes, lack evolutionary signatures expected for dual-coding regions, indicating they do not produce functional proteins. ORF9b has ambiguous protein-coding signatures, preventing us from resolving its protein-coding status. ORF8 shows extremely fast nucleotide-level evolution, lacks a known function, and was deactivated in SARS-CoV-1, but shows clear signatures indicating protein-coding function worthy of further investigation given its rapid evolution and potential role in replication. SARS-CoV-2 mutations are preferentially excluded from evolutionarily-constrained amino acid residues and synonymously-constrained nucleotides, indicating purifying constraint acting at both coding and non-coding levels. In contrast, we find a conserved region in the nucleocapsid that is enriched for recent mutations, which could indicate a selective signal, and find that several spike-protein mutations previously identified as candidates for increased transmission and several mutations in isolates found to generate higher viral load in-vitro disrupt otherwise-perfectly-conserved amino-acids, consistent with adaptations for human-to-human transmission.

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SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant

Abstract: 147/150 words 24

Cited by 63 publications

References 42 publications

SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids

SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids

Coronavirus biology and replication: implications for SARS-CoV-2

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

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