Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

Lin, Jing-wen; Tang, Chao; Hong, Wei; Du, Baowen; Chen, Chuan.; Wang, Minjin; Zhou, Yongzhao; Mu, Yu; Cheng, Lu; Kuivanen, Suvi; Ogando, Natacha S.; Levanov, Lev; Zhao, Yuancun; Li, Changling; Zhou, Ran; Li, Zhidan; Zhang, Yiming; Sun, Ke; Wang, Chengdi; Chen, Li; Xiao, Xia; Zheng, Xiuran; Chen, Shasha; Zhou, Zhen; Yang, Ruirui; Zhang, Dan Ning; Xu, Mengying; Song, Junwei; Wang, Danrui; Li, Yupeng; Lei, Shikun; Zeng, Wen; Yang, Qingxin; He, Ping; Zhang, Yaoyao; Zhou, Lifang; Cao, Ling; Luo, Feng; Liu, Huayi; Wang, Liping; Ye, Fei; Zhang, Ming; Li, Mengjiao; Fan, Wei; Li, Xinqiong; Li, Kaiju; Ke, Bowen; Xu, Jiannan; Yang, Huiping; He, Shusen; Pan, Ming; Yan, Yichen; Zha, Yi; Jiang, Ling-Yu; Yu, Changxiu; Liu, Yingfen; Xu, Zhiyong; Li, Qingfeng; Jiang, Yongmei; Sun, Jiufeng; Hong, Wei; Wei, Hongping; Lu, Guangwen; Vapalahti, Olli; Luo, Yunzi; Wei, Yuquan; Connor, Thomas R.; Tan, Wenjie; Snijder, Eric J.; Smura, Teemu; Liu, Weimin; Geng, Jia; Ying, Binwu; Lu, Ciyong

doi:10.1016/j.chom.2021.01.015

Cited by 103 publications

(105 citation statements)

References 54 publications

(54 reference statements)

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“…Samples of the supernatant were collected at 1 h, 24 h and 48 h post infection for qRT-PCR and at 24 h and 48 h for the TCID50 assay. Viral RNA was extracted using RNeasy Mini Kit (Qiagen, Germany), and SARS-CoV-2 qRT-PCR was performed using primers, probe and an in vitro synthesized control for RNA-dependent RNA polymerase (RdRp) as described earlier (Corman et al, 2020;Lin et al, 2021). Infectious virus titers were determined by TCID50 measurement of VeroE6-TMPRSS2 cells (Virtanen et al, 2021).…”

Section: Detection Of Viral Infection By Pseudotyped Sars-cov-2 or Vsv-g Viruses And Native Sars-cov-2mentioning

confidence: 99%

Antidepressant and antipsychotic drugs reduce viral infection by SARS-CoV-2 and fluoxetine show antiviral activity against the novel variants in vitro

Fred

Kuivanen

Uğurlu

et al. 2021

Preprint

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Background and Purpose: Repurposing of currently available drugs is a valuable strategy to tackle the consequences of COVID-19. Recently, several studies have investigated the effect of psychoactive drugs on SARS-CoV-2 in cell culture models as well as in clinical practice. Our aim was to expand these studies and test some of these compounds against newly emerged variants. Experimental Approach: Several antidepressant drugs and antipsychotic drugs with different primary mechanisms of action were tested in ACE2/TMPRSS2-expressing human embryonic kidney cells against the infection by SARS-CoV-2 spike protein-dependent pseudoviruses. Some of these compounds were also tested in human lung epithelial cell line, Calu-1, against the first wave (B.1) lineage of SARS-CoV-2 and the variants of concern, B.1.1.7 and B.1.351. Key Results: Several clinically used antidepressants, including fluoxetine, citalopram, reboxetine, imipramine, as well as antipsychotic compounds chlorpromazine, flupenthixol, and pimozide inhibited the infection by pseudotyped viruses with minimal effects on cell viability. The antiviral action of several of these drugs was verified in Calu-1 cells against the (B.1) lineage of SARS-CoV-2. By contrast, the anticonvulsant carbamazepine, and novel antidepressants ketamine and its derivatives as well as MAO and phosphodiesterase inhibitors phenelzine and rolipram, respectively, showed no activity in the pseudovirus model. Furthermore, fluoxetine remained effective against pseudo viruses with N501Y, K417N, and E484K spike mutations, and the VoC-1 (B.1.1.7) and VoC-2 (B.1.351) variants of SARS-CoV-2. Conclusion and Implications: Our study confirms previous data and extends information on the repurposing of these drugs to counteract SARS-CoV-2 infection including different variants of concern.

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Section: Detection Of Viral Infection By Pseudotyped Sars-cov-2 or Vsv-g Viruses And Native Sars-cov-2mentioning

confidence: 99%

Antidepressant and antipsychotic drugs reduce viral infection by SARS-CoV-2 and fluoxetine show antiviral activity against the novel variants in vitro

Fred

Kuivanen

Uğurlu

et al. 2021

Preprint

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“…Unlike cellular mRNA, viral mRNA remains robustly translated in the presence of nsp1 6,30,33,46 . As shown for both SARS-CoV and CoV-2, preservation of viral gene expression in the presence of nsp1 requires a conserved stem loop (termed SL1) within the 5’ leader sequence present on viral mRNAs 6,24,30,31 .…”

Section: Discussionmentioning

confidence: 99%

“…It is therefore possible that specific nsp1 mutations such as R99, R124 and R125 could impair viral pathogenesis as a consequence of translational suppression of viral transcripts in addition to impaired shutoff of host genes such as those involved in interferon signaling. It will be of interest to determine whether this underlies the lower viral load and decreased pathogenesis reported for the recurrent CoV-2 variant that contains an 11 aa nsp1 N-terminal domain deletion, or other variants that may emerge with changes to these regions of nsp1 33 . Likewise, small molecule drugs that phenocopy these mutations could serve as therapies or prophylactics for viral infection.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, deciphering the mechanistic contributions of domains outside of the C-terminal region in nsp1-induced host shutoff and viral escape will be key to ultimately understanding CoV virulence. Indeed, a recent CoV-2 genomic monitoring study reported a recurrent viral variant found in 37 countries containing an 11 amino acid (aa) deletion in the N-terminus of nsp1 that is associated with lower viral load, lower serum IFN-β and enrichment of less severe disease 32,33 .…”

Section: Introductionmentioning

confidence: 99%

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The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression

et al. 2021

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Nonstructural protein 1 (nsp1) is the first viral protein synthesized during coronavirus (CoV) infection and is a key virulence factor that dampens the innate immune response. It restricts cellular gene expression through a combination of inhibiting translation by blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We performed a detailed structure-guided mutational analysis of CoV-2 nsp1 coupled with in vitro and cell-based functional assays, revealing insight into how it coordinates these activities against host but not viral mRNA. We found that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, thereby enhancing its restriction of host gene expression. These residues are also critical for the ability of mRNA containing the CoV-2 leader sequence to escape translational repression. Notably, we identify CoV-2 nsp1 mutants that gain the ability to repress translation of viral leader-containing transcripts. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in CoV-2 nsp1 could attenuate the virus.

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“…Currently, over half a million complete and high coverage genomes are accessible on GISAID 10,11 , which aids immensely in tracking the viral sequences globally 12 . Novel SARS-CoV-2 variants are continuously arising and besides providing signals for epidemiological tracking, a subset of the resulting variants will have a functional impact on transmission and infection [13][14][15] . It is therefore critical to monitor the genetic viral diversity throughout the pandemic.…”

Section: Mainmentioning

confidence: 99%

Saudi Arabian SARS-CoV-2 genomes implicate a mutant Nucleocapsid protein in modulating host interactions and increased viral load in COVID-19 patients

Mourier

Shuaib

Hala

et al. 2021

Preprint

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Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. The availability of patient hospital records is crucial for linking the genomic sequence information to virus function during the course of infections. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. From the assembled sequences, we estimate the SARS-CoV-2 effective population size and infection rate and outline the epidemiological dynamics of import and transmission events during this period in Saudi Arabia. We show that two consecutive mutations (R203K/G204R) in the SARS-CoV-2 nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein by mass-spectrometry analysis. Furthermore, analysis of the host cell transcriptome suggests that the mutant N protein results in dysregulated interferon response genes. We provide crucial information in linking the R203K/G204R mutations in the N protein as a major modulator of host-virus interactions and increased viral load and underline the potential of the nucleocapsid protein as a drug target during infection.

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Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

Cited by 103 publications

References 54 publications

Antidepressant and antipsychotic drugs reduce viral infection by SARS-CoV-2 and fluoxetine show antiviral activity against the novel variants in vitro

Antidepressant and antipsychotic drugs reduce viral infection by SARS-CoV-2 and fluoxetine show antiviral activity against the novel variants in vitro

The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression

Saudi Arabian SARS-CoV-2 genomes implicate a mutant Nucleocapsid protein in modulating host interactions and increased viral load in COVID-19 patients

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