Exogenous coronavirus interacts with endogenous retrotransposon in human cells

Yin, Ying; Liu, Xiao-zhao; He, Ximiao; Zhou, Li-Quan

doi:10.21203/rs.3.rs-40063/v1

Cited by 14 publications

(31 citation statements)

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“…We next quantified the reads that partly mapped to the human genome and partly mapped to the SARS-CoV2 genome (see methods ). We found that nearly 0.05-1% of all viral reads are formed of hybrid sequences between host and virus RNAs, a frequency consistent with that recently reported by others 15,16 ( Fig. 1C ).…”

Section: Resultssupporting

confidence: 92%

“…RNA-sequencing reads that partly align to the host genome and partly align to the viral genome are the signature of HVC events in RNA-sequencing datasets. Recent reports 15,16 suggesting the presence of HVC events in SARS-CoV2-infected cells have been interpreted as supporting viral integration into the human genome as a mechanism of viral persistence. To gain insights into the authenticity of these events, we re-analyzed the 3 available RNA-seq datasets from patients with COVID-19 (n=57 samples) and in vitro SARS-CoV2 infected cells (n=64 samples).…”

Section: Resultsmentioning

confidence: 99%

“…In particular, relatively little is known about the processes following viral infection and why some individuals develop little to no symptoms, while others develop life-threatening or persistent (“long”) COVID-19. Recent studies have identified host-virus chimeric (HVC) reads in RNA-sequencing data from SARS-CoV2 infected cells and samples from COVID-19 patients 15,16 . Both studies have suggested that HVC events support potential “human genome invasion” and “integration” by SARS-CoV2.…”

Section: Introductionmentioning

confidence: 99%

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Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual

Yan

Chakravorty

Mirabelli

et al. 2021

Preprint

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Pathogenic mechanisms underlying severe SARS-CoV2 infection remain largely unelucidated. High throughput sequencing technologies that capture genome and transcriptome information are key approaches to gain detailed mechanistic insights from infected cells. These techniques readily detect both pathogen and host-derived sequences, providing a means of studying host-pathogen interactions. Recent studies have reported the presence of host-virus chimeric (HVC) RNA in RNA-seq data from SARS-CoV2 infected cells and interpreted these findings as evidence of viral integration in the human genome as a potential pathogenic mechanism. Since SARS-CoV2 is a positive sense RNA virus that replicates in the cytoplasm it does not have a nuclear phase in its life cycle, it is biologically unlikely to be in a location where splicing events could result in genome integration. Here, we investigated the biological authenticity of HVC events. In contrast to true biological events such as mRNA splicing and genome rearrangement events, which generate reproducible chimeric sequencing fragments across different biological isolates, we found that HVC events across >100 RNA-seq libraries from patients with COVID-19 and infected cell lines, were highly irreproducible. RNA-seq library preparation is inherently error-prone due to random template switching during reverse transcription of RNA to cDNA. By counting chimeric events observed when constructing an RNA-seq library from human RNA and spike-in RNA from an unrelated species, such as fruit-fly, we estimated that ~1% of RNA-seq reads are artifactually chimeric. In SARS-CoV2 RNA-seq we found that the frequency of HVC events was, in fact, not greater than this background noise. Finally, we developed a novel experimental approach to enrich SARS-CoV2 sequences from bulk RNA of infected cells. This method enriched viral sequences but did not enrich for HVC events, suggesting that the majority of HVC events are, in all likelihood, artifacts of library construction. In conclusion, our findings indicate that HVC events observed in RNA-sequencing libraries from SARS-CoV2 infected cells are extremely rare and are likely artifacts arising from either random template switching of reverse-transcriptase and/or sequence alignment errors. Therefore, the observed HVC events do not support SARS-CoV2 fusion to cellular genes and/or integration into human genomes.

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Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual

Yan

Chakravorty

Mirabelli

et al. 2021

Preprint

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“…We thank Dr. Bing Li from Shanghai Jiao Tong University for assistance of data analysis on retrotransposon expression. This manuscript has been released as a pre-print at ResearchSquare ( Yin Y et al., 2020 ).…”

Section: Acknowledgmentsmentioning

confidence: 99%

Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells

Yin

Liu

et al. 2021

Front. Cell. Infect. Microbiol.

Self Cite

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There is an increased global outbreak of diseases caused by coronaviruses affecting respiratory tracts of birds and mammals. Recent dangerous coronaviruses are MERS-CoV, SARS-CoV, and SARS-CoV-2, causing respiratory illness and even failure of several organs. However, profound impact of coronavirus on host cells remains elusive. In this study, we analyzed transcriptome of MERS-CoV, SARS-CoV, and SARS-CoV-2 infected human lung-derived cells, and observed that infection of these coronaviruses all induced increase of retrotransposon expression with upregulation of TET genes. Upregulation of retrotransposon was also observed in SARS-CoV-2 infected human intestinal organoids. Retrotransposon upregulation may lead to increased genome instability and enhanced expression of genes with readthrough from retrotransposons. Therefore, people with higher basal level of retrotransposon such as cancer patients and aged people may have increased risk of symptomatic infection. Additionally, we show evidence supporting long-term epigenetic inheritance of retrotransposon upregulation. We also observed chimeric transcripts of retrotransposon and SARS-CoV-2 RNA for potential human genome invasion of viral fragments, with the front and the rear part of SARS-CoV-2 genome being easier to form chimeric RNA. Thus, we suggest that primers and probes for nucleic acid detection should be designed in the middle of virus genome to identify live virus with higher probability. In summary, we propose our hypothesis that coronavirus invades human cells and interacts with retrotransposon, eliciting more severe symptoms in patients with underlying diseases. In the treatment of patients with coronavirus infection, it may be necessary to pay more attention to the potential harm contributed by retrotransposon dysregulation.

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“…Recent studies reported a high frequency of reverse transcription and integration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in infected cells (Zhang et al, 2020;Ying et al, 2021), with implications for diagnostic detection of SARS-CoV-2 nucleic acids by RT-qPCR and for viral antigen persistence. These findings were partly based on the identification of chimeric reads between viral and human RNA in next-generation RNA-sequencing (RNA-seq) data (Zhang et al, 2020;Ying et al, 2021). Here, we examined the potential source of such chimeric reads and found that they are more likely to be a methodological product, than the result of genuine reverse transcription, integration and expression.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA

Kazachenka

Kassiotis

2021

Preprint

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The human genome bears evidence of extensive invasion by retroviruses and other retroelements, as well as by diverse RNA and DNA viruses. High frequency of somatic integration of the RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the DNA of infected cells was recently suggested, partly based on the detection of chimeric RNA-sequencing (RNA-seq) reads between SARS-CoV-2 RNA and RNA transcribed from human host DNA. Here, we examined the possible origin of human-SARS-CoV-2 chimeric reads in RNA-seq libraries and provide alternative explanations for their origin. Chimeric reads were frequently detected also between SARS-CoV-2 RNA and RNA transcribed from mitochondrial DNA or episomal adenoviral DNA present in transfected cell lines, which was unlikely the result of SARS-CoV-2 integration. Furthermore, chimeric reads between SARS-CoV-2 RNA and RNA transcribed from nuclear DNA was highly enriched for host exonic, than intronic or intergenic sequences and often involved the same, highly expressed host genes. These findings suggest that human-SARS-CoV-2 chimeric reads found in RNA-seq data may arise during library preparation and do not necessarily signify SARS-CoV-2 reverse transcription, integration in to host DNA and further transcription.

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Exogenous coronavirus interacts with endogenous retrotransposon in human cells

Cited by 14 publications

References 50 publications

Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual

Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual

Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells

SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA

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