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Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence of PCR-positive tests have Desonide Gel (Desonate)- FDA widely reported in patients after Desonide Gel (Desonate)- FDA from COVID-19, but some of these patients do not appear to shed infectious virus.

We investigated the possibility that SARS-CoV-2 RNAs tretinoin retin a be reverse-transcribed and integrated into the DNA of human cells in culture and that transcription of the integrated sequences Desonide Gel (Desonate)- FDA account for some of the positive PCR tests seen in patients. In support of this hypothesis, we found that DNA copies of SARS-CoV-2 sequences can be integrated into the genome of infected human cells.

We found target site duplications flanking the viral sequences and consensus LINE1 endonuclease recognition sequences at the integration sites, consistent with a LINE1 retrotransposon-mediated, target-primed reverse transcription and retroposition mechanism. The integration and transcription of viral sequences may thus contribute to the detection of viral RNA by PCR in patients after infection and clinical recovery.

SARS-CoV-2 is a positive-stranded RNA virus. One possible explanation for the continued detection of SARS-CoV-2 viral RNA Desonide Gel (Desonate)- FDA the absence of virus reproduction Desonide Gel (Desonate)- FDA that, in some cases, DNA copies of viral subgenomic RNAs may integrate into the DNA of the host cell by a reverse transcription mechanism. Transcription of the integrated DNA copies could be responsible for positive PCR tests long after the initial infection was cleared.

Indeed, nonretroviral RNA virus sequences have been detected in the Desonide Gel (Desonate)- FDA of many vertebrate species (25, 26), with several integrations exhibiting signals consistent with the integration of DNA Desonide Gel (Desonate)- FDA of viral mRNAs into the germline via ancient long interspersed nuclear element (LINE) retrotransposons (reviewed in ref.

In addition, cellular RNAs, for example the human APP Desonide Gel (Desonate)- FDA, have been shown to be reverse-transcribed by endogenous RT in neurons with the resultant APP fragments integrated into the genome and expressed (31). Endogenous LINE1 elements have been shown to be expressed in aged human tissues (35) and LINE1-mediated somatic retrotransposition is common in cancer patients (36, 37).

In this study, we show that SARS-CoV-2 sequences can integrate into the Desonide Gel (Desonate)- FDA cell genome by a LINE1-mediated retroposition mechanism. We provide evidence that the integrated viral sequences can be transcribed and that, in some patient samples, the majority of viral transcripts appear to be derived from integrated viral sequences. We used three different approaches to detect genomic SARS-CoV-2 sequences integrated into the genome of infected cells.

These approaches were Nanopore long-read sequencing, Illumina paired-end whole genomic sequencing, and Tn5 tagmentation-based DNA integration site enrichment sequencing. All three methods provided evidence that SARS-CoV-2 sequences can be integrated into the genome of the host cell.

To increase the likelihood of detecting rare integration events, we transfected HEK293T cells with LINE1 expression plasmids prior to infection with SARS-CoV-2 and isolated DNA from the cells 2 d after infection (SI Appendix, Fig.

We detected DNA copies of SARS-CoV-2 nucleocapsid (NC) sequences in the infected cells by PCR (SI Appendix, Fig. S1B) and cloned the complete NC gene (SI Appendix, Fig. S1D) from large-fragment cell genomic DNA that had been gel-purified (SI Appendix, Fig.

The odor DNA sequence (NC) was confirmed by Sanger sequencing (Dataset S1). These results suggest that SARS-CoV-2 RNA can be reverse-transcribed, and the resulting DNA could be integrated into the genome of the host cell. To demonstrate directly that the SARS-CoV-2 sequences were integrated into the host cell genome, DNA isolated from infected LINE1-overexpressing HEK293T cells was used for Nanopore long-read sequencing (Fig.

Importantly, the flanking sequences included a 20-bp direct repeat. This target site duplication is a signature of LINE1-mediated retro-integration (41, 42). Another viral integrant Desonide Gel (Desonate)- FDA a partial NC subgenomic RNA sequence that was flanked by a duplicated host cell DNA target sequence is shown in SI Appendix, Glipizide Extended Release (Glucotrol XL)- FDA In both cases, the flanking sequences contained a consensus recognition sequence of the LINE1 endonuclease (43).

These results indicate that SARS-CoV-2 sequences can Desonide Gel (Desonate)- FDA integrated into the genomes of cultured human cells by a LINE1-mediated retroposition mechanism. DNA copies of portions of the viral genome were found in almost all human chromosomes. In addition to the two examples given in Fig.

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