Reverse Transcriptase and Coronaviruses

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Articles review

This abstract comprises a simple analysis and description of the virus genome.

Human coronaviruses, or HCoVs consist of HCoV-229E and HCoV-NL63 in the Alphacoronavirus family and HCoV-OC43 and HCoV-HKU1 in the Betacoronavirus family.

Four CoVs, for instance, HKU1, NL63, 229E and OC43, are mainly responsible for mild respiratory disorders in human circulation.

SARS-CoV-2 is a β-coronavirus carrying a single positive RNA strand as genetic material, it has a lipidic envelope that confers an elliptic morphology.

CoVs evolved a relatively complex multiplication mechanism to facilitate virus reproduction. In their viral life cycle CoVs transmit genomes and subgenomic RNAs only from RNA templates, and do not need a step of DNA. CoVs use exonuclease NSP14, the first known RNA virus-encoded proofreading enzyme that in comparison with other error-prone RNA viruses, could be adapted to handle CoVs‘ large RNA genome.

Source: Genetic analysis of the 2019 coronavirus pandemic with from real-time reverse transcriptase polymerase chain reaction (

From original article report:

“Prolonged SARS-CoV-2 RNA shedding, and recurrence of PCR-positive tests have been widely reported in patients after recovery, yet these patients most commonly are non-infectious”. The researchers in this article have investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the human genome and that transcription of the integrated sequences may be responsible for PCR-positive tests.

In support of this hypothesis, they found chimeric transcripts consisting of viral fused to cellular sequences in published data sets of SARS-CoV-2 infected cultured cells and primary cells of patients, consistent with the transcription of viral sequences integrated into the genome.

To experimentally corroborate the possibility of viral retro-integration, they describe evidence that SARS-CoV-2 RNAs can be reverse transcribed in human cells by reverse transcriptase, RT from LINE-1 elements or by HIV-1 RT, and that these DNA sequences can be integrated into the cell genome and subsequently be transcribed.

-This is, of course, referred to an infection with SARS-CoV-2, and not to the genetic material (mRNA) introduced with the vaccine-


SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome | bioRxiv

In this last article slightly modified and reduced from myself also is commented about the reverse transcription of SARS-CoV-2.

The authors report that: “The researchers explored the occurrence of reverse transcription of the SARS-CoV-2 RNA into the human genome. This would result in positive PCR tests due to the continuing transcription of viral RNAs.

Reverse transcriptase activity has been detected within human cells, so as integration of the reverse transcription products.

The endogenous RT is potentially present in the form of human LINE-1 elements, which make up 17% of the human genome. These are autonomous retrotransposon elements that can transpose themselves as well as other elements of the genome back into the DNA of the nucleus for future transcription.

The researchers looked at the published RNA-sequences from SARS-CoV-2 infected cells, their purpose was to find chimeric transcripts, fusing human and viral RNA into the same genome. They found a good number of these in several different cell types, and from cells recovered from the bronchoalveolar lavage fluid obtained from COVID-19 patients.

The proportion of these chimeric sequences was directly correlated with the level of viral RNA in each sample. The greatest proportion was in cells recovered from the bronchoalveolar lavage fluid of severe COVID-19 patients, while there were almost none in blood cells.

Most of the host-viral chimeric protein contained the nucleocapsid sequences, as expected since this is the most abundant viral particles. This would, therefore, be the most likely to be reverse transcribed and then integrated. These findings for the researchers support the occurrence of this event within infected cells.

They conducted then an experiment inducing the overexpression of human LINE-1 elements or HIV-1 RT, in the cell line.

These cells were then infected with SARS-CoV-2. At two days post-infection, they carried out polymerase chain reaction, PCR, tests to detect the viral sequences, using the N-targeting primer sets used in the commonly used COVID-19 PCR tests.

PCR amplification of the purified cell DNA from infected cells showed the presence of the N protein bands. This did not occur in non-transfected or uninfected cells.

They also conducted an in vitro RT experiment, which showed that cell lysates from cells expressing RT of either type could cause reverse transcription of purified viral RNA from infected cells.

Using fluorescent in situ hybridization, FISH, technology, they trapped down the presence and ongoing transcription of the viral N sequences within the cell nucleus with the help of Ntargeting fluorescent probes. The N sequences were found in the cytoplasm, as expected of cells infected by SARS-CoV-2.

However, FISH also picked up N RNA signals from the nucleus of cells that overexpressed LINE-1, showing that integrated N sequences in the host genome were being transcribed there.

The integrated sequences are probably sub-genomic and cannot produce live infectious virions. This explains the positivity of later PCR tests for viral RNA in clinically recovered patients.

The authors suggest that the site of insertion and regulation by epigenetic factors, besides the existing immune state of the patient, may affect the translation of these sequences and their possible clinical consequences.

In conclusion, the study suggests that many PCR positive results could be due to viral transcripts from chimeric sequences instead of reflecting the presence of replicating virus in the host. If validated, this will require better tests to be used when assessing the efficacy of COVID-19 therapies in clinical trials, for example, in the future.


SARS-CoV-2 RNA can be reverse-transcribed (

-As we can see, the role of the immune system and of the epigenetics factors is one of the major compounds in any disease, and especially considered with Covid-19 infections-

Thanks for Reading

Mariarosaria M.

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