Even though SARS-CoV-2 doesn’t encode a reverse transcriptase in its genome, the MIT scientists postulated that the SARS-CoV-2 RNA may still be reverse transcribed at some point during its replication cycle by endogenous copies of reverse transcriptase, encoded in the host genome. Biologists know that DNA sequences associated with retrotransposons (such as LINE sequences) found in the host cell’s genome encode for proteins with reverse transcriptase activity.

LINE sequences comprise about 20 percent of the human genome. These mobile DNA elements can make copies of themselves, with the copies becoming randomly inserted throughout the genome. Some LINE DNA sequences lie dormant in the human genome. Others can be transcribed into mRNA that, in turn, can be translated into a protein with reverse transcriptase activity. The LINE reverse transcriptase can make a copy of the LINE mRNA, converting it into DNA that can be integrated into the genome at a new location.

The research team speculated that once it has been synthesized by endogenous reverse transcriptase activity, the SARS-CoV-2 DNA can become integrated into the host cell’s genome. Here, the SARS-CoV-2 DNA sequences can be transcribed, producing viral RNAs that are detected by PCR tests.

1) Cultured human cells exposed to SARS-CoV-2 in the laboratory and cells taken from patients infected with SARS-CoV-2 both produce mRNA molecules that include those with hybrid sequences made up of host cell genes and viral genes. This observation suggests that viral genetic material has been incorporated in the host cell’s genome.

2) The predominant viral gene sequences that occur in the hybrid RNA molecules encode the capsid proteins. mRNA molecules that encode the capsid proteins are the most abundant of the viral mRNAs in the cell. These mRNA molecules would be readily available to be transcribed by endogenously sourced reverse transcriptase.

3) In the laboratory, when cells belonging to the HEK293 line are forced to overexpress LINE DNA sequences, SARS-CoV-2 RNA becomes reverse transcribed upon exposure of the cells to virions. The resulting SARS-CoV-2 DNA becomes incorporated into the genome of the HEK293 cells.

4) Exposure of cells to SARS-CoV-2 virions induces LINE expression.

Collectively, these findings provide compelling circumstantial evidence that endogenous reverse transcriptase converts SARS-CoV-2 RNA into DNA and this DNA, in turn, becomes integrated into the host cell’s genome. The evidence also indicates that only portions of the SARS-CoV-2 genome become incorporated into the host cell’s genome. As a result, when the host cell’s machinery transcribes these sequences to produce RNA, it can’t produce virions that can be transmitted to other people.

This discovery carries several important scientific and biomedical implications.

• It explains the unusual PCR results returned for patients who have recovered from COVID–19.

• It will help guide the development of antiviral therapies if the presence of SARS-CoV-2 genetic material in the patient is used to monitor the effectiveness of the antiviral treatment.

• It indicates that the reverse transcription of viral genetic material and its incorporation into the host cell genome may not be limited to SARS-CoV-2. It might be a general feature of other RNA viruses.

This discovery also has implications for the RTB creation model. It gives insight as to why ERV sequences are found in genomes. By doing so, it becomes increasingly reasonable to view ERV sequence elements as the intentional handiwork of a Creator, instead of a reflection of our evolutionary history.