Study investigates recombinant SARS-CoV-2 variants in immunocompromised individuals

By Tarun Sai LomteMar 28 2022Reviewed by Aimee Molineux

In a recent study posted to the medRxiv* preprint server, researchers identified the recombination of two severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Background

Genetic recombination of ribonucleic acid (RNA) viruses is an important evolutionary mechanism and is frequently observed in coronaviruses. There are speculations that genetic recombination might be involved in SARS-CoV-2 origin. Moreover, coinfections with distinct SARS-CoV-2 variants in the same patient are documented, with few reports speculating possible genetic recombination. However, these conclusions were drawn based on the identification of coexisting signature mutations of SARS-CoV-2 variants in the isolated viral genomes. They did not report the isolation of distinct variants in culture.

In the United Kingdom (UK), in 2021, 16 inter-lineage recombinants between non-Alpha and Alpha viruses were reported based on the analysis of more than 270,000 genome sequences. Further, it has been reported that nearly 5% of SARS-CoV-2 circulating in the UK and United States might be recombinants.

The study

In the present study, researchers reported recombination of two SARS-CoV-2 variants in a patient leading to the generation of a hybrid SARS-CoV-2 variant. The subject was an immunocompromised patient with chronic SARS-CoV-2 infection for 14 months until death. The authors’ laboratory processed over a million respiratory samples for SARS-CoV-2 by real-time reverse transcription-polymerase chain reaction (RT-qPCR) since January 2020, and sequential samples from multiple patients were available. This enabled them to detect reinfections and chronic infections in severely immunosuppressed individuals.

The researchers sequenced the viral genome obtained from the respiratory specimens of the patient. The viral RNA was extracted from nasopharyngeal swabs using an EZ1 virus mini kit and was subject to next-generation sequencing (NGS) with the Illumina COVIDSeq protocol or by ARTIC multiplex PCR sequencing using nanopore technology. Additionally, PCR amplification was carried out on sequences overlapping the putative sites of recombination and sequenced with nanopore technology. Lastly, virus culture analysis was performed on Vero E6 cells using respiratory samples, and the isolated viruses were sequenced.

Findings

The patient was first diagnosed with COVID-19 in 2020, and he had been previously diagnosed with Hodgkin and follicular lymphoma. He developed severe pneumonia associated with COVID-19. SARS-CoV-2 was persistent, i.e., viral clearance was not observed, despite clinical improvement in the subject. The patient tested negative in the fifth month post-infection but positive at month 7.

The research team identified a viral genome that was a hybrid of two SARS-CoV-2 variants – B.1.160 and Alpha (B.1.1.7). The recombinant genome contained a matrix of B.1.160 genome with a few regions being replaced by those of the Alpha variant – one was located at the 5’ end of the genome harboring C913U (a synonymous mutation), and the other was spanned at the 17,109 – 18,877 and 25,710 – 27,972 sites. The recombinant contained all mutations of the Alpha variant in the spike (S) gene but lacked the characteristic S477N mutation of the B.1.160 variant. Coinfection or contamination of two variants was ruled out as the nucleotide diversity was low at 35 sites harboring characteristic mutations of B.1.160 or Alpha variants.

The patient’s samples when he was first diagnosed in Summer 2020 were examined, and the researchers determined that infection was with the B.1.160 variant, as it was epidemic at that time. While the B.1.160 variant was not retrospectively isolated, they observed that the genome sequence was typical of the variant without any significant nucleotide diversity. At four months post-infection, when he was still PCR-positive, his samples were unavailable for NGS, and therefore, it was undetermined if this (sample) contained B.1.160 or Alpha variant. The hybrid virus was first observed in his sample(s) after eight months of infection.

Conclusions

The current study reported that an immunocompromised individual who developed chronic COVID-19 infection had a hybrid variant resulting from recombination between B.1.160 and Alpha variants at three sites. Notably, samples before the first detection of the hybrid genome were unavailable for sequencing; hence (super)infection with Alpha variant could not be dated in that period (months 0-8).

Nonetheless, it is implausible that random mutations could have led to the appearance of Alpha variant sequences in the recombinant genome. These observations shed light on the mechanism of the genetic recombination of SARS-CoV-2 viruses and suggest intensive genomic surveillance in patients with SARS-CoV-2 coinfections and those coinfected with other RNA viruses.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources