Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Bolze, Alexandre; Basler, Tracy; White, Simon; Rossi, Andrew Dei; Wyman, Dana; Dai, Hang; Roychoudhury, Pavitra; Greninger, Alexander L.; Hayashibara, Kathleen; Beatty, Mark E.; Shah, Seema; Stous, Sarah; McCrone, John; Kil, Eric; Cassens, Tyler; Tsan, Kevin; Nguyen, Jason; Ramirez, Jimmy M.; Carter, Scotty; Cirulli, Elizabeth T.; Barrett, Kelly M Schiabor; Washington, Nicole; Belda-Ferre, Pedro; Jacobs, Sharoni; Sandoval, Efren; Becker, David G.; Lu, James T.; Isaksson, Magnus; Lee, William; Luo, Shishi

doi:10.1016/j.medj.2022.10.002

Cited by 48 publications

(49 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among all recombinants, the likely most well-known and controversial recombinant is the Omicron-Delta recombinant. 29 , 30 , 31 Profiling Delta and Omicron polymutants on these 2 recombinants (eTable 19 in Supplement 1 ), we found that the virus carried L452R and I82T polymutants unique to Delta, while the remaining polymutants were unique to Omicron. Similarly, the Omicron-Alpha recombinants carried T183I, S982A, R52I, D3L, and S235F mutations unique to Alpha, while Omicron-Zeta recombinants carried L71F, A119S, and M234I mutations unique to Zeta (eTable 20 in Supplement 1 ).…”

Section: Resultsmentioning

confidence: 88%

“…The most frequently occurring recombinant type among all 657 MVs was Omicron-Epsilon (609 recombinants [92.7%]). Among all recombinants, the likely most well-known and controversial recombinant is the Omicron-Delta recombinant . Profiling Delta and Omicron polymutants on these 2 recombinants (eTable 19 in Supplement 1), we found that the virus carried L452R and I82T polymutants unique to Delta, while the remaining polymutants were unique to Omicron.…”

Section: Resultsmentioning

confidence: 95%

See 1 more Smart Citation

Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations

et al. 2023

View full text Add to dashboard Cite

ImportanceEarlier detection of emerging novel SARS-COV-2 variants is important for public health surveillance of potential viral threats and for earlier prevention research. Artificial intelligence may facilitate early detection of SARS-CoV2 emerging novel variants based on variant-specific mutation haplotypes and, in turn, be associated with enhanced implementation of risk-stratified public health prevention strategies.ObjectiveTo develop a haplotype-based artificial intelligence (HAI) model for identifying novel variants, including mixture variants (MVs) of known variants and new variants with novel mutations.Design, Setting, and ParticipantsThis cross-sectional study used serially observed viral genomic sequences globally (prior to March 14, 2022) to train and validate the HAI model and used it to identify variants arising from a prospective set of viruses from March 15 to May 18, 2022.Main Outcomes and MeasuresViral sequences, collection dates, and locations were subjected to statistical learning analysis to estimate variant-specific core mutations and haplotype frequencies, which were then used to construct an HAI model to identify novel variants.ResultsThrough training on more than 5 million viral sequences, an HAI model was built, and its identification performance was validated on an independent validation set of more than 5 million viruses. Its identification performance was assessed on a prospective set of 344 901 viruses. In addition to achieving an accuracy of 92.8% (95% CI within 0.1%), the HAI model identified 4 Omicron MVs (Omicron-Alpha, Omicron-Delta, Omicron-Epsilon, and Omicron-Zeta), 2 Delta MVs (Delta-Kappa and Delta-Zeta), and 1 Alpha-Epsilon MV, among which Omicron-Epsilon MVs were most frequent (609/657 MVs [92.7%]). Furthermore, the HAI model found that 1699 Omicron viruses had unidentifiable variants given that these variants acquired novel mutations. Lastly, 524 variant-unassigned and variant-unidentifiable viruses carried 16 novel mutations, 8 of which were increasing in prevalence percentages as of May 2022.Conclusions and RelevanceIn this cross-sectional study, an HAI model found SARS-COV-2 viruses with MV or novel mutations in the global population, which may require closer examination and monitoring. These results suggest that HAI may complement phylogenic variant assignment, providing additional insights into emerging novel variants in the population.

show abstract

Section: Resultsmentioning

confidence: 88%

Section: Resultsmentioning

confidence: 95%

Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations

et al. 2023

View full text Add to dashboard Cite

show abstract

“…In contrast, multiple putative Delta-Omicron recombinants have been reported so far [29][30][31]. Previously, these recombinants featured elements of both parental lineages, the highly pathogenic Delta variant and, the highly transmissible Omicron variant, thus they were nicknamed "Deltacron" by Kostrikis et al [32].…”

Section: Inter-voc Recombinationsmentioning

confidence: 99%

Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages

et al. 2023

View full text Add to dashboard Cite

The SARS-CoV-2 Omicron is currently the predominant circulating variant in the COVID-19 pandemic. The dominating Omicron sublineages respond to host immune pressure and develop advantageous mutations or genetic recombination, which result in variants that are more contagious or better at escaping immune responses in response to previous infection or vaccination. Meanwhile, multiple genetic recombination events have been reported in coinfection cases, the majority of which have resulted from the recombination between co-circulating Omicron BA.1 (or BA.1.1) and Delta variant or BA.2. Here, we review the knowledge and characterization of recombination for SARS-CoV-2 at the population level, provide an update on the occurrence of newly circulating Omicron sublineages, and discuss the effectiveness of novel vaccines/therapeutic drugs against the Omicron variant.

show abstract

“…The recombination of Delta and Omicron can result in mutations with different viral properties and characteristics. Bolze et al identified cases of Delta and Omicron co-infection in the United States of America between November 2021 and February 2022 (14). An analysis of the first 87 695 SARS-CoV-2 genomes shared on GISAID in 2021 identified 225 sequences of likely recombinant origin (15).…”

Section: Genomic Surveillance and Sequencing Across South Americamentioning

confidence: 99%

Genomic surveillance and sequencing of SARS-CoV-2 across South America

Dias¹,

Andriolo

Silvestre

et al. 2023

Revista Panamericana De Salud Pública

View full text Add to dashboard Cite

After 2 years of the COVID-19 pandemic, the protocols used to control infection lack attention and analysis. We present data about deposits of complete genomic sequences of SARS-CoV-2 in the Global Initiative on Sharing All Influenza Data (GISAID) database made between January 2021 and May 31, 2022. We build the distribution profile of SARS-CoV-2 variants across South America, highlighting the contribution and influence of each variant over time. Monitoring the genomic sequences in GISAID illustrates negligence in the follow up of infected patients in South America and also the discrepancies between the number of complete genomes deposited throughout the pandemic by developed and developing countries. While Europe and North America account for more than 9 million of the genomes deposited in GISAID, Africa and South America deposited less than 400 000 genome sequences. Genomic surveillance is important for detecting early warning signs of new circulating viruses, assisting in the discovery of new variants and controlling pandemics.

show abstract

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Cited by 48 publications

References 26 publications

Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations

Using Haplotype-Based Artificial Intelligence to Evaluate SARS-CoV-2 Novel Variants and Mutations

Characterization of SARS-CoV-2 recombinants and emerging Omicron sublineages

Genomic surveillance and sequencing of SARS-CoV-2 across South America

Contact Info

Product

Resources

About