key: cord-0814285-pxmqvdtp
authors: Lacek, Kristine A.; Rambo-Martin, Benjamin L.; Batra, Dhwani; Zheng, Xiao-yu; Sakaguchi, Hitoshi; Peacock, Thomas; Keller, Matthew; Wilson, Malania M.; Sheth, Mili; Davis, Morgan L.; Borroughs, Mark; Gerhart, Jonathan; Hassell, Norman; Shepard, Samuel S.; Cook, Peter W.; Lee, Justin; Wentworth, David E.; Barnes, John R.; Kondor, Rebecca; Paden, Clinton R.
title: Identification of a Novel SARS-CoV-2 Delta-Omicron Recombinant Virus in the United States
date: 2022-03-21
journal: bioRxiv
DOI: 10.1101/2022.03.19.484981
sha: 301d0306fa0f268929572a2361db4e5f866b8309
doc_id: 814285
cord_uid: pxmqvdtp

Recombination between SARS-CoV-2 virus variants can result in different viral properties (e.g., infectiousness or pathogenicity). In this report, we describe viruses with recombinant genomes containing signature mutations from Delta and Omicron variants. These genomes are the first evidence for a Delta-Omicron hybrid Spike protein in the United States.

Emerging variants of SARS-CoV-2, the virus that causes COVID-19, are characterized and monitored closely via national genomic surveillance. In addition to sequencing efforts from US public health, academic, and commercial laboratories, the Centers for Disease Control and Prevention (CDC) collects and sequences SARS-CoV-2 specimens from 64 states and jurisdictions via the National SARS-CoV-2

Strain Surveillance Program (NS3), and funds SARS-CoV-2 sequencing via a nationwide network of commercial laboratory testing companies. These efforts have contributed over 1.8 million SARS-CoV-2 genomes from the United States to public repositories since January 2021. The purpose of this genomic surveillance system is to detect and respond dynamically to new and changing SARS-CoV-2 variants (1).

Recombination is common in coronaviruses (2, 3) , and can lead to rapid accumulation of mutations and heightened transmissibility (4) . SARS-CoV-2 recombination events have also been found to arise disproportionately in the Spike [S] gene (5) . Recombination between Alpha and Delta SARS-CoV-2 variants has been documented (6) (7) (8) , but through the end of 2021, there was no clear evidence of recombination between co-circulating Delta and Omicron variants.

Given the divergence of Delta and Omicron genomes, as well as Omicron's known immune escape properties (9, 10), a Delta-Omicron recombinant strain could alter the landscape of vaccine and therapeutic efficacy. In early 2022, there were reports of viruses resulting from recombination between Delta and Omicron, but upon further inspection, these appeared to be due to laboratory artifact or coinfections (11) .

In this report, we identify candidate Delta-Omicron recombinant genomes from CDC's national genomic surveillance and describe efforts to rule out laboratory contamination or sequencing error. We show that these genomes are likely the result of recombination within the Spike gene, containing substitutions common to Delta lineages at the 5' end and Omicron lineages at the 3' end.

A group of nine candidate recombinant sequences (Table 1) were identified from CDC's national genomic surveillance dataset made publicly available in Genbank and GISAID EpiCoV TM . Using Bolotie, a rapid inter-clade recombination detection method (3), these sequences were identified as candidate recombinant genomes, with one parent in Delta (Clade 21J) and another in Omicron (Clade 21K). Bolotie describes a single breakpoint between nucleotide (nt) position 22035 and 22577 (referenced to Genbank accession NC_045512.2)-there are no differentiating mutations between clades 21J and 21K within this range. These sequences (EPI_ISL_8720194, EPI_ISL_9147438, EPI_ISL_9147935, EPI_ISL_8981459, EPI_ISL_8981824, EPI_ISL_9088187, EPI_ISL_8981712, EPI_ISL_10389339, EPI_ISL_10389336) contain hallmark mutation sets from both Omicron and Delta SARS-CoV-2 lineages, changing from Delta-associated substitutions to Omicron-associated substitutions between Spike amino acids 158 and 339 ( Figure 1A ). This breakpoint is distinct from the two clusters of apparent Delta-Omicron recombinants identified in the United Kingdom (https://github.com/cov-lineages/pangodesignation/issues/422 and https://github.com/cov-lineages/pango-designation/issues/441), which have a breakpoint upstream of Spike in orf1ab ( Figure 1A ).

To rule out laboratory contamination, Delta and Omicron co-infection, and bioinformatic error, we examined the raw read data from the nine candidate recombinants created from molecular loop and amplicon based sequencing strategies. Two of these specimens were readily available from the original diagnostic lab, and extracted RNA was shipped to CDC for confirmatory sequencing. We used Illumina and PacBio sequencing of two different whole genome amplicon strategies, as well as S-gene amplification followed by Nanopore sequencing (detailed in Appendix). All sequencing strategies yielded functionally identical consensus sequences compared to the corresponding original sequencing strategies. Given the potential public health consequences of new variants emerging from recombination, investigations involving laboratory and bioinformatic components, such as the one presented here, are critical to correctly identify and track these viruses.

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I G S T A L R S I A V L I L A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D L I G S T A L R S I A V L I L A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D L I G S T A I A V L I L T Q N G L S L S V I D V Y Y --G D K L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I E T L G ---K R DĨ G S T A L R S I A V L I L A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D L I G S T A L R S I A V L I F A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F N K S N K A R S R Y H K G Y K H A K Y K K F I G E T L G ---K R D L I G S T A L R S I A V L I L A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D L I G S T V R S T A V L I L A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F N K A R S R Y H K G Y K H A K Y K H K F I G E L~--~K R D L I G S T A L R S I A V L I L A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F K N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D L I G S T A L R S I A V L I L A Q N G L S L S V L R A H V I D V Y Y --G N L D K L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D L T D S T A L R S I V A L I L A Q K E L S L A V L R A H V I D V Y H --G -I D R L P F N K A R S R Y H K G Y K H V Y K H K F I G E T L G ---K R A L T G S I A L R S I V A L I L A H K E L S L A A L T V --I ---D E F R -I D R L P F N K S N K A R S R Y H K G Y K H V K Y K H K F I G E T L G ---K R D L T G S I A L R S I V A L I L K E L A A L T V --I ---D E F R -I D R L P F N K A R S R Y H K G Y K H V K Y K H K F I G E T L G ---K R D L T G S I A L R S I V A L I L A H K E L S L A A L T V --I ---D E F R -I D R L P F N K A R S R Y H K G Y K H V Y K H K F I G E T L G ---K R D L T G S I A L R S I V A L I L A H K E L S L A A L T V --I ---D E F R -I D R L P F N K A R S R Y H K G Y K H V Y K H K F I G E T L G ---K R D L G S T A W S I V A L I L A Q K E L L A V F R V --I ---D E F R -I D R L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D L T G S T A L W S I V A L I L A Q K E L L A V F R V --I ---D E F R -I D R L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D F T G S T A L W S I V A L I L A Q K E L S L A V F R V --I ---D E F R -I D R L P F N K S N K A R S R Y H K G Y K H A K Y K H K F I G E T L G ---K R D F T G SY Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y V V V V V V V T T S S S S S S S S S S R R R R R R R R R R R R R Q Q Q Q Q Q P P P N N N N N N N N N N N N N N N N L L L L L L L L L L K K K K G G G G F F F F F F F E E D D D D D D D D D D D A A A A A A - - - - - - - - - - - - % allele

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