key: cord-0429339-kovi3uyz
authors: Gonzalez-Reiche, A. S.; Alshammary, H.; Schaefer, S.; Patel, G.; Polanco, J.; Amoako, A.; Rooker, A.; Cognigni, C.; Floda, D.; van de Guchte, A.; Khalil, Z.; Farrugia, K.; Assad, N.; Zhang, J.; Alburquerque, B.; Sominsky, L.; Srivastava, K.; Sebra, R.; Ramirez, J. D.; Banu, R.; Shrestha, P.; Paniz-Mondolfi, A.; Sordillo, E. M.; Simon, V.; van Bakel, H.
title: Intrahost evolution and forward transmission of a novel SARS-CoV-2 Omicron BA.1 subvariant
date: 2022-05-27
journal: nan
DOI: 10.1101/2022.05.25.22275533
sha: 15506be475eac09571058c43dfc1ca0621dda2b7
doc_id: 429339
cord_uid: kovi3uyz

Persistent SARS-CoV-2 infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. It has been speculated that the emergence of antigenically diverse SARS-CoV-2 variants such as the Omicron variant may be the result of intra-host viral evolution driven by suboptimal immune responses, which must be followed by forward transmission. However, while intrahost evolution has been documented, to our knowledge no direct evidence of subsequent forward transmission is available to date. Here we describe the emergence of an Omicron BA.1 sub-lineage with 8 additional amino acid substitutions within the spike (E96D, L167T, R346T, L455W, K458M, A484V, H681R, A688V) in an immune-compromised host along with evidence of 5 forward transmission cases. Our findings show that the Omicron BA.1 lineage can further diverge from its exceptionally mutated genome during prolonged SARS-CoV-2 infection; highlighting an urgent need to employ therapeutic strategies to limit duration of infection and spread in vulnerable patients.

Emergence of antigenically diverse SARS-CoV-2 variants of concern (VOC) poses a 53 challenge to SARS-CoV-2 vaccine-induced immunity. Prolonged evolution in 54 immunocompromised hosts is thought to have played a role in the emergence of 55 several SARS-CoV-2 VOC such as Alpha and Omicron 1,2 . However, although persistent 56 SARS-CoV-2 replication with stepwise acquisition of mutations in spike within 57 immunocompromised COVID-19 patients has been documented 3-7 , clear evidence for 58 forward transmission has been lacking. 59 The Mount Sinai Pathogen Surveillance Program (MS-PSP) has profiled the evolving 60 landscape of SARS-CoV-2 in New York City (NYC) since the beginning of the 61 pandemic 8,9 . We routinely perform complete viral genome sequencing from at least 10% 62 of randomly selected contemporaneous SARS-CoV-2 positive specimens collected from 63 patients seeking care at our health system. 64 We describe a persistent SARS-CoV-2 Omicron BA.1 infection in an immuno- (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. amplicons were sequenced on a MiSeq instrument. SARS-CoV-2 genomes were 106 assembled using a custom reference-based pipeline as previously described 8 . The final 107 sequencing depth per genome ranged between ~135k to ~415k reads. Medium containing 10% heat-inactivated fetal bovine serum and 1% Minimum Essential 129 Medium (MEM) Amino Acids Solution, supplemented with 100 U/ml penicillin, 100 μg/ml 130 streptomycin, 100 μg/ml normocin, and 3 μg/ml puromycin. 200ul of viral transport 131 media from the nasopharyngeal or anterior nares swab specimen was added to Vero-132 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. In this study we report the genomic analysis of serially collected nasopharyngeal (NP) individuals. In one case, infection persisted for more than three weeks resulting in 162 All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 acquisition of an additional mutation in the spike RBD (V445A) (Figure 1) . In some 163 specimens we detected minority alleles at variant positions suggesting ongoing intra-164 host selection (Figure 1 and Figure 3) . Although viral isolation failed for specimens 165 available for the index case, we successfully cultured SARS-CoV-2 from the initial 166 positive specimens of the three forward transmission cases, confirming the transmission 167 of replication-competent virus.

Lastly, two additional related SARS-CoV-2 genomes from the NYC area were identified 169 from the GISAID database (Figure 1) . Based on the metadata provided, these two (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 since without their assistance and help, none of this surveillance work would be 193 possible. 194 We gratefully acknowledge the authors and originating and submitting laboratories of 195 sequences from GISAID's EpiCoV (www.gisaid.org) that were used as background for 196 our phylogenetic inferences. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 8. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

Mash: fast genome and metagenome 264 distance estimation using MinHash

Nextstrain build for novel coronavirus 267 SARS-CoV-2

Nextstrain: real-time tracking of pathogen 269 evolution

Nextclade: 272 clade assignment, mutation calling and quality control for viral genomes

Phylogenetic assignment of named global outbreak 275 lineages

Tracking the international spread of SARS-277

CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch

Activity of convalescent and 280 vaccine serum against SARS-CoV-2 Omicron

All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101/2022.05.25.22275533 doi: medRxiv preprint All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 325 All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted May 27, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022