COVID‐19 severity from Omicron and Delta SARS‐CoV‐2 variants

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Abstract

The Omicron variant of SARS‐CoV‐2 achieved worldwide dominance in late 2021. Early work suggests that infections caused by the Omicron variant may be less severe than those caused by the Delta variant. We sought to compare clinical outcomes of infections caused by these two strains, confirmed by whole genome sequencing, over a short period of time, from respiratory samples collected from SARS‐CoV‐2 positive patients at a large medical center. We found that infections caused by the Omicron variant caused significantly less morbidity, including admission to the hospital and requirement for oxygen supplementation, and significantly less mortality than those caused by the Delta variant.

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Most cited references 11

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Andrew Rambaut, Edward C. Holmes, Aine O’Toole … (2020)

The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. We present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and de-labelling virus lineages that become unobserved and hence are likely inactive. By focusing on active virus lineages and those spreading to new locations this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.

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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Raquel Viana, Sikhulile Moyo, Daniel G. Amoako … (2022)

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function 4 . Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

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Author and article information

Contributors

Suman R. Das:

ORCID: https://orcid.org/0000-0003-2496-9724

suman.r.das@vumc.org

Journal

Journal ID (nlm-ta): Influenza Other Respir Viruses

Journal ID (iso-abbrev): Influenza Other Respir Viruses

Journal ID (doi): 10.1111/(ISSN)1750-2659

Journal ID (publisher-id): IRV

Title: Influenza and Other Respiratory Viruses

Publisher: John Wiley and Sons Inc. (Hoboken )

ISSN (Print): 1750-2640

ISSN (Electronic): 1750-2659

Publication date (Electronic): 13 April 2022

Publication date PMC-release: 13 April 2022

Electronic Location Identifier: 10.1111/irv.12982

Affiliations

[ ¹ ] Department of Emergency Medicine Vanderbilt University Medical Center Nashville Tennessee USA

[ ² ] Division of Infectious Disease, Department of Medicine Vanderbilt University Medical Center Nashville Tennessee USA

[ ³ ] Department of Pathology Microbiology and Immunology Vanderbilt University Medical Center Nashville Tennessee USA

[ ⁴ ] Department of Otolaryngology Vanderbilt University Medical Center Nashville Tennessee USA

Author notes

[*] [* ] Correspondence

Suman R. Das, Division of Infectious Diseases, Vanderbilt University Medical Center, 1211 21st Avenue South, S2108 Medical Center North, Nashville, TN 37232, USA.

Email: suman.r.das@ 123456vumc.org

Author information

Suman R. Das https://orcid.org/0000-0003-2496-9724

Article

Publisher ID: IRV12982

DOI: 10.1111/irv.12982

PMC ID: 9111734

PubMed ID: 35415869

SO-VID: e01cfd39-9a30-4734-bb97-7eba04c8a73b

License:

This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

History

Date received : 09 March 2022

Date accepted : 13 March 2022

Page count

Figures: 1, Tables: 1, Pages: 5, Words: 2908

Funding

Funded by: National Institute of Allergy and Infectious Diseases , doi 10.13039/100000060;

Award ID: R21AI142321‐02S1

Award ID: R21AI149262

Award ID: R21AI154016

Award ID: R21AI142321

Funded by: National Institutes of Health , doi 10.13039/100000002;

Award ID: G20RR030956

Award ID: P30EY08126

Award ID: P30CA68485

Award ID: UL1RR024975

Funded by: National Heart, Lung, and Blood Institute , doi 10.13039/100000050;

Award ID: R01HL146401

Award ID: K23HL148638

Funded by: Centers for Disease Control and Prevention , doi 10.13039/100000030;

Award ID: 75D3012110094

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source-schema-version-number 2.0

edited-state corrected-proof

details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.6 mode:remove_FC converted:17.05.2022

ScienceOpen disciplines: Infectious disease & Microbiology

Keywords: covid‐19,delta,omicron,sars‐cov‐2,severity,whole genome sequencing (wgs)

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ScienceOpen disciplines: Infectious disease & Microbiology

Keywords: covid‐19, delta, omicron, sars‐cov‐2, severity, whole genome sequencing (wgs)

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COVID‐19 severity from Omicron and Delta SARS‐CoV‐2 variants

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Novel Coronavirus Disease COVID-19

Most cited references 11

Fast and accurate short read alignment with Burrows–Wheeler transform

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

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