Investigation of a SARS-CoV-2 B.1.1.529 (Omicron) Variant Cluster - Nebraska, November-December 2021

Abstract

The B.1.1.529 (Omicron) variant of SARS-CoV-2 (the virus that causes COVID-19) was first detected in specimens collected on November 11, 2021, in Botswana and on November 14 in South Africa;* the first confirmed case of Omicron in the United States was identified in California on December 1, 2021 (1). On November 29, the Nebraska Department of Health and Human Services was notified of six probable cases^† of COVID-19 in one household, including one case in a man aged 48 years (the index patient) who had recently returned from Nigeria. Given the patient's travel history, Omicron infection was suspected. Specimens from all six persons in the household tested positive for SARS-CoV-2 by reverse transcription-polymerase chain reaction (RT-PCR) testing on December 1, and the following day genomic sequencing by the Nebraska Public Health Laboratory identified an identical Omicron genotype from each specimen (Figure). Phylogenetic analysis was conducted to determine if this cluster represented an independent introduction of Omicron into the United States, and a detailed epidemiologic investigation was conducted. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.^§.

FIGURE

Global phylogeny of B.1.1.529 (Omicron) samples available on Global Initiative on Sharing All Influenza Data* as of December 6, 2021 (650 total genomes) (A) and expanded view of Omicron sequences (B) — Nebraska, November–December 2021^,,,, Abbreviation: SNP = single nucleotide polymorphism. * https://www.gisaid.org ^† Branch lengths are shown in number of mutations from the root. The maximum-likelihood phylogenetic trees are rooted with the original SARS-CoV-2 genome Wuhan/Hu-1/2019. ^§ Each of the six SARS-CoV-2 genomes generated from this cluster is >94% complete and shares 100% nucleotide identity across the length of the genome, consistent with household transmission. ^¶ Genomes from the five secondary cases have SNPs at nucleotide positions T1552C and C23709T that are not yet found in other Omicron genomes sampled. ** The genome from the index patient, NCOV21-42615, has the ambiguous nucleotide “N” at positions 1552 and 23709 and further inspection of the read-level data showed nucleotide variability at both sites. The SNP allele frequency at these sites in the NCOV21-42615 genome is >50%, consistent with epidemiologic findings of household transmission from the index patient to all secondary cases. ^†† https://academic.oup.com/bioinformatics/article/34/23/4121/5001388 ^§§ https://onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12628