Viral load of SARS‐CoV‐2 Omicron BA.5 is lower than that of BA.2 despite the higher infectivity of BA.5

Takatsuki, Yuna; Takahashi, Yuta; Nakajima, Jun; Iwasaki, Yumi; Nagano, Katsutoshi; Tani‐Sassa, Chihiro; Yuasa, Sonoka; Kanehira, Saki; Sonobe, Kazunari; Nukui, Yoko; Takeuchi, Hiroaki; Tanimoto, Kousuke; Tanaka, Yukië; Kimura, Akinori; Ichimura, Naoya; Tohda, Shuji

doi:10.1002/iid3.783

Cited by 2 publications

(1 citation statement)

References 8 publications

(17 reference statements)

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“…An intrinsic limitation of the study may be due also to the lower viral loads usually found in the nasopharyngeal swabs of patients infected with some of the Omicron variants (e.g. BA.1 [ 18 ] or BA.5 [ 19 ]) compared to those with other variants. By limiting the sequencing of those positive samples with Ct ≤30, some patients infected with these Omicron variants may have been missed, possibly biasing the results.…”

Section: Discussionmentioning

confidence: 99%

Reinfection rate and disease severity of the BA.5 Omicron SARS-CoV-2 lineage compared to previously circulating variants of concern in the Canary Islands (Spain)

Ciuffreda

Lorenzo-Salazar

Artola

et al. 2023

Emerging Microbes & Infections

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The emergence of the Omicron SARS-CoV-2 variant of concern has changed the COVID-19 scenario as this variant is characterized by high transmissibility and immune evasion ability. To evaluate the impact of this variant on the Canary Islands (Spain) population, we determined the reinfection rates and disease severity associated with the Omicron sublineages and the previously circulating variants of concern. We performed a retrospective observational study on 21,745 SARS-CoV-2 viral genomes collected from December 2020 to July 2022 in the Canary Islands (Spain). We compared the reinfection rates between lineages using pairwise proportion and Fisher’s exact tests. To assess disease severity, we studied the association of Alpha, Delta, BA.1, BA.2, BA.5, and other risk factors on 28-day hospital mortality using logistic regression and Cox proportional hazard models. We observed 127 bona fide reinfection cases throughout the study period. We found that BA.5 had the highest reinfection rate compared to other lineages (vs. Delta p = 2.89 × 10 −25 ; vs. BA.1 p = 5.17 × 10 −11 ; vs. BA.2 p = 0.002). Among the 1,094 hospitalized patients, multivariate logistic regression showed that Alpha (Odds Ratio [OR] = 0.45, 95% Confidence Interval [CI] = 0.23-0.87, p = 0.02), BA.2 (OR = 0.38, 95% CI = 0.22-0.63, p = 1.91 × 10 −4 ), and BA.5 (OR = .30, 95% CI = 0.16-0.55, p = 1.05 × 10 −4 ) had lower 28-day hospital mortality compared to Delta. These results were confirmed by using Cox proportional hazard models. Omicron lineages, and in particular BA.5, were associated with higher reinfection rates and lower disease severity (28-day hospital mortality) than previously circulating variants of concern.

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Section: Discussionmentioning

confidence: 99%

Reinfection rate and disease severity of the BA.5 Omicron SARS-CoV-2 lineage compared to previously circulating variants of concern in the Canary Islands (Spain)

Ciuffreda

Lorenzo-Salazar

Artola

et al. 2023

Emerging Microbes & Infections

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A highly divergent SARS-CoV-2 lineage B.1.1 sample in a patient with long-term COVID-19

Nabieva,

Komissarov,

Klink

et al. 2023

Preprint

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We report the genomic analysis of a highly divergent SARS-CoV-2 sample obtained in October 2022 from an HIV+ patient with presumably long-term COVID-19 infection. Phylogenetic analysis indicates that the sample is characterized by a gain of 89 mutations since divergence from its nearest sequenced neighbor, which had been collected in September 2020 and belongs to the B.1.1 lineage, largely extinct in 2022. 33 of these mutations were coding and occurred in the Spike protein. Of these, 17 are lineage-defining in some of the variants of concern (VOCs) or are in sites where another mutation is lineage-defining in a variant of concern, and/or shown to be involved in antibody evasion, and/or detected in other cases of persistent COVID-19; these include some "usual suspects," such as Spike:L452R, E484Q, K417T, Y453F, and N460K. Molecular clock analysis indicates that mutations in this lineage accumulated at an increased rate compared to the ancestral B.1.1 strain. This increase is driven by the accumulation of nonsynonymous mutations, for an average dN/dS value of 2.2, indicating strong positive selection during within-patient evolution. Additionally, there is reason to believe that the virus had persisted for at least some time in the gastrointestinal tract, as evidenced by the presence of mutations that are rare in the general population samples but common in samples from wastewater. Our analysis adds to the growing body of research on evolution of SARS-CoV-2 in chronically infected patients and its relationship to the emergence of variants of concern.

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Viral load of SARS‐CoV‐2 Omicron BA.5 is lower than that of BA.2 despite the higher infectivity of BA.5

Cited by 2 publications

References 8 publications

Reinfection rate and disease severity of the BA.5 Omicron SARS-CoV-2 lineage compared to previously circulating variants of concern in the Canary Islands (Spain)

Reinfection rate and disease severity of the BA.5 Omicron SARS-CoV-2 lineage compared to previously circulating variants of concern in the Canary Islands (Spain)

A highly divergent SARS-CoV-2 lineage B.1.1 sample in a patient with long-term COVID-19

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