Comparison of SARS-CoV-2 Viral Loads in the Nasal Mucosa of Patients Infected With BA.1, BA.2, or BA.5 Omicron Lineages

Tozer, Kyla; Sjaarda, Calvin; Moslinger, Emily; Wong, Henry; Mubareka, Samira; Maguire, Finlay; Fattouh, Ramzi; Brabant-Kirwan, Danielle; Kozak, Robert; Sheth, Prameet M.

doi:10.1093/ofid/ofac564

Cited by 3 publications

(4 citation statements)

References 17 publications

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“…The symptoms of ‘runny nose’ and ‘cough’ occurred significantly more frequently in BA.2- and BA.5-infected individuals than in BA.1 cases. One possible explanation for this could be that there is evidence that patients infected with the BA.2 and BA.5 sub-lineages have a higher upper respiratory viral load compared to patients infected with BA.1 [ 14 , 15 ]. However, in accordance with the results of Whitaker et al [ 24 ], respiratory symptoms were the most prominent in all three sub-lineages.…”

Section: Discussionmentioning

confidence: 99%

“…Differences between BA.5 and BA.2 could also be observed in terms of BA.5 having a higher transmissibility and being more pathogenic than BA.2. Additionally, the genetic differences among the Omicron subvariants could also imply potential differences in clinical presentations, probably caused by different viral loads in the respiratory tract [14,15]. However, despite the data on mortality [16], direct comparisons of the symptoms caused by BA.1 and BA.2 infections are rare, but suggest somewhat milder symptoms in BA.1 infections [17].…”

Section: Introductionmentioning

confidence: 99%

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Clinical Manifestations of Infections with the Omicron Sub-Lineages BA.1, BA.2, and BA.5: A Retrospective Follow-Up Analysis of Public Health Data from Mecklenburg-Western Pomerania, Germany

Goller,

Ziemann,

Kohler

et al. 2024

Viruses

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The Omicron variants BA.1, BA.2, and BA.5 caused several waves of SARS-CoV-2 in Germany in 2022. In this comparative study, public health data on SARS-CoV-2 infections from Mecklenburg-Western Pomerania, Germany, between January and October 2022 were examined retrospectively using Pearson’s chi-squared tests and Fisher’s exact tests for testing for statistical significance. Compared to BA.5 infections, BA.1 and BA.2 infections affected younger individuals aged up to 19 years significantly more often, whereas BA.5 infections occurred significantly more frequently in patients between 40 and 59 years of age when compared to BA.1 and BA.2. Infections with all three variants predominantly caused flu-like symptoms; nevertheless, there were significant differences between the reported symptoms of BA.1, BA.2, and BA.5 infections. Especially, the symptoms of ‘fever’, ‘severe feeling of sickness’, ‘loss of taste’, and ‘loss of smell’ were significantly more often present in patients with BA.5 infections compared to BA.1 and BA.2 cases. Additionally, BA.2 and BA.5 cases reported significantly more often the symptoms of ‘runny nose’ and ‘cough’ than BA.1-infected cases. Our findings indicate remarkable differences in the clinical presentations among the sub-lineages, especially in BA.5 infections. Furthermore, the study demonstrates a powerful tool to link epidemiological data with genetic data in order to investigate their potential impact on public health.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Clinical Manifestations of Infections with the Omicron Sub-Lineages BA.1, BA.2, and BA.5: A Retrospective Follow-Up Analysis of Public Health Data from Mecklenburg-Western Pomerania, Germany

Goller,

Ziemann,

Kohler

et al. 2024

Viruses

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Section: Methodsmentioning

confidence: 99%

“…Samples that were positive for SARS-CoV-2 using reverse-transcription polymerase chain reaction testing with a cycle threshold less than 30 cycles underwent whole-genome sequencing, as has been previously described. 10 In a single center, the Illumina platform was used, and data consensus sequences and variants were called using FreeBayes. 11 The other 3 centers used the Oxford Nanopore Technologies platform, with Nanopore v3 Midnight primers using the native barcode, ARTIC SARS-CoV-2 bioinformatic protocol.…”

Section: Methodsmentioning

confidence: 99%

Prevalence of Low-Frequency, Antiviral Resistance Variants in SARS-CoV-2 Isolates in Ontario, Canada, 2020-2023

et al. 2023

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ImportanceNirmatrelvir-ritonavir is an oral antiviral medication that improves outcomes in SARS-CoV-2 infections. However, there is concern that antiviral resistance will develop and that these viruses could be selected for after treatment.ObjectiveTo determine the prevalence of low-frequency SARS-CoV-2 variants in patient samples that could be selected for by nirmatrelvir-ritonavir.Design, Setting, and ParticipantsThis retrospective cohort study was conducted at 4 laboratories that serve community hospitals, academic tertiary care centers, and COVID-19 assessment centers in Ontario, Canada. Participants included symptomatic or asymptomatic patients who tested positive for SARS-CoV-2 virus and submitted virus samples for diagnostic testing between March 2020 and January 2023.ExposureSARS-CoV-2 infection.Main Outcomes and MeasuresSamples with sufficient viral load underwent next-generation genome sequencing to identify low-frequency antiviral resistance variants that could not be identified through conventional sequencing.ResultsThis study included 78 866 clinical samples with next-generation whole-genome sequencing data for SARS-CoV-2. Low-frequency variants in the viral nsp5 gene were identified in 128 isolates (0.16%), and no single variant associated with antiviral resistance was predominate.Conclusions and RelevanceThis cohort study of low-frequency variants resistant to nirmatrelvir-ritonavir found that these variants were very rare in samples from patients with SARS-CoV-2, suggesting that selection of these variants by nirmatrelvir-ritonavir following the initiation of treatment may also be rare. Surveillance efforts that involve sequencing of viral isolates should continue to monitor for novel resistance variants as nirmatrelvir-ritonavir is used more broadly.

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Dynamic changes of Ct values of N gene and ORF1ab genes and laboratory parameters in patients with COVID-19 caused by SARS-CoV-2 B.1, BA.2 and BA.5 variants and their correlation with clinical characteristics

Yang,

Chen,

Zhou

et al. 2024

Preprint

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This study investigated the patterns of variation in the Ct values of the ORF1ab and N genes in oropharyngeal swabs of COVID-19 patients with different variants and to evaluate their associations with clinical and laboratory parameters. Total of 259 individuals with COVID-19 from 2021 to 2023 in Jilin Province were retrospectively included. Analysis was performed to compare the Ct values of the gene of SARS-CoV-2 in patients, with negative conversion time of nucleic acid, and the levels of blood tests during the patients' hospitalization.The majority of B.1 variant-infected individuals were asymptomatic; the median ORF1ab gene and N gene Ct values in oropharyngeal swabs from heavy patients were the lowest; and all ORF1ab gene Ct values were lower than N gene Ct values; with the longest negative conversion time of nucleic acid in these patients being 18 days.The median Ct values of the ORF1ab gene and the N gene were the highest in BA. 2 variant infected patients, and the Ct values of the ORF1ab gene and the N gene were higher in male patients than in female patients, and the shortest negative conversion time of nucleic acid was 14 days in patients with this variant, and the negative conversion time of nucleic acid was shorter in vaccinated patients than in unvaccinated patients.While the negative conversion time of nucleic acid was similar between BA.2 patients and BA.5 patients, the median Ct values of the ORF1ab and N genes were considerably lower in BA.5 patients than in BA.2 patients. The CREA, WBC, and NE% were significantly higher, and the ALB and LY% were significantly lower in BA.2 and BA.5 patients compared with B.1 patients. With disease aggravation, CREA, NE%, APTT, PT, and D-D increased, and LY% decreased. In conclusion, The most asymptomatic and longest transitional cycles were shown in patients with the ancestral lineage B.1 variation. Patients with the OmicronBA.2 variant showed the highest Ct values for the ORF1ab and N genes, while patients with the BA.2 and BA.5 variants had more serious coagulation and renal impairment.

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Comparison of SARS-CoV-2 Viral Loads in the Nasal Mucosa of Patients Infected With BA.1, BA.2, or BA.5 Omicron Lineages

Cited by 3 publications

References 17 publications

Clinical Manifestations of Infections with the Omicron Sub-Lineages BA.1, BA.2, and BA.5: A Retrospective Follow-Up Analysis of Public Health Data from Mecklenburg-Western Pomerania, Germany

Clinical Manifestations of Infections with the Omicron Sub-Lineages BA.1, BA.2, and BA.5: A Retrospective Follow-Up Analysis of Public Health Data from Mecklenburg-Western Pomerania, Germany

Prevalence of Low-Frequency, Antiviral Resistance Variants in SARS-CoV-2 Isolates in Ontario, Canada, 2020-2023

Dynamic changes of Ct values of N gene and ORF1ab genes and laboratory parameters in patients with COVID-19 caused by SARS-CoV-2 B.1, BA.2 and BA.5 variants and their correlation with clinical characteristics

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