“Rapid reinfections with different or same Omicron SARS-CoV-2 sub-variants”

Vera-Lise, Ihm; Dominik, Ensle; Elisabeth, Reiter; Huber, Kerstin; Raffael, Förster; Angelika, Xaver; Tibor, Aßheuer; Jusztina, Barna; Karnthaler, Ursula; Jochen, Haidvogel; Krass, David; John-Hendrik, Jordan

doi:10.1016/j.jinf.2022.07.003

Cited by 7 publications

(7 citation statements)

References 3 publications

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“…In one study, spike gene target failure, which could be detected in Delta but not Omicron in the TaqPath RT-PCR, was used as a proxy marker to assign the variant ( 11 ). In another study, variants of concern (VOCs) were inferred by determining changes in the melting patterns of probes used in RT-PCR to target regions where marker SNVs are located ( 4 ). Although such inferences are useful and practicable, they can only assign reinfections involving certain VOCs, thereby missing possible early reinfections involving the same lineages or even sublineages, which can only be addressed by WGS characterization.…”

Section: Discussionmentioning

confidence: 99%

“…Centers for Disease Control and Prevention (CDC) guidelines for consideration of SARS-CoV-2 reinfection require evidence of 2 sequential COVID-19 episodes separated by > 90 days and > 1 negative RT-PCR in between ( 2 ). However, inclusion criterion for most studies that have focused on COVID-19 reinfection have usually required 45–60 days between sequential episodes ( 3 , 4 ). This timeframe maximizes factors that increase the likelihood of reinfection, including the chance of cure of the first episode, clearance of the strain involved in the first episode, and possibility of reexposure to another positive case.…”

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confidence: 99%

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Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain

Rodríguez‐Grande¹,

Estévez²,

Palomino-Cabrera³

et al. 2023

Emerg. Infect. Dis.

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Centers for Disease Control and Prevention guidelines consider SARS-CoV-2 reinfection when sequential COVID-19 episodes occur > 90 days apart. However, genomic diversity acquired over recent COVID-19 waves could mean previous infection provides insufficient cross-protection. We used genomic analysis to assess the percentage of early reinfections in a sample of 26 patients with 2 COVID-19 episodes separated by 20–45 days. Among sampled patients, 11 (42%) had reinfections involving different SARS-CoV-2 variants or subvariants. Another 4 cases were probable reinfections; 3 involved different strains from the same lineage or sublineage. Host genomic analysis confirmed the 2 sequential specimens belonged to the same patient. Among all reinfections, 36.4% involved non-Omicron, then Omicron lineages. Early reinfections showed no specific clinical patterns; 45% were among unvaccinated or incompletely vaccinated persons, 27% were among persons <18 years of age, and 64% of patients had no risk factors. Time between sequential positive SARS-CoV-2 PCRs to consider reinfection should be re-evaluated.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain

Rodríguez‐Grande¹,

Estévez²,

Palomino-Cabrera³

et al. 2023

Emerg. Infect. Dis.

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“…There are several limitations to our study. First, this PCR assay cannot distinguish between co‐existing Omicron variants due to re‐infection or co‐infection of various variants that may lead to the co‐existence of distinct RNA of circulating sublineages as described by Vera‐Lise et al and Combes et al 22,23 Second, our novel RT‐PCR assay targeting the existing BA.2, BA.4, and BA.5 may not be suitable for detecting newly emerging sublineages. To circumvent this, samples showing unexpected mutational profiles by our PCR typing method should be further submitted for WGS analysis for epidemiological investigation.…”

Section: Discussionmentioning

confidence: 93%

Accelerating pandemic response with the emergency Omicron RT‐PCR test: A comprehensive solution for COVID‐19 diagnosis and tracking

Chung

Jian

Chang

et al. 2023

Journal of Medical Virology

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The Omicron variant of concern (VOC) has surged in many countries and replaced the previously reported VOC. To identify different Omicron strains/sublineages on a rapid, convenient, and precise platform, we report a novel multiplex real‐time reverse transcriptase polymerase chain reaction (RT‐PCR) method in one tube based on the Omicron lineage sequence variants' information. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) subvariants were used in a PCR‐based assay for rapid identification of Omicron sublineage genotyping in 1000 clinical samples. Several characteristic mutations were analyzed using specific primers and probes for the spike gene, del69–70, and F486V. To distinguish Omicron sublineages (BA.2, BA.4, and BA.5), the NSP1:141–143del in the ORF1a region and D3N mutation in membrane protein occurring outside the spike protein region were analyzed. Results from the real‐time PCR assay for one‐tube accuracy were compared to those of whole genome sequencing. The developed PCR assay was used to analyze 400 SARS‐CoV‐2 positive samples. Ten samples determined as BA.4 were positive for NSP1:141–143del, del69–70, and F486V mutations; 160 BA.5 samples were positive for D3N, del69–70, and F486V mutations, and 230 BA.2 samples were without del69–70. Screening these samples allowed the identification of epidemic trends at different time intervals. Our novel one‐tube multiplex PCR assay was effective in identifying Omicron sublineages.

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“…Previous studies have demonstrated that reinfection with Omicron BA.2 can occur within 60 days, especially in unvaccinated individuals ( 24 ). In this study, the variant of Omicron was determined as BA.2.…”

Section: Discussionmentioning

confidence: 99%

Older age and depressive state are risk factors for re-positivity with SARS-CoV-2 Omicron variant

Peng

Duan

et al. 2022

Front. Public Health

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BackgroundThe reinfection rate of SARS-CoV-2 Omicron variant is high; thus, exploring the risk factors for reinfection is important for the effective control of the epidemic. This study aimed to explore the effects of psychological and sleep factors on re-positivity with Omicron.MethodsThrough a prospective cohort study, 933 adult patients diagnosed with Omicron BA.2.2 infection and testing negative after treatment were included for screening and follow-up. We collected data on patients' demographic characteristics, SARS-CoV-2 Omicron vaccination status, anxiety, depression, and sleep status. Patients underwent nucleic acid testing for SARS-CoV-2 Omicron for 30 days. Regression and Kaplan-Meier analyses were used to determine the risk factors for re-positivity of Omicron.ResultsUltimately, 683 patients were included in the analysis. Logistic regression analysis showed that older age (P = 0.006) and depressive status (P = 0.006) were two independent risk factors for Omicron re-positivity. The odds ratios of re-positivity in patients aged ≥60 years and with a Patient Health Questionnaire-9 (PHQ-9) score ≥5 was 1.82 (95% confidence interval:1.18–2.78) and 2.22 (1.27–3.85), respectively. In addition, the time from infection to recovery was significantly longer in patients aged ≥60 years (17.2 ± 4.5 vs. 16.0 ± 4.4, P = 0.003) and in patients with PHQ-9≥5 (17.5 ± 4.2vs. 16.2 ± 4.5, P = 0.026). Kaplan–Meier analysis showed that there was a significantly higher primary re-positivity rate in patients aged ≥60 years (P = 0.004) and PHQ-9 ≥ 5 (P = 0.007).ConclusionThis study demonstrated that age of ≥60 years and depressive status were two independent risk factors for re-positivity with Omicron and that these factors could prolong the time from infection to recovery. Thus, it is necessary to pay particular attention to older adults and patients in a depressive state.

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“Rapid reinfections with different or same Omicron SARS-CoV-2 sub-variants”

Cited by 7 publications

References 3 publications

Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain

Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain

Accelerating pandemic response with the emergency Omicron RT‐PCR test: A comprehensive solution for COVID‐19 diagnosis and tracking

Older age and depressive state are risk factors for re-positivity with SARS-CoV-2 Omicron variant

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