Dataset Information

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021.

ABSTRACT: Routine genomic surveillance on samples from COVID-19 patients collected in Poland during summer 2021 revealed the emergence of a SARS-CoV-2 Delta variant with a large 872 nt deletion. This change, confirmed by Sanger and deep sequencing, causes complete loss of ORF7a, ORF7b, and ORF8 genes. The index case carrying the deletion is unknown. The standard pipeline for sequencing may mask this deletion with a long stretch of N's. Effects of this deletion on phenotype or immune evasion needs further study.

SUBMITTER: Mazur-Panasiuk N

PROVIDER: S-EPMC8485581 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Publications

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021.

Mazur-Panasiuk Natalia N Rabalski Lukasz L Gromowski Tomasz T Nowicki Grzegorz G Kowalski Michal M Wydmanski Witold W Szulc Piotr P Kosinski Maciej M Gackowska Karolina K Drweska-Matelska Natalia N Grabowski Jakub J Piotrowska-Mietelska Anna A Szewczyk Boguslaw B Bienkowska-Szewczyk Krystyna K Swadzba Jakub J Labaj Pawel P Grzybek Maciej M Pyrc Krzysztof K

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 20210901 39

Routine genomic surveillance on samples from COVID-19 patients collected in Poland during summer 2021 revealed the emergence of a SARS-CoV-2 Delta variant with a large 872 nt deletion. This change, confirmed by Sanger and deep sequencing, causes complete loss of ORF7a, ORF7b, and ORF8 genes. The index case carrying the deletion is unknown. The standard pipeline for sequencing may mask this deletion with a long stretch of N's. Effects of this deletion on phenotype or immune e ...[more]

PMID: 34596017

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Project description:BackgroundThe extent to which vaccinated persons who become infected with SARS-CoV-2 contribute to transmission is unclear. During a SARS-CoV-2 Delta variant outbreak among incarcerated persons with high vaccination rates in a federal prison, we assessed markers of viral shedding in vaccinated and unvaccinated persons.MethodsConsenting incarcerated persons with confirmed SARS-CoV-2 infection provided mid-turbinate nasal specimens daily for 10 consecutive days and reported symptom data via questionnaire. Real-time reverse transcription-polymerase chain reaction (RT-PCR), viral whole genome sequencing, and viral culture was performed on these nasal specimens. Duration of RT-PCR positivity and viral culture positivity was assessed using survival analysis.ResultsA total of 957 specimens were provided by 93 participants, of whom 78 (84 %) were vaccinated and 17 (16 %) were unvaccinated. No significant differences were detected in duration of RT-PCR positivity among vaccinated participants (median: 13 days) versus those unvaccinated (median: 13 days; p = 0.50), or in duration of culture positivity (medians: 5 days and 5 days; p = 0.29). Among vaccinated participants, overall duration of culture positivity was shorter among Moderna vaccine recipients versus Pfizer (p = 0.048) or Janssen (p = 0.003) vaccine recipients. In post-hoc analyses, Moderna vaccine recipients demonstrated significantly shorter duration of culture positivity compared to unvaccinated participants (p = 0.02). When restricted to participants without reported prior infection, the difference between Moderna vaccine recipients and unvaccinated participants was more pronounced (medians: 3 days and 6 days, p = 0.002).ConclusionsInfectious periods for vaccinated and unvaccinated persons who become infected with SARS-CoV-2 are similar and can be highly variable, though some vaccinated persons are likely infectious for shorter durations. These findings are critically important, especially in congregate settings where viral transmission can lead to large outbreaks. In such settings, clinicians and public health practitioners should consider vaccinated, infected persons to be no less infectious than unvaccinated, infected persons.

Project description:ImportanceThe COVID-19 pandemic led to widespread lockdowns and school closures that may have affected screen time among children. Although restrictions were strongest early in the pandemic, it is unclear how screen time changed as the pandemic progressed.ObjectiveTo evaluate change in children's screen time from before the pandemic to during the pandemic, from July 2019 through August 2021.Design, setting, and participantsThis is a longitudinal cohort study with repeated measures of screen time collected before the pandemic and during 2 pandemic periods. Children aged 4 to 12 years and their parent were enrolled in 3 pediatric cohorts across 3 states in the US participating in the Environmental Influences of Child Health Outcomes (ECHO) Program. Data analysis was performed from November 2021 to July 2022.ExposuresCOVID-19 pandemic period: prepandemic (July 2019 to March 2020), pandemic period 1 (December 2020 to April 2021), and pandemic period 2 (May 2021 to August 2021).Main outcomes and measuresThe primary outcomes were total, educational (not including remote school), and recreational screen time assessed via the ECHO Child Media Use questionnaire. Linear mixed-effects models were used for screen time adjusted for child's age, number of siblings, sex, race, ethnicity, and maternal education.ResultsThe cohort included 228 children (prepandemic mean [SD] age, 7.0 [2.7] years; 100 female [43.9%]) with screen time measured during the prepandemic period and at least once during the pandemic period. Prepandemic mean (SD) total screen time was 4.4 (3.9) hours per day and increased 1.75 hours per day (95% CI, 1.18-2.31 hours per day) in the first pandemic period and 1.11 hours per day (95% CI, 0.49-1.72 hours per day) in the second pandemic period, in adjusted models. Prepandemic mean (SD) recreational screen time was 4.0 (3.5) hours per day and increased 0.89 hours per day (95% CI, 0.39-1.39 hours per day) in the first pandemic period and 0.70 hours per day (95% CI, 0.16-1.25 hours per day) in the second pandemic period. Prepandemic mean (SD) educational screen time was 0.5 (1.2) hours per day (median [IQR], 0.0 [0.0-0.4] hours per day) and increased 0.93 hours per day (95% CI, 0.67-1.19 hours per day) in the first pandemic period and 0.46 hours per day (95% CI, 0.18-0.74 hours per day) in the second pandemic period.Conclusions and relevanceThese findings suggest that screen time among children increased during the COVID-19 pandemic and remained elevated even after many public health precautions were lifted. The long-term association of increased screen time during the COVID-19 pandemic with children's health needs to be determined.

Dataset Information

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021.

Publications

Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing <i>ORF7a</i>, <i>ORF7b</i> and <i>ORF8</i>, Poland, July to August 2021.

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