28 days to alpha pdf
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Although the sample size used in our study is small, these findings suggest the possibility of changes in the viral replication kinetics, unlike previous reports for ancestral (wild-type) strain (Wu01) strains ( 8, 9). In symptomatic case-patients with infectious virus detected on days 6–9 after symptom onset, infectious virus was also detected 0–2 days after symptom resolution. Omicron RNA detection was highest 2–5 days after diagnosis or after symptom onset and then decreased over time, markedly 10 days after diagnosis or symptom onset. Of the 18 case-patients, 15 were symptomatic and 3 were asymptomatic.
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The median (interquartile range ) duration between vaccination and diagnosis was 117 (71–131) days. Statistical significance was set at p14 days before coronavirus disease (COVID-19) diagnosis ( Table). To compare the Cq values, we used Mann-Whitney t and Friedman tests with Dunn multiple comparisons. For data analysis and visualization, we used GraphPad Prism version 8.4.3 ( ). For cases in which multiple samples were collected in each time segment, we used the sample with the highest amount of viral RNA (i.e., lowest Cq values) in each time segment for each case for comparison. To examine infectious virus shedding, we classified samples according to date of diagnosis, date of symptom onset, and date of symptom resolution. All laboratory analyses were performed at the NIID. We performed the virus isolation assay according to described procedure ( 7). We analyzed samples with Cq values that were reported as negative after 40 cycles by substituting a value of 45. We measured Cq values (i.e., viral RNA levels) by using qRT-PCR targeting the SARS-CoV-2 nucleocapsid gene ( Appendix Figure 1). We performed qRT-PCR as described previously ( 6). We quantified SARS-CoV-2 RNA by using quantitative reverse transcription PCR (qRT-PCR) and virus isolation testing. Nasopharyngeal samples were collected serially during hospitalization, stored at −80☌, and transported to NIID. The date of sample collection of the first Omicron-positive sample for each patient was defined as the diagnosis date (day 0). We used the residual samples for this study. We sequenced the Omicron variant by using whole-genome sequencing as described ( 2) and uploaded the consensus sequences to GISAID ( ) ( Table).įor cases detected by SARS-CoV-2 testing at airport quarantines, samples collected for diagnosis (saliva or nasopharyngeal) were transported to the NIID to confirm Omicron. We conducted our retrospective study on leftover clinical samples collected from Omicron-infected patients in Japan during November 29–December 18, 2021. We obtained written informed consent to publish the article. NCGM-G-003472–03) and the Medical Research Ethics Committee of the National Institute of Infectious Diseases (NIID) for the use of human subjects (approval no. This study was approved by the ethics committee of the National Center for Global Health and Medicine (approval no. To help determine the criteria for patient isolation, we evaluated the duration of shedding of Omicron variant virus isolated from upper respiratory samples collected from the reported case-patients in Japan. However, the relationship between duration of virus shedding and infectivity of Omicron is unknown. The clinical course and the duration of virus shedding based on cycle quantification (Cq) values among 11 Omicron-infected patients has been reported ( 5). Several reports describe high infectivity and transmissibility of Omicron ( 3, 4). The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern belonging to the Pango lineage B.1.1.529, known as the Omicron variant, has spread rapidly worldwide ( 1, 2).