![]() ![]() We fitted incubation period data for each subvariant to the gamma distribution model and calculated parameters and 95% CI within a Bayesian inference framework.įigure. When we fitted incubation period data from the BA.5–dominant period to parametric distribution models, the Akaike information criterion for gamma distribution was smaller than that for Gaussian, lognormal, and Weibull distribution models. The mean ( +SD) incubation periods were 2.6 ( +1.0) days during the BA.5–dominant period, 2.9 ( +1.3) days during the BA.1–dominant period, and 3.7 ( +1.6) days during the Delta-dominant period. Patient data during the BA.1–dominant and Delta-dominant periods were obtained from previous studies ( 6, 7). We extracted data for 266 infector/infectee pairs who had 1 definite date of SARS-CoV-2 exposure as follows: 122 infectees from 108 infectors during the Omicron BA.5–dominant period, 68 infectees from 49 infectors during the BA.1–dominant period, and 76 infectees from 51 infectors during the Delta-dominant period. ![]() Genomic sequencing detected variants of concern in Japan from July 19–September 13, 2001, as follows: 26,963 cases of B.1.617.2 (Delta), 15,009 cases of B.1.1.7 (Alpha), and 5 cases of other variants ( 9) the L452R mutation was found mostly in the Delta variant. We defined patients in the Delta-dominant period as those who had symptom onset during July 23–September 14, 2021, and either they or their contacts were confirmed to have L452R-positive SARS-CoV-2. Genomic sequencing showed that 92% of 22,953 variants of concern sampled in Japan during January 3–February 6 were BA.1 ( 9). Of the 1,216 samples collected during January 3–February 6 in Ibaraki, a total of 1,158 (95%) were negative for the SARS-CoV-2 spike protein mutation L452R ( 8). We defined patients in the BA.1–dominant period as those who had symptom onset during January 1–February 2, 2022. Genomic sequencing of 528 samples collected in Ibaraki showed 481 (91%) samples were BA.5, 40 were BA.2, and 7 were BA.1 subvariants. We defined patients in the Omicron BA.5–dominant period as those who had symptoms during July 4–August 19, 2022. We defined the patient with the later symptom onset in each pair as the infected patient. Persons exposed to SARS-CoV-2 in household, workplace, or school settings were excluded if they might have been exposed at another time. Procedures used for contact tracing and data collection for patient pairs with COVID-19 were similar to those described previously ( 6, 7). Other transmission settings included conversations in the home, a building or car, or outdoors. If the pair shared meals on both July 4 and 5, we excluded all data from this pair. If a pair shared meals on July 4 and the infectee had COVID-19 symptoms on July 7, we calculated an incubation period of 3 days. We calculated the incubation period by using the calendar dates of contact and symptom onset, regardless of duration or number of contacts. We enrolled COVID-19 infector/infectee pairs who lived within the Itako PHC jurisdiction and had a single definite close contact date with patients who had COVID-19 without other potential transmission settings. ![]()
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