SARS-CoV-2 Omicron Virus Shedding Duration by Vaccinees

Information from Industry

View All

Conclusions

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. 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. 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] Cq values were frequently lower for the B.1.617.2 (Delta) variant than for the other variants (B.1.1.7 [Alpha]), and virus clearance was faster in vaccinated than in unvaccinated persons.^[10] Similar to findings for the Wu01 strain, the Alpha variant, and the Delta variant,^[11–13] RNA of the Omicron variant was detectable 10 days after diagnosis or symptom onset, but no virus was isolated.

In the United States, the isolation period for COVID-19 patients is 5 days after symptom onset if the symptoms are improving.^[14] In Japan, based on the outbreak situation, the results of this study, and isolation criteria in other countries, the isolation criteria for Omicron patients were changed on January 6, 2022. Two consecutive negative test results 10 days after diagnosis or symptom onset are no longer required for patients who received 2 vaccine doses.

Our first study limitation is that we identified infectious virus by infection assays among only 18 patients. We do not know about the infectivity outside of this study. In addition, there are no epidemiologic data about whether secondary infections occurred from patients with these infectious viruses. Therefore, comparing theses results with future epidemiologic studies of more samples is necessary. Our second study limitation is that the virus isolation and infectivity assay results depend on the sample collection method, storage period, and storage conditions. Therefore, negative results do not guarantee that there was no infectious virus in the sample at the time of collection. Last, for some case-patients, virus was not isolated in samples collected at the time of diagnosis. For these persons, the samples used for diagnosis were collected at the airport quarantine and were saliva, for which the quality may not be suitable for virus isolation. Although our results are insufficient to show a difference in efficiency of virus isolation between saliva and nasopharyngeal samples in Omicron-infected persons, this difference may have underestimated the presence of infectious virus at diagnosis. In conclusion, fully vaccinated COVID-19 case-patients with mild or asymptomatic infection shed infectious virus in their upper respiratory tract for 6–9 days after illness onset or diagnosis, even after symptom resolution, but not after day 10.

Acknowledgment
We thank Akiko Sataka, Asato Kojima, Izumi Kobayashi, Yuki Iwamoto, Yuko Sato, Seiya Ozono, Milagros Virhuez Mendoza, Noriko Nakajima, Kenta Takahashi, Yuichiro Hirata, Shun Iida, Harutaka Katano, Makoto Kuroda, Tsuyoshi Sekizuka, Naomi Nojiri, Hazuka, Yoshida, Nozomu Hanaoka, and Masumichi Saito for technical support. We also thank Kenji Sadamasu and Mami Nagashima for technical support with respect to SARS-CoV-2 viral RNA genome sequencing and all staff members for providing care for COVID-19 patients.

Table. Overview of 18 cases of SARS-CoV-2 infection caused by the Omicron variant, Japan, November 29–December 18, 2021*
Case no.	Patient age, y/sex	Disease severity	Vaccine, no. doses (type)	Duration of symptoms, d	Lowest Cq values (days after diagnosis, days after symptom onset)	Virus isolation, since diagnosis (days)‡
1	39/M	Mild	2 (M, M)	5	21.6 (3, 3)	Positive (3)
2	30/M	Asymptomatic	2 (M, M)	NA	25.3 (5, NA)	Positive (5)
3	25/M	Mild	2 (P, P)	6	23.2 (4, 3)	Negative
4	46/M	Mild	3 (J, P, P)	11	24.7 (9, 11)	Positive (6)
5	50/M	Asymptomatic	2 (P, P)	NA	23.1 (5, NA)	Positive (5)
6	31/M	Mild	2 (P, P)	5	25.4 (0, 0)	Negative
7	47/M	Asymptomatic	2 (P, P)	NA	34.2 (9, NA)	Negative
8	33/F	Mild	2 (M, M)	12	32.4 (0, 1)	Negative
9	64/M	Mild	2 (P, P)	4	23.9 (0, −1)	Positive (0)
10	42/M	Mild	2 (M, M)	4	27.0 (0, −1)	Negative
11	49/M	Mild	2 (M, M)	5	26.5 (0, −1)	Positive (8)
12	31/M	Mild	2 (M, M)	4	25.4 (5, 4)	Positive (7)
13	50/M	Mild	2 (M, M)	6	24.7 (5, 7)	Positive (5)
14	30/F	Mild	2 (M, M)	11	30.0 (0, 2)	Negative
15	27/M	Mild	2 (P, P)	8	25.8 (6, 10)	Negative
16	23/M	Mild	2 (P, P)	5	18.7 (3, 4)	Positive (3)
17	47/M	Mild	2 (M, M)	6	24.2 (7, 7)	Positive (0)
18	38/M	Mild	2 (P, P)	6	29.0 (7, 8)	Negative

*The consensus sequences of the viral genome have been uploaded to GISAID (https://www.gisaid.org) (identification nos. EPI_ISL_6913953, EPI_ISL_6914908, EPI_ISL_7194610, EPI_ISL_7834392, EPI_ISL_7860184, EPI_ISL_7860185, EPI_ISL_7860188, EPI_ISL_7860189, EPI_ISL_7860190, EPI_ISL_7860193, EPI_ISL_7860197, EPI_ISL_7889642, EPI_ISL_7889643, EPI_ISL_8096984, EPI_ISL_8096995, EPI_ISL_8605240, EPI_ISL_8605241, EPI_ISL_8605242). Cq, quantification cycle; J, Johnson & Johnson; M, Moderna; NA, not available; P, Pfizer/BioNTech; SARS-CoV-2, severe acute respiratory syndrome. coronavirus 2.