Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Variant Kinetics in Natural Infection: A Case Study

Year 2024, , 69 - 73, 29.01.2024

Daisuke Tamura , Hirokazu Yamagishi Kiri Koshu Toshihiro Tajima Hiroshi Osaka

https://doi.org/10.46310/tjim.1352394

Abstract

Background Omicron has become the mainstream epidemic variant of severe acute respiratory syndrome coronavirus 2 worldwide. One reason for the high infectivity of this variant is its ability to multiply rapidly in the human body. It has been speculated that, in general, the short period required for virus multiplication affects the incubation period and timing of viral shedding that begins during the incubation period. However, it is unclear whether these effects can be related to the Omicron variant. Similar to a recent human challenge study, in this study, patients with known timing of Omicron infection were followed up in a hospital before the onset of the disease.
Methods In two patients, the viral shedding was investigated and analysed along with symptoms before and after the disease onset.
Results The incubation period for Omicron was 30-36 h; this was shorter than the average incubation period of the alpha variant in the human challenge study and that reported in a systematic review and meta-analysis (3.5 days). Viral shedding at the nasal site began 19-22 h after infection, approximately 10 h before symptom onset.
Conclusion The results of this study demonstrated that in some instances with Omicron (BA.5), the time to viral shedding and the time to disease onset were considerably shorter after infection than those previously reported for Omicron and Alpha variants. We showed the importance of early detection of the viral antigen after viral exposure and early isolation initiation to prevent infection spread.

Keywords

SARS-CoV-2, Omicron variant, incubation period, viral shedding, infection, epidemic

References

• World Health Organization. WHO Coronavirus (COVID-19) Dashboard. Available at: https://covid19.who.int. Accessed April 19, 2023.
• World Health Organization. Tracking SARS-CoV-2 variants. Available at: https://www.who.int/activities/tracking-SARS-CoV-2-variants. Accessed April 19, 2023.
• World Health Organization. Update on Omicron. Available at: https://www.who.int/news/item/28-11-2021-update-on-omicron. Accessed April 19, 2023.
• Puhach O, Adea K, Hulo N, Sattonnet P, Genecand C, Iten A, Jacquérioz F, Kaiser L, Vetter P, Eckerle I, Meyer B. Infectious viral load in unvaccinated and vaccinated individuals infected with ancestral, Delta or Omicron SARS-CoV-2. Nat Med. 2022 Jul;28(7):1491-500. doi: 10.1038/s41591-022-01816-0.
• World Health Organization. Therapeutics and COVID-19. Available at: https://www.who.int/teams/health-care-readiness/covid-19/therapeutics. Accessed April 19, 2023.
• Chen J, Wang R, Gilby NB, Wei GW. Omicron variant (B.1.1.529): Infectivity, vaccine breakthrough, and antibody resistance. J Chem Inf Model. 2022 Jan 24;62(2):412-422. doi: 10.1021/acs.jcim.1c01451.
• Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J; COVID-19 Genomics UK Consortium; Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol. 2023 Mar;21(3):162-177. doi: 10.1038/s41579-022-00841-7.
• Guo Z, Zhao S, Mok CKP, So RTY, Yam CHK, Chow TY, Chan TCP, Wei Y, Jia KM, Wang MH, Chong KC, Yeoh EK. Comparing the incubation period, serial interval, and infectiousness profile between SARS-CoV-2 Omicron and Delta variants. J Med Virol. 2023 Mar;95(3):e28648. doi: 10.1002/jmv.28648.
• Wu Y, Kang L, Guo Z, Liu J, Liu M, Liang W. Incubation period of COVID-19 caused by unique SARS-CoV-2 strains: A systematic review and meta-analysis. JAMA Netw Open. 2022 Aug 1;5(8):e2228008. doi: 10.1001/jamanetworkopen.2022.28008.
• Galmiche S, Cortier T, Charmet T, Schaeffer L, Chény O, von Platen C, Lévy A, Martin S, Omar F, David C, Mailles A, Carrat F, Cauchemez S, Fontanet A. SARS-CoV-2 incubation period across variants of concern, individual factors, and circumstances of infection in France: a case series analysis from the ComCor study. Lancet Microbe. 2023 Jun;4(6):e409-17. doi: 10.1016/S2666-5247(23)00005-8.
• Killingley B, Mann AJ, Kalinova M, Boyers A, Goonawardane N, Zhou J, Lindsell K, Hare SS, Brown J, Frise R, Smith E, Hopkins C, Noulin N, Löndt B, Wilkinson T, Harden S, McShane H, Baillet M, Gilbert A, Jacobs M, Charman C, Mande P, Nguyen-Van-Tam JS, Semple MG, Read RC, Ferguson NM, Openshaw PJ, Rapeport G, Barclay WS, Catchpole AP, Chiu C. Safety, tolerability and viral kinetics during SARS-CoV-2 human challenge in young adults. Nat Med. 2022 May;28(5):1031-41. doi: 10.1038/s41591-022-01780-9.
• National Institute of Infectious Disease, Laboratory Manuals for Pathogen Detection. Manual for the Detection of Pathogen (2019).nCoV. ver.2.6. Available at: https://www.niid.go.jp/niid/images/epi/corona/2019-nCoVmanual20200217-en.pdf; 2020. Accessed April 19, 2023.
• Tamura D, Yamagishi H, Morisawa Y, Mato T, Nunomiya S, Maehara Y, Ochiai Y, Okuyama S, Ohmika N, Yamagata T, Osaka H. Diagnostic accuracy of a novel SARS CoV-2 rapid antigen test and usefulness of specimens collected from the anterior nasal cavity. Int J Infect Dis. 2022 Nov;124:199-205. doi: 10.1016/j.ijid.2022.09.018.
• Ogata T, Tanaka H. SARS-CoV-2 Incubation period during the Omicron BA.5-dominant period in Japan. Emerg Infect Dis. 2023 Mar;29(3):595-8. doi: 10.3201/eid2903.221360.
• Vitiello A, Ferrara F, Auti AM, Di Domenico M, Boccellino M. Advances in the Omicron variant development. J Intern Med. 2022 Jul;292(1):81-90. doi: 10.1111/joim.13478.