Osong Public Health and Research Perspectives

Brief Report

Replication kinetics and infectivity of SARS-CoV-2 Omicron variant sublineages recovered in the Republic of Korea: Jeong-Min Kim, Dongju Kim, Jee Eun Rhee, Cheon Kwon Yoo, Eun-Jin Kim; Osong Public Health Res Perspect. 2024;15(3):260-264. Published online June 27, 2024; DOI: https://doi.org/10.24171/j.phrp.2023.0216

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Objectives
We analyzed the correlation between the infectivity and transmissibility of the severe acute respiratory syndrome coronavirus 2 Omicron sublineages BA.1, BA. 2, BA.4, and BA.5. Methods: We assessed viral replication kinetics and infectivity at the cellular level. Nasopharyngeal and oropharyngeal specimens were obtained from patients with coronavirus disease 2019, confirmed using whole-genome sequencing to be caused by the Omicron sublineages BA.1, BA.2, BA.4, or BA.5. These specimens were used to infect Vero E6 cells, derived from monkey kidneys, for the purpose of viral isolation. Viral stocks were then passaged in Vero E6 cells at a multiplicity of infection of 0.01, and culture supernatants were harvested at 12-hour intervals for 72 hours. To evaluate viral replication kinetics, we determined the cycle threshold values of the supernatants using real-time reverse transcription polymerase chain reaction and converted these values to genome copy numbers. Results: The viral load was comparable between BA.2, BA.4, and BA.5, whereas BA.1 exhibited a lower value. The peak infectious load of BA.4 was approximately 3 times lower than that of BA.2 and BA.5, while the peak load of BA.2 and BA.5 was about 7 times higher than that of BA.1. Notably, BA.1 demonstrated the lowest infectivity over the entire study period. Conclusion: Our results suggest that the global BA.5 wave may have been amplified by the higher viral replication and infectivity of BA.5 compared to other Omicron sublineages. These analyses could support the rapid assessment of the impact of novel variants on case incidence.

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최근 코로나바이러스감염증-19 변이 바이러스 유행 현황 및 세포기반의 오미크론 세부계통 KP.3 감염성 분석
정민 김, 진선 노, 동주 김, 지영 노, 채영 이, 상희 우, 남주 이, 지은 이, 일환 김, 은진 김
Public Health Weekly Report.2024; 17(39): 1671. CrossRef

Original Article

Increased viral load in patients infected with severe acute respiratory syndrome coronavirus 2 Omicron variant in the Republic of Korea: Jeong-Min Kim, Dongju Kim, Nam-Joo Lee, Sang Hee Woo, Jaehee Lee, Hyeokjin Lee, Ae Kyung Park, Jeong-Ah Kim, Chae Young Lee, Il-Hwan Kim, Cheon Kwon Yoo, Eun-Jin Kim; Osong Public Health Res Perspect. 2023;14(4):272-278. Published online July 27, 2023; DOI: https://doi.org/10.24171/j.phrp.2023.0024

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Objectives
Coronavirus disease 2019 (COVID-19) has been declared a global pandemic owing to the rapid spread of the causative agent, severe acute respiratory syndrome coronavirus 2. Its Delta and Omicron variants are more transmissible and pathogenic than other variants. Some debates have emerged on the mechanism of variants of concern. In the COVID-19 wave that began in December 2021, the Omicron variant, first reported in South Africa, became identifiable in most cases globally. The aim of this study was to provide data to inform effective responses to the transmission of the Omicron variant.
Methods
The Delta variant and the spike protein D614G mutant were compared with the Omicron variant. Viral loads from 5 days after symptom onset were compared using epidemiological data collected at the time of diagnosis.
Results
The Omicron variant exhibited a higher viral load than other variants, resulting in greater transmissibility within 5 days of symptom onset.
Conclusion
Future research should focus on vaccine efficacy against the Omicron variant and compare trends in disease severity associated with its high viral load.

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Replication kinetics and infectivity of SARS-CoV-2 Omicron variant sublineages recovered in the Republic of Korea
Jeong-Min Kim, Dongju Kim, Jee Eun Rhee, Cheon Kwon Yoo, Eun-Jin Kim
Osong Public Health and Research Perspectives.2024; 15(3): 260. CrossRef
Diagnostic Accuracy of the Abbott BinaxNOW COVID‐19 Antigen Card Test, Puerto Rico
Zachary J. Madewell, Chelsea G. Major, Nathan Graff, Cameron Adams, Dania M. Rodriguez, Tatiana Morales, Nicole A. Medina Lopes, Rafael Tosado, Liliana Sánchez‐González, Janice Perez‐Padilla, Hannah R. Volkman, Jorge Bertrán‐Pasarell, Diego Sainz de la Pe
Influenza and Other Respiratory Viruses.2024;[Epub] CrossRef

Brief Report

The effectiveness of Paxlovid treatment in long-term care facilities in South Korea during the outbreak of the Omicron variant of SARS-CoV-2: Hanul Park, Young Joon Park, Hye Young Lee, Mi Yu, Yeong-Jun Song, Sang Eun Lee, Ji-Joo Lee, Eun-Sol Lee, Yeonjung Kim; Osong Public Health Res Perspect. 2022;13(6):443-447. Published online December 23, 2022; DOI: https://doi.org/10.24171/j.phrp.2022.0262

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Objectives
On November 5, 2021, Pfizer Inc. announced Paxlovid (nirmatrelvir +ritonavir) asa treatment method that could reduce the risk of hospitalization or death for patients withconfirmed coronavirus disease 2019 (COVID-19).Methods: From February 6, 2022 to April 2, 2022, the incidence of COVID-19 and the effectsof treatment with Paxlovid were analyzed in 2,241 patients and workers at 5 long-term carefacilities during the outbreak of the Omicron variant of severe acute respiratory syndromecoronavirus 2 in South Korea.Results: The rate of severe illness or death in the group given Paxlovid was 51% lower thanthat of the non-Paxlovid group (adjusted risk ratio [aRR], 0.49; 95% confidence interval [CI],0.24−0.98). Compared to unvaccinated patients, patients who had completed 3 doses of thevaccine had a 71% reduced rate of severe illness or death (aRR, 0.29; 95% CI, 0.13−0.64) and a65% reduced death rate (aRR, 0.35; 95% CI, 0.15−0.79).Conclusion: Patients given Paxlovid showed a lower rate of severe illness or death and alower fatality rate than those who did not receive Paxlovid. Patients who received 3 dosesof the vaccine had a lower rate of severe illness or death and a lower fatality rate than theunvaccinated group.

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American Journal of Infection Control.2025; 53(3): 348. CrossRef
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Meital Zur, Thalia Peselev, Stav Yanko, Victoria Rotshild, Ilan Matok
Antiviral Research.2024; 221: 105768. CrossRef
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Sydney Paltra, Tim O. F. Conrad
Advances in Respiratory Medicine.2024; 92(1): 66. CrossRef
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Sien Ombelet, Diego Castanares‐Zapatero, Fabian Desimpel, Frank Hulstaert, Sabine Stordeur, Dominique Roberfroid
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Medicina de Familia. SEMERGEN.2024; 50(6): 102274. CrossRef
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Chienhsiu Huang, Sufang Kuo, Lichen Lin
Tungs' Medical Journal.2024; 18(Suppl 1): S35. CrossRef
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Eric Y. F. Wan, Zoey C. T. Wong, Vincent K. C. Yan, Celine S. L. Chui, Francisco T. T. Lai, Xue Li, Ian C. K. Wong, Esther W. Y. Chan
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COVID‐19 infection in patients with haematological malignancies: A single‐centre survey in the latest Omicron wave in China
Xiaolu Zhu, Qian Jiang, Jin Lu, Yuqian Sun, Xiaosu Zhao, Shenmiao Yang, Feifei Tang, Wenjing Yu, Ting Zhao, Xiaohong Liu, Jinsong Jia, Wenbing Duan, Lijuan Hu, Jing Wang, Yang Liu, Nan Peng, Xuelin Dou, Rui Ma, Qiang Fu, Huifang Wang, Kaiyan Liu, Xiaojun
British Journal of Haematology.2023; 202(1): 31. CrossRef
The association mental health of adolescents with economic impact during the COVID-19 pandemic: a 2020 Korean nationally representative survey
Hanul Park, Kang-Sook Lee
BMC Public Health.2023;[Epub] CrossRef
Efficacy and safety of paxlovid (nirmatrelvir/ritonavir) in the treatment of COVID‐19: An updated meta‐analysis and trial sequential analysis
Haokun Tian, Changsen Yang, Tiangang Song, Kechen Zhou, Lequan Wen, Ye Tian, Lirui Tang, Weikai Xu, Xinyuan Zhang
Reviews in Medical Virology.2023;[Epub] CrossRef
Real-World Effectiveness of Nirmatrelvir-Ritonavir and Its Acceptability in High-Risk COVID-19 Patients
Min-Kyung Kim, Kyung-Shin Lee, Sin Young Ham, Youn Young Choi, Eunyoung Lee, Seungjae Lee, Bora Lee, Jaehyun Jeon, BumSik Chin, Yeonjae Kim, Gayeon Kim, Hee-Chang Jang, Jae-Phil Choi, Sang-Won Park
Journal of Korean Medical Science.2023;[Epub] CrossRef
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Hye Rim Park, Min-Gyu Yoo, Jong Mu Kim, Soon Jong Bae, Hyungmin Lee, Jungyeon Kim
Infection & Chemotherapy.2023; 55(4): 490. CrossRef
Nirmatrelvir combined with ritonavir for preventing and treating COVID-19
Stefanie Reis, Maria-Inti Metzendorf, Rebecca Kuehn, Maria Popp, Ildiko Gagyor, Peter Kranke, Patrick Meybohm, Nicole Skoetz, Stephanie Weibel
Cochrane Database of Systematic Reviews.2023;[Epub] CrossRef

Original Articles

mRNA vaccine effectiveness against SARS-CoV-2 B.1.617.2 (Delta) and B.1.1.529 (Omicron) variant transmission from home care cases to household contacts in South Korea: Hanul Park, Young Joon Park, Sang Eun Lee, Min Jei Lee, Hyungtae Ahn; Osong Public Health Res Perspect. 2022;13(6):435-442. Published online November 28, 2022; DOI: https://doi.org/10.24171/j.phrp.2022.0243

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Objectives
Household contacts of confirmed cases of coronavirus disease 2019 (COVID-19) areexposed to a high risk of viral transmission, and secondary incidence is an important indicatorof community transmission. This study analyzed the secondary attack rate and mRNA vaccineeffectiveness against transmission (VET) for index cases (patients treated at home) confirmedto be infected with the Delta and Omicron variants.Methods: The subjects of the study were 4,450 index cases and 10,382 household contacts.Logistic regression analysis was performed to compare the secondary attack rate byvaccination status, and adjusted relative risk and 95% confidence intervals were identified.Results: The secondary attack rate of the Delta variant was 27.3%, while the secondary attackrate of the Omicron variant was 29.8%. For the Delta variant, groups with less than 90 daysand more than 90 days after 2 doses of mRNA vaccination both showed a VET of 37%. For theOmicron variant, a 64% VET was found among those with less than 90 days after 2 doses ofmRNA vaccination.Conclusion: This study provides useful data on the secondary attack rate and VET of mRNAvaccines for household contacts of COVID-19 cases in South Korea.

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Impact of disease severity, age, sex, comorbidity, and vaccination on secondary attack rates of SARS-CoV-2: a global systematic review and meta-analysis
Dewan Md. Sumsuzzman, Yang Ye, Zhen Wang, Abhishek Pandey, Joanne M. Langley, Alison P. Galvani, Seyed M. Moghadas
BMC Infectious Diseases.2025;[Epub] CrossRef
Child Transmission of SARS-CoV-2 Throughout the Pandemic: An Updated Systematic Review and Meta-Analysis
Eugene Kwon, Gabriel Blank, Samantha Starkey, Cassidy Chapman, Conné Lategan, Hennady Shulha, Vanessa Kitchin, Sarah Silverberg, Laura Sauvé, Manish Sadarangani
Pediatric Infectious Disease Journal.2025;[Epub] CrossRef
Household secondary attack rates and risk factors during periods of SARS-CoV-2 Delta and Omicron variant predominance in the Republic of Korea
Jin Lee, Mijeong Ko, Seontae Kim, Dosang Lim, Gemma Park, Sang-Eun Lee
Osong Public Health and Research Perspectives.2023; 14(4): 263. CrossRef

Investigation of SARS-CoV-2 lineages and mutations circulating in a university-affiliated hospital in South Korea analyzed using Oxford Nanopore MinION sequencing: Hyaekang Kim, Sung Hee Chung, Hyun Soo Kim, Han-Sung Kim, Wonkeun Song, Ki Ho Hong, Jae-Seok Kim; Osong Public Health Res Perspect. 2022;13(5):360-369. Published online October 11, 2022; DOI: https://doi.org/10.24171/j.phrp.2022.0183

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Abstract PDF Supplementary Material

Objectives
Despite the introduction of vaccines, treatments, and massive diagnostic testing, the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to overcome barriers that had slowed its previous spread. As the virus evolves towards increasing fitness, it is critical to continue monitoring the occurrence of new mutations that could evade human efforts to control them. Methods: We performed whole-genome sequencing using Oxford Nanopore MinION sequencing on 58 SARS-CoV-2 isolates collected during the ongoing coronavirus disease 2019 pandemic at a tertiary hospital in South Korea and tracked the emergence of mutations responsible for massive spikes in South Korea. Results: The differences among lineages were more pronounced in the spike gene, especially in the receptor-binding domain (RBD), than in other genes. Those RBD mutations could compromise neutralization by antibodies elicited by vaccination or previous infections. We also reported multiple incidences of Omicron variants carrying mutations that could impair the diagnostic sensitivity of reverse transcription-polymerase chain reaction-based testing. Conclusion: These results provide an understanding of the temporal changes of variants and mutations that have been circulating in South Korea and their potential impacts on antigenicity, therapeutics, and diagnostic escape of the virus. We also showed that the utilization of the nanopore sequencing platform and the ARTIC workf low can provide convenient and accurate SARS-CoV-2 genomic surveillance even at a single hospital.

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Understanding large scale sequencing datasets through changes to protein folding
David Shorthouse, Harris Lister, Gemma S Freeman, Benjamin A Hall
Briefings in Functional Genomics.2024; 23(5): 517. CrossRef
Molecular epidemiology of SARS‐CoV‐2 in Mongolia, first experience with nanopore sequencing in lower‐ and middle‐income countries setting
Munkhtuya Erendereg, Suvd Tumurbaatar, Otgonjargal Byambaa, Gerelmaa Enebish, Natsagdorj Burged, Tungalag Khurelsukh, Nomin‐Erdene Baatar, Badmaarag Munkhjin, Jargaltulga Ulziijargal, Anuujin Gantumur, Oyunbaatar Altanbayar, Ochbadrakh Batjargal, Delgermu
Immunity, Inflammation and Disease.2023;[Epub] CrossRef

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