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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Graphical Abstract Abstract PDF Supplementary Material: 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.

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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Graphical Abstract Abstract PDF

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.

Citations

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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
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Brief Report

Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020: Ae Kyung Park, Il-Hwan Kim, Junyoung Kim, Jeong-Min Kim, Heui Man Kim, Chae young Lee, Myung-Guk Han, Gi-Eun Rhie, Donghyok Kwon, Jeong-Gu Nam, Young-Joon Park, Jin Gwack, Nam-Joo Lee, SangHee Woo, Jin Sun No, Jaehee Lee, Jeemin Ha, JeeEun Rhee, Cheon-Kwon Yoo, Eun-Jin Kim; Osong Public Health Res Perspect. 2021;12(1):37-43. Published online February 23, 2021; DOI: https://doi.org/10.24171/j.phrp.2021.12.1.06

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Abstract PDF

Since a novel beta-coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019, there has been a rapid global spread of the virus. Genomic surveillance was conducted on samples isolated from infected individuals to monitor the spread of genetic variants of SARS-CoV-2 in Korea. The Korea Disease Control and Prevention Agency performed whole genome sequencing of SARS-CoV-2 in Korea for 1 year (January 2020 to January 2021). A total of 2,488 SARS-CoV-2 cases were sequenced (including 648 cases from abroad). Initially, the prevalent clades of SARS-CoV-2 were the S and V clades, however, by March 2020, GH clade was the most dominant. Only international travelers were identified as having G or GR clades, and since the first variant 501Y.V1 was identified (from a traveler from the United Kingdom on December 22^nd, 2020), a total of 27 variants of 501Y.V1, 501Y.V2, and 484K.V2 have been classified (as of January 25^th, 2021). The results in this study indicated that quarantining of travelers entering Korea successfully prevented dissemination of the SARS-CoV-2 variants in Korea.

Citations

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Osong Public Health and Research Perspectives.2024; 15(3): 260. CrossRef
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Influenza and Other Respiratory Viruses.2024;[Epub] CrossRef
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Virus Research.2024; 350: 199471. CrossRef
Increased viral load in patients infected with severe acute respiratory syndrome coronavirus 2 Omicron variant in the Republic of Korea
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Original Articles

2019 Tabletop Exercise for Laboratory Diagnosis and Analyses of Unknown Disease Outbreaks by the Korea Centers for Disease Control and Prevention: Il-Hwan Kim, Jun Hyeong Jang, Su-Kyoung Jo, Jin Sun No, Seung-Hee Seo, Jun-Young Kim, Sang-Oun Jung, Jeong-Min Kim, Sang-Eun Lee, Hye-Kyung Park, Eun-Jin Kim, Jun Ho Jeon, Myung-Min Choi, Boyeong Ryu, Yoon Suk Jang, Hwami Kim, Jin Lee, Seung-Hwan Shin, Hee Kyoung Kim, Eun-Kyoung Kim, Ye Eun Park, Cheon-Kwon Yoo, Sang-Won Lee, Myung-Guk Han, Gi-Eun Rhie, Byung Hak Kang; Osong Public Health Res Perspect. 2020;11(5):280-285. Published online October 22, 2020; DOI: https://doi.org/10.24171/j.phrp.2020.11.5.03

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Abstract PDF: Objectives
The Korea Centers for Disease Control and Prevention has published “A Guideline for Unknown Disease Outbreaks (UDO).” The aim of this report was to introduce tabletop exercises (TTX) to prepare for UDO in the future.
Methods
The UDO Laboratory Analyses Task Force in Korea Centers for Disease Control and Prevention in April 2018, assigned unknown diseases into 5 syndromes, designed an algorithm for diagnosis, and made a panel list for diagnosis by exclusion. Using the guidelines and laboratory analyses for UDO, TTX were introduced.
Results
Since September 9^th, 2018, the UDO Laboratory Analyses Task Force has been preparing TTX based on a scenario of an outbreak caused by a novel coronavirus. In December 2019, through TTX, individual missions, epidemiological investigations, sample treatments, diagnosis by exclusions, and next generation sequencing analysis were discussed, and a novel coronavirus was identified as the causal pathogen.
Conclusion
Guideline and laboratory analyses for UDO successfully applied in TTX. Conclusions drawn from TTX could be applied effectively in the analyses for the initial response to COVID-19, an ongoing epidemic of 2019 – 2020. Therefore, TTX should continuously be conducted for the response and preparation against UDO.

Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome: Jun-Sub Kim, Jun-Hyeong Jang, Jeong-Min Kim, Yoon-Seok Chung, Cheon-Kwon Yoo, Myung-Guk Han; Osong Public Health Res Perspect. 2020;11(3):101-111. Published online May 14, 2020; DOI: https://doi.org/10.24171/j.phrp.2020.11.3.05

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Abstract PDF

Objectives

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019 and has been rapidly spreading worldwide. Although the causal relationship among mutations and the features of SARS-CoV-2 such as rapid transmission, pathogenicity, and tropism, remains unclear, our results of genomic mutations in SARS-CoV-2 may help to interpret the interaction between genomic characterization in SARS-CoV-2 and infectivity with the host.

Methods

A total of 4,254 genomic sequences of SARS-CoV-2 were collected from the Global Initiative on Sharing all Influenza Data (GISAID). Multiple sequence alignment for phylogenetic analysis and comparative genomic approach for mutation analysis were conducted using Molecular Evolutionary Genetics Analysis (MEGA), and an in-house program based on Perl language, respectively.

Results

Phylogenetic analysis of SARS-CoV-2 strains indicated that there were 3 major clades including S, V, and G, and 2 subclades (G.1 and G.2). There were 767 types of synonymous and 1,352 types of non-synonymous mutation. ORF1a, ORF1b, S, and N genes were detected at high frequency, whereas ORF7b and E genes exhibited low frequency. In the receptor-binding domain (RBD) of the S gene, 11 non-synonymous mutations were observed in the region adjacent to the angiotensin converting enzyme 2 (ACE2) binding site.

Conclusion

It has been reported that the rapid infectivity and transmission of SARS-CoV-2 associated with host receptor affinity are derived from several mutations in its genes. Without these genetic mutations to enhance evolutionary adaptation, species recognition, host receptor affinity, and pathogenicity, it would not survive. It is expected that our results could provide an important clue in understanding the genomic characteristics of SARS-CoV-2.

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Detection and Isolation of SARS-CoV-2 in Serum, Urine, and Stool Specimens of COVID-19 Patients from the Republic of Korea: Jeong-Min Kim, Heui Man Kim, Eun Jung Lee, Hye Jun Jo, Youngsil Yoon, Nam-Joo Lee, Junseock Son, Ye-Ji Lee, Mi Seon Kim, Yong-Pyo Lee, Su-Jin Chae, Kye Ryeong Park, Seung-Rye Cho, Sehee Park, Su Jin Kim, Eunbyeol Wang, SangHee Woo, Aram Lim, Su-Jin Park, JunHyeong Jang, Yoon-Seok Chung, Bum Sik Chin, Jin-Soo Lee, Duko Lim, Myung-Guk Han, Cheon Kwon Yoo; Osong Public Health Res Perspect. 2020;11(3):112-117. Published online May 8, 2020; DOI: https://doi.org/10.24171/j.phrp.2020.11.3.02

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Abstract PDF

Objectives

Coronavirus Disease-19 (COVID-19) is a respiratory infection characterized by the main symptoms of pneumonia and fever. It is caused by the novel coronavirus severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), which is known to spread via respiratory droplets. We aimed to determine the rate and likelihood of SARS-CoV-2 transmission from COVID-19 patients through non-respiratory routes.

Methods

Serum, urine, and stool samples were collected from 74 hospitalized patients diagnosed with COVID-19 based on the detection of SARS-CoV-2 in respiratory samples. The SARS-CoV-2 RNA genome was extracted from each specimen and real-time reverse transcription polymerase chain reaction performed. CaCo-2 cells were inoculated with the specimens containing the SARS-COV-2 genome, and subcultured for virus isolation. After culturing, viral replication in the cell supernatant was assessed.

Results

Of the samples collected from 74 COVID-19 patients, SARS-CoV-2 was detected in 15 serum, urine, or stool samples. The virus detection rate in the serum, urine, and stool samples were 2.8% (9/323), 0.8% (2/247), and 10.1% (13/129), and the mean viral load was 1,210 ± 1,861, 79 ± 30, and 3,176 ± 7,208 copy/µL, respectively. However, the SARS-CoV-2 was not isolated by the culture method from the samples that tested positive for the SARS-CoV-2 gene.

Conclusion

While the virus remained detectable in the respiratory samples of COVID-19 patients for several days after hospitalization, its detection in the serum, urine, and stool samples was intermittent. Since the virus could not be isolated from the SARS-COV-2-positive samples, the risk of viral transmission via stool and urine is expected to be low.

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Identification of Coronavirus Isolated from a Patient in Korea with COVID-19: Jeong-Min Kim, Yoon-Seok Chung, Hye Jun Jo, Nam-Joo Lee, Mi Seon Kim, Sang Hee Woo, Sehee Park, Jee Woong Kim, Heui Man Kim, Myung-Guk Han; Osong Public Health Res Perspect. 2020;11(1):3-7. Published online February 28, 2020; DOI: https://doi.org/10.24171/j.phrp.2020.11.1.02

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Abstract PDF

Objectives

Following reports of patients with unexplained pneumonia at the end of December 2019 in Wuhan, China, the causative agent was identified as coronavirus (SARS-CoV-2), and the 2019 novel coronavirus disease was named COVID-19 by the World Health Organization. Putative patients with COVID-19 have been identified in South Korea, and attempts have been made to isolate the pathogen from these patients.

Methods

Upper and lower respiratory tract secretion samples from putative patients with COVID-19 were inoculated onto cells to isolate the virus. Full genome sequencing and electron microscopy were used to identify the virus.

Results

The virus replicated in Vero cells and cytopathic effects were observed. Full genome sequencing showed that the virus genome exhibited sequence homology of more than 99.9% with SARS-CoV-2 which was isolated from patients from other countries, for instance China. Sequence homology of SARS-CoV-2 with SARS-CoV, and MERS-CoV was 77.5% and 50%, respectively. Coronavirus-specific morphology was observed by electron microscopy in virus-infected Vero cells.

Conclusion

SARS-CoV-2 was isolated from putative patients with unexplained pneumonia and intermittent coughing and fever. The isolated virus was named BetaCoV/Korea/KCDC03/2020.

Citations

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