Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020

Park, Ae Kyung; Kim, Il-Hwan; Kim, Junyoung; Kim, Jeong‐Min; Kim, Heui Man; Lee, Chang Kyu; Han, Myung Guk; Rhie, Gi‐eun; Kwon, Donghyok; Nam, Jung Gwon; Park, Young Joon; Gwack, Jin; Lee, Nam Joo; Woo, Sang Hee; No, Jin Sun; Lee, Jaehee; Ha, Jeemin; Rhee, Jee Eun; Yoo, Cheon-Kwon; Kim, Eun Jin

doi:10.24171/j.phrp.2021.12.1.06

Cited by 29 publications

(26 citation statements)

References 12 publications

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“…Genomic surveillance by the South Korea Disease Control and Prevention Agency from January 2020 to January 2021 showed that amongst 2,488 COVID-19 cases, including 648 from abroad, Variant B.1.1.7 and B.1.351 were only identified from international travelers. This supports the efficacy of South Korea's rapid implementation of nonpharmaceutical public health interventions, such as quarantining incoming travelers, for preventing dissemination of SARS-CoV-2 variants (210,211). Further strengthening of global sequencing capacity will facilitate ending the current pandemic and early detection and management of future outbreaks (208,212).…”

Section: Other Methods Of Viral Rna Detectionmentioning

confidence: 54%

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Mardian¹,

Kosasih²,

et al. 2021

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Diagnostic testing plays a critical role in addressing the coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Rapid and accurate diagnostic tests are imperative for identifying and managing infected individuals, contact tracing, epidemiologic characterization, and public health decision making. Laboratory testing may be performed based on symptomatic presentation or for screening of asymptomatic people. Confirmation of SARS-CoV-2 infection is typically by nucleic acid amplification tests (NAAT), which requires specialized equipment and training and may be particularly challenging in resource-limited settings. NAAT may give false-negative results due to timing of sample collection relative to infection, improper sampling of respiratory specimens, inadequate preservation of samples, and technical limitations; false-positives may occur due to technical errors, particularly contamination during the manual real-time polymerase chain reaction (RT-PCR) process. Thus, clinical presentation, contact history and contemporary phyloepidemiology must be considered when interpreting results. Several sample-to-answer platforms, including high-throughput systems and Point of Care (PoC) assays, have been developed to increase testing capacity and decrease technical errors. Alternatives to RT-PCR assay, such as other RNA detection methods and antigen tests may be appropriate for certain situations, such as resource-limited settings. While sequencing is important to monitor on-going evolution of the SARS-CoV-2 genome, antibody assays are useful for epidemiologic purposes. The ever-expanding assortment of tests, with varying clinical utility, performance requirements, and limitations, merits comparative evaluation. We herein provide a comprehensive review of currently available COVID-19 diagnostics, exploring their pros and cons as well as appropriate indications. Strategies to further optimize safety, speed, and ease of SARS-CoV-2 testing without compromising accuracy are suggested. Access to scalable diagnostic tools and continued technologic advances, including machine learning and smartphone integration, will facilitate control of the current pandemic as well as preparedness for the next one.

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Section: Other Methods Of Viral Rna Detectionmentioning

confidence: 54%

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Mardian¹,

Kosasih²,

et al. 2021

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“…1 Libraries were prepared using the Nextera DNA Flex Library Prep Kit (Illumina, San Diego, CA, United States), and sequencing was performed on an MiSeq instrument using a MiSeq reagent kit V2 (Illumina, San Diego, CA, United States) to obtain an average genome coverage of >1,000 × for all samples. The reads were trimmed and mapped to the reference genome Wuhan-Hu-1 (GenBank: MN908947.3) using CLC Genomics Workbench version 20.0.3 (CLC Bio, Aarhus, Denmark) ( Park et al, 2021 ). The lineages and clades of the SARS-CoV-2 sequences were assigned using Nextclade v1.7.1 ( Nextstrain Project ) and PANGOLIN ( Rambaut et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Increase in Viral Load in Patients With SARS-CoV-2 Delta Variant Infection in the Republic of Korea

et al. 2022

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread rapidly, causing in COVID-19 being declared a global pandemic by the World Health Organization. The key variants include alpha, beta, gamma, and delta; these exhibit high viral transmission, pathogenicity, and immune evasion mechanisms. The delta variant, first confirmed in India, was detected in the majority of COVID-19 patients at the recent wave in the Republic of Korea. Here, the features of the delta variant were compared to the earlier waves, with focus on increased transmissibility. The viral load, from the initial days of infection to 14 days later, was compared based on epidemiological data collected at the time of confirmed diagnosis. The increased viral load observed in the delta variant-led infections influences the scale of the wave, owing to the increased rate of transmission. Infections caused by the delta variant increases the risk of hospitalization within 14 days after symptom onset, and the high viral load correlates with COVID-19 associated morbidity and mortality. Therefore, the future studies should compare the trend of disease severity caused by the high viral load of delta variant with previous waves and analyze the vaccine effects in light of the delta variant of fourth wave.

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“…YUMC-2021-03-012). COVID-19-convalescent patients had been diagnosed using RT-PCR during the first wave of COVID-19 (from February 2020 to April 2020) [19]. They had been discharged from either hospitals or residential treatment centers and visited Yeungnam University Medical Center four times for blood sampling after recovery.…”

Section: Participants and Study Designmentioning

confidence: 99%

Humoral and Cellular Responses to COVID-19 Vaccines in SARS-CoV-2 Infection-Naïve and -Recovered Korean Individuals

et al. 2022

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In the face of a global COVID-19 vaccine shortage, an efficient vaccination strategy is required. Therefore, the immunogenicity of single or double COVID-19 vaccination doses (ChAdOX1, BNT162b2, or mRNA-1273) of SARS-CoV-2-recovered individuals was compared to that of unvaccinated individuals with SARS-CoV-2 infection at least one year post-convalescence. Moreover, the immunogenicity of SARS-CoV-2-naïve individuals vaccinated with a complete schedule of Ad26.CoV2.S, ChAdOX1, BNT162b2, mRNA-1273, or ChAdOX1/BNT162b2 vaccines was evaluated. Anti-SARS-CoV-2 S1 IgG antibody (S1-IgG), pseudotyped virus-neutralizing antibody titer (pVNT50), and IFN-γ ELISpot counts were measured. Humoral immune responses were significantly higher in vaccinated than in unvaccinated recovered individuals, with a 43-fold increase in the mean pVNT50 values. However, there was no significant difference in the pVNT50 and IFN-γ ELISpot values between the single- and double-dose regimens. In SARS-CoV-2-naïve individuals, antibody responses varied according to the vaccine type: BNT162b2 and mRNA-1273 induced similar levels of S1-IgG to those observed in vaccinated, convalescent individuals; in contrast, pVNT50 was much lower in SARS-CoV-2-naïve vaccinees than in vaccinated recovered individuals. Therefore, a single dose of ChAdOX1, BNT162b2, or mRNA-1273 vaccines would be a good alternative for recovered individuals instead of a double-dose regimen.

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Genomic Surveillance of SARS-CoV-2: Distribution of Clades in the Republic of Korea in 2020

Cited by 29 publications

References 12 publications

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Increase in Viral Load in Patients With SARS-CoV-2 Delta Variant Infection in the Republic of Korea

Humoral and Cellular Responses to COVID-19 Vaccines in SARS-CoV-2 Infection-Naïve and -Recovered Korean Individuals

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