Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020

Kwon, Jungh-Hoon; Kim, Jeong‐Min; Lee, Donghun; Park, Ae Kyung; Kim, Il-Hwan; Kim, Da-Won; Kim, Jiyun; Lim, Noori; Cho, Kyeong-Yeon; Kim, Heui Man; Lee, Nam-Joo; Woo, SangHee; Lee, Chang Kyu; No, Jin Sun; Kim, Junyoung; Rhee, JeeEun; Han, Myung Guk; Rhie, Gi‐eun; Yoo, Cheon-Kwon; Kim, Eun Jin

doi:10.1093/ve/veab077

Cited by 11 publications

(12 citation statements)

References 34 publications

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“…COVID-19 infections surged in the Republic of Korea during the first wave in the first half of 2020, second wave in the second half of 2020, third wave between November 2020 and early 2021, and delta variant-led fourth wave which is still ongoing. Most deaths occurred in patients with comorbidities or in elderly patients with compromised immunity ( Cherian et al, 2021 ; Kwon et al, 2021 ).…”

Section: Introductionmentioning

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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Section: Introductionmentioning

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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“…Human interventions such as isolation or quarantine of the population, restricting mobility between countries, and vaccination programs could impact negatively on the Ne of the variants. Other studies have reported that the COVID-19 control programs have had a negative impact on the Ne of SARS-CoV-2 ( Kwon et al, 2021 ). Interestingly, the Mexican variant presented a strong bottleneck from April 2021 onwards, which coincided with the decline of the number of cases at the end of the second wave, and the emergence and spread of the Alpha, Gamma, and Delta VOCs, which are more transmissible ( Thye et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

et al. 2022

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BackgroundThe advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs).ObjectiveThis study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs.Methods30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed.Results148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes.ConclusionThe COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.

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“…The B.1.497 lineage was first detected in South Korea in March 2020 and was a dominant subgroup until April 2021 [ 32 ]. This lineage was dynamically associated with visitors to clubs and bars in Itaewon, Seoul, from April 29 to 6 May 2020, and caused one of the major local and long-term epidemics in South Korea [ 33 ]. A total of 3180 sequences in Korea have been uploaded in GISAID.…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequencing of SARS-CoV-2 in Cats and Dogs in South Korea in 2021

Shin

Kwon

Heo

et al. 2022

Veterinary Sciences

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SARS-CoV-2 infections have caused unprecedented damage worldwide by affecting humans and various animals. The first reported animal infection was observed in a pet dog in Hong Kong in March 2020. 36 countries reported 692 SARS-CoV-2 infections in 25 different animal species by 31 August 2022. Most outbreaks were caused by contact with SARS-CoV-2 infected humans. In South Korea, the first SARS-CoV-2 infection in an animal was reported in a cat in February 2021. As of 31 December 2021, 74 dogs and 42 cats have been confirmed to have SARS-CoV-2 in South Korea. Here, we identified various SARS-CoV-2 genomic lineages in SARS-CoV-2 confirmed cats and dogs. Among the 40 animal samples sequenced for lineage identification, a total of eight Pango lineages (B.1.1.7 (Alpha variant), B.1.429 (Epsilon variant), B.1.470, B.1.497, B.1.619.1, B.1.620, AY.69 (Delta variant), and AY.122.5 (Delta variant)) were identified. The dominant lineages were AY.69 (Delta variant; 37.5%), B.1.497 (35.0%), and B.1.619.1 (12.5%). This study provides the first reported cases of six lineages (B.1.470, B.1.497, B.1.620, B.1.619.1, AY.69 (Delta variant)), and AY.122.5 (Delta variant) in cats and dogs. Our results emphasize the importance of monitoring SARS-CoV-2 in pets because they are dynamic hosts of variant Pango lineages of SARS-CoV-2.

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Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020

Cited by 11 publications

References 34 publications

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

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

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

Whole Genome Sequencing of SARS-CoV-2 in Cats and Dogs in South Korea in 2021

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