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CCDC Weekly: COVID-19 Variant 501Y.V2 Detected in Airplane Pilot — Guangdong Province, Jan 6th 2021
#15,701
Although China carefully manages the release of `sensitive' information via their government websites and state run media - and has a history of sometimes being less than forthcoming with the international community - Chinese scientific publications are generally top-notch.
At least, in those papers that actually see the light of day.
A little over a year ago, China launched their own version of the U.S. CDC's MMWR, called the CCDC Weekly. It is published in English, and It's format is quite similar to the MMWR, including a `Notes From The Field' style report.
Below you'll find a `Notes From The Field' report describing China's first detection of the 501Y.V2 Covid variant, which carries the 501Y mutation, along with the E484K mutation, that has been making major inroads in South Africa.
Although not as well distributed internationally as the B.1.1.7 variant which first emerged in the UK, this variant is worrisome because it carries the E484K mutation, which has been has been tentatively linkedto reduced antibody recognition, which in turn may decrease immune protection acquired from prior infection or vaccination.
The patient is a 55 y.o. airline pilot from South Africa, who arrived at Guangzhou City from Singapore on the evening of December 8, 2020, and tested positive for COVID. He was transferred to a hospital for treatment and isolation. As of the time of the paper's publication (Jan 6th), he was still receiving treatment.
Genomic sequencing takes time, and there is often a backlog, so it was more than three weeks after admission that samples were sent to China's CDC for analysis. On January 5, 2021, the sample and virus isolates were sequenced and identified as being the 501Y.V2 variant.
Follow the link for the full report, and graphics. I'll have a brief postscript when you return.
Fengjuan Chen1,&; Bosheng Li2,&; Peter Hao3; Yang Song4; Wenbo Xu4; Nankun Liu3; Chunliang Lei1, , ; Changwen Ke2, , View author affiliations
On January 6, 2021, Guangdong CDC successfully isolated the 501Y.V2 variant of coronavirus disease 2019 (COVID-19) virus from a throat swab of a patient. The 501Y.V2 variant was first detected in South Africa, and the patient is a 55-year-old male airline pilot of South African nationality.
He entered Guangzhou City, the capital of Guangdong Province, from Singapore on the evening of December 8, 2020 and was subject to a COVID-19 test. The result returned positive and he was transferred to the designated hospital for further isolation and treatment.
The patient is still receiving treatment.
On January 5, 2021, the sample and virus isolates were sequenced using Nanopore MK1C. Compared with the Wuhan reference strain (EPI_ISL_402119) (1-2), this strain displayed 23 nucleotide variation sites including the single nucleotide polymorphisms (SNPs) that defined the L-lineage European branch II.1 and belonged to the Pangolin lineage B.1.351 (3) (Figure 1). Furthermore, 10 amino acid mutation sites (D80A, L242del, A243del, L244del, R246I, K417N, E484K, N501Y, D614G, and A701V) were detected in the spike protein that corresponded to the features of the South African 501Y.V2 variant.
The 501Y.V2 variant has 3 specific mutations, K417N, E484K, and N501Y, on the spike protein (4) and shares the N501Y and D614G mutations with the 501Y.V1 variant (also known as the B.1.1.7 lineage and variant of concern (VOC) 202012/01) recently detected in the United Kingdom.
This is the second recent detection of a major international variant following the detection of the United Kingdom 501Y.V1 variant in a patient in Shanghai (NC20SCU2740-1) in December 2020 (5).
The transmissibility and pathogenicity of these mutant variants urgently needs further study.
Copyright ? 2019 Chinese Center for Disease Control and Prevention (China CDC)
No.155 Changbai Road, Changping District, Beijing 102206, China
Tel：+86-10-63150501, 63150701
Supported by: Beijing Renhe Information Technology Co., Ltd.
For more on this potentially problematic E484K mutation, you may wish to revisit:
PrePrint: Genomic Evidence of a Sars-Cov-2 Reinfection Case With E484K Spike Mutation in Brazil
Argentina: PAIS Report On COVID E484K Variant In South America
PrePrint: Emergence & Rapid Spread of a New SARS-CoV-2 Lineage with Multiple Spike Mutations in South Africa
https://afludiary.blogspot.com/2021/01/ccdc-weekly-covid-19-variant-501yv2.html
#15,701
Although China carefully manages the release of `sensitive' information via their government websites and state run media - and has a history of sometimes being less than forthcoming with the international community - Chinese scientific publications are generally top-notch.
At least, in those papers that actually see the light of day.
A little over a year ago, China launched their own version of the U.S. CDC's MMWR, called the CCDC Weekly. It is published in English, and It's format is quite similar to the MMWR, including a `Notes From The Field' style report.
Below you'll find a `Notes From The Field' report describing China's first detection of the 501Y.V2 Covid variant, which carries the 501Y mutation, along with the E484K mutation, that has been making major inroads in South Africa.
Although not as well distributed internationally as the B.1.1.7 variant which first emerged in the UK, this variant is worrisome because it carries the E484K mutation, which has been has been tentatively linkedto reduced antibody recognition, which in turn may decrease immune protection acquired from prior infection or vaccination.
The patient is a 55 y.o. airline pilot from South Africa, who arrived at Guangzhou City from Singapore on the evening of December 8, 2020, and tested positive for COVID. He was transferred to a hospital for treatment and isolation. As of the time of the paper's publication (Jan 6th), he was still receiving treatment.
Genomic sequencing takes time, and there is often a backlog, so it was more than three weeks after admission that samples were sent to China's CDC for analysis. On January 5, 2021, the sample and virus isolates were sequenced and identified as being the 501Y.V2 variant.
Follow the link for the full report, and graphics. I'll have a brief postscript when you return.
Fengjuan Chen1,&; Bosheng Li2,&; Peter Hao3; Yang Song4; Wenbo Xu4; Nankun Liu3; Chunliang Lei1, , ; Changwen Ke2, , View author affiliations
Author Affiliations
1. Guangzhou Eighth People’s Hospital, Guangzhou, Guangdong, China
2. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
3. Chinese Center for Disease Control and Prevention, Beijing, China
4. National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
Corresponding authors:
1. Guangzhou Eighth People’s Hospital, Guangzhou, Guangdong, China
2. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China
3. Chinese Center for Disease Control and Prevention, Beijing, China
4. National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
Corresponding authors:
Online Date: January 07 2021
doi: 10.46234/ccdcw2021.007
doi: 10.46234/ccdcw2021.007
On January 6, 2021, Guangdong CDC successfully isolated the 501Y.V2 variant of coronavirus disease 2019 (COVID-19) virus from a throat swab of a patient. The 501Y.V2 variant was first detected in South Africa, and the patient is a 55-year-old male airline pilot of South African nationality.
He entered Guangzhou City, the capital of Guangdong Province, from Singapore on the evening of December 8, 2020 and was subject to a COVID-19 test. The result returned positive and he was transferred to the designated hospital for further isolation and treatment.
On December 31, 2020, Guangdong CDC received the samples and began virus isolation and gene sequencing analysis. The analysis and subsequent verification have concluded that the virus genome belongs to lineage B.1.351, inferring classification as the 501Y.V2 variant.
The patient is still receiving treatment.
On January 5, 2021, the sample and virus isolates were sequenced using Nanopore MK1C. Compared with the Wuhan reference strain (EPI_ISL_402119) (1-2), this strain displayed 23 nucleotide variation sites including the single nucleotide polymorphisms (SNPs) that defined the L-lineage European branch II.1 and belonged to the Pangolin lineage B.1.351 (3) (Figure 1). Furthermore, 10 amino acid mutation sites (D80A, L242del, A243del, L244del, R246I, K417N, E484K, N501Y, D614G, and A701V) were detected in the spike protein that corresponded to the features of the South African 501Y.V2 variant.
The 501Y.V2 variant has 3 specific mutations, K417N, E484K, and N501Y, on the spike protein (4) and shares the N501Y and D614G mutations with the 501Y.V1 variant (also known as the B.1.1.7 lineage and variant of concern (VOC) 202012/01) recently detected in the United Kingdom.
This is the second recent detection of a major international variant following the detection of the United Kingdom 501Y.V1 variant in a patient in Shanghai (NC20SCU2740-1) in December 2020 (5).
The transmissibility and pathogenicity of these mutant variants urgently needs further study.
Copyright ? 2019 Chinese Center for Disease Control and Prevention (China CDC)
No.155 Changbai Road, Changping District, Beijing 102206, China
Tel：+86-10-63150501, 63150701
Supported by: Beijing Renhe Information Technology Co., Ltd.
For more on this potentially problematic E484K mutation, you may wish to revisit:
PrePrint: Genomic Evidence of a Sars-Cov-2 Reinfection Case With E484K Spike Mutation in Brazil
Argentina: PAIS Report On COVID E484K Variant In South America
PrePrint: Emergence & Rapid Spread of a New SARS-CoV-2 Lineage with Multiple Spike Mutations in South Africa
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