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Pandemic Potentials Blog

UK COVID Variant in Singapore Missing NSB 6 Deletion

niman
in Sequences (COVID)

Featured Replies

  • Author
 

What does that mean?

This sequence appears to have been removed from the database

Virus name Passage details/history Accession ID Collection date Submission Date info_gray.png Length Host Location Originating lab Submitting lab
hCoV-19/Singapore/1465/2020
Original
EPI_ISL_728201
2020-12-08
2020-12-22
warn_sign.png
29,852
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1464/2020
Original
EPI_ISL_728200
2020-12-12
2020-12-22
warn_sign.png
29,877
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1463/2020
Original
EPI_ISL_728199
2020-12-10
2020-12-22
 
29,852
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1462/2020
Original
EPI_ISL_728198
2020-12-13
2020-12-22
 
29,880
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1461/2020
Original
EPI_ISL_728197
2020-12-11
2020-12-22
warn_sign.png
29,853
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1460/2020
Original
EPI_ISL_728196
2020-12-11
2020-12-22
 
29,810
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1459/2020
Original
EPI_ISL_728195
2020-12-10
2020-12-22
 
29,879
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1458/2020
Original
EPI_ISL_728194
2020-12-06
2020-12-22
 
29,891
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1457/2020
Original
EPI_ISL_728193
2020-12-11
2020-12-22
 
29,874
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1456/2020
Original
EPI_ISL_728192
2020-12-11
2020-12-22
 
29,874
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1455/2020
Original
EPI_ISL_728191
2020-12-09
2020-12-22
 
29,883
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1454/2020
Original
EPI_ISL_728190
2020-12-05
2020-12-22
 
29,886
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1452/2020
Original
EPI_ISL_728188
2020-12-02
2020-12-22
 
29,841
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1451/2020
Original
EPI_ISL_728187
2020-12-04
2020-12-22
 
29,796
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1450/2020
Original
EPI_ISL_728186
2020-12-04
2020-12-22
 
29,861
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1449/2020
Original
EPI_ISL_728185
2020-12-06
2020-12-22
 
29,817
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1448/2020
Original
EPI_ISL_728184
2020-12-07
2020-12-22
 
29,885
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1447/2020
Original
EPI_ISL_728183
2020-12-07
2020-12-22
 
29,887
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1446/2020
Original
EPI_ISL_728182
2020-12-06
2020-12-22
 
29,889
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1445/2020
Original
EPI_ISL_728181
2020-12-05
2020-12-22
 
29,874
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1444/2020
Original
EPI_ISL_728180
2020-12-07
2020-12-22
 
29,890
Human
Asia / Singapore
National Public Health Laboratory, National Centre for Infectious Diseases
National Public Health Laboratory, National Centre for Infectious Diseases
hCoV-19/Singapore/1443/2020
Original
EPI_ISL_728179
2020-12-05
2020-12-22
 
29,887
Human
Asia / Singapore
National  Public Health Laboratory, National Centre for Infectious Diseases

Are these sequences from residents of Singapore or are the sequences simply being processed from a lab located in Singapore? My daughter is in Singapore right now.

  • Author
 

Are these sequences from residents of Singapore or are the sequences simply being processed from a lab located in Singapore? My daughter is in Singapore right now.

The list above are those submitted yesterday.  Only the variant has been removed, but these are presumed to be from samples from people in Singapore on the collection date.

  • Author
 

Have you ever known sequence submissions to be withdrawn?

Finding withdrawn sequences is difficult, but sequences are frequently modified after submission at Genbank, but the original sequence(s) remain available and a new number is assigned to the new sequence (as .1, .2, etc)

  • Author

SINGAPORE: Singapore reported 21 new COVID-19 cases on Wednesday (Dec 23), the Ministry of Health (MOH) said.

All the new cases were imported and were placed on stay-home notice upon arrival in Singapore.

 

MOH also confirmed that a COVID-19 case reported on Dec 8 was found to carry the coronavirus strain circulating in the United Kingdom.

"In light of recent reports that the B117 strain, a potentially more contagious strain of the COVID-19 virus, is circulating in the UK, the National Public Health Laboratory is performing viral genomic sequencing for confirmed COVID-19 cases who had arrived from Europe recently," said MOH.

The case, known as Case 58504, is a 17-year-old female who had been studying in the UK from August.

She returned to Singapore on Dec 6 and served her stay-home notice at a dedicated facility upon arrival.

 

The ministry said there is "currently no evidence no evidence that the B117 strain is circulating in the community".

https://www.channelnewsasia.com/news/singapore/covid-19-dec-23-new-cases-imported-community-moh-13828506?cid=TWTcna

  • Author
 

National Health labs in Singapore released full sequence (at GISAID), hCoV-19/Singapore/1453/2020, from 17F collected Dec 8. 

Has all 10 of the Spike mutations, but missing the 9 BP del in NSP6.

All six sequences from Naples ex-London are also missing the 9 BP del in NSP6

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