8 May 2020

Commentary: COG-UK Report 5, 7th May 2020


Commentary: COG-UK Report 5, 7th May 2020

The 5th report from COG-UK includes analysis of a total of 10,483 SARS-CoV-2 genomes, sequenced before 7th May 2020.

The report also includes analysis of viral genomes sequenced from five care homes in London. The samples were taken from staff and residents between 13th and 15th of April 2020. Of the 210 samples assessed, 91 were positive for SARS-CoV-2. 55 of these samples were of high enough quality for analysis. These data were used for phylogenetic studies within each care home, and for comparison with 277 non-care home viral genomes originating in London.

Analysis of the data suggests that in one care home, there were at least four separate introductions of the virus. A similar pattern of multiple introductions of the virus was observed in two other care homes, although less data were available for these sites. There was also some evidence that following an introduction of the virus, in some cases, there was transmission within a care home.

No common pattern or direction was seen for transmission, either between staff and residents or between symptomatic and asymptomatic people.

Further analysis identified a putative cluster of viral sequences, containing samples from multiple care homes. The presence of similar sequences across different care homes could suggest either transmission of SARS-CoV-2 between care homes, or separate introductions of the same viral lineage to different care homes from the community or other healthcare settings. Since the completion of this report, additional sequence data have been analysed. This analysis indicated that the sequences from care homes are part of a widespread viral lineage and consequently it is not possible to determine which of these scenarios is the case.

The findings highlight the importance of ongoing, larger studies, with additional metadata. Such studies will be vital to study transmission in care settings and inform control strategies.

The researchers anticipate that as the number of genomes sequenced increases, they will be able to provide a high resolution view of viral lineage diversity in the UK. This will make it possible to distinguish dominant local lineages and track viral spread from one part of the UK to another.

In such a fast-moving situation, the consortium members note it is important to consider the limitations of phylogenetic analysis, and the importance of caveats when interpreting data.

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Events / Women in COG

24 Aug 2022

Women in COG: in Conversation with Dr Mariana Viegas

On Thursday 10th November, at 13:15 – 14:00 BST, we will be hosting our next ‘Women in COG’ event featuring Dr Mariana Viegas, professor of clinical virology  at the Faculty of Exact Sciences of the Universidad Nacional de La Plata (UNLP), Argentina, and coordinator of the Argentine Consortium for SARS-CoV-2 Genomics (PAIS project).

On Thursday 10th November, at 13:15 – 14:00 BST, we will be hosting our ‘Women in COG’ event featuring Dr Mariana Viegas, professor of clinical virology  at the Faculty of Exact Sciences of the Universidad Nacional de La Plata (UNLP), Argentina, and coordinator of the Argentine Consortium for SARS-CoV-2 Genomics (PAIS project).

This event will feature a conversation with Mariana followed by an informal Q&A.


When? 10th November 13:15h
Where? Virtual
Who can attend? Everyone


Dr Mariana Viegas

Mariana Viegas is a biochemist and has a PhD from the Faculty of Exact Sciences of the Universidad Nacional de La Plata (UNLP). She is a professor of clinical virology at that faculty since 2006. Mariana has been working on viral evolution studies of respiratory viruses in paediatric patients at the Virology Laboratory of the Ricardo Gutiérrez Children’s Hospital (HNRG) in Buenos Aires, Argentina since 1999, where she is currently an independent CONICET researcher. She has collaborated as an External Advisor to the World Health Organization since 2019 within the WHO Global Respiratory Syncytial Virus (RSV) Surveillance program. In 2013, Mariana ventured into Next Generation Sequencing technologies to begin with the genomic approach in her work. Since 2015, her team developed and implemented a genomic surveillance of RSV in paediatrics at their hospital. Then, they expanded their experience into the genomic studies of other respiratory viruses and new approaches, such as metagenomics. Due to her previous experience, she was the right person to brainstorm, create, and coordinate the Argentine Consortium for SARS-CoV-2 Genomics (PAIS project).


COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.