The first SARS-CoV-2 genome, Wuhan-Hu-1, sequenced by Yong-Zhen Zhang, Fudan University, Shanghai, was released by Edward Holmes, University of Sydney, on Virological.

Virological is a discussion forum for analysis and interpretation of virus molecular evolution and epidemiology. It was important during the COVID-19 Response as it allowed rapid outbreak data and report sharing.

Read the Virological article: First report of COVID-19 in Scotland

Using emerging data on COVID-19 cases from China, a basic reproductive number of 3.11 (95%CI, 2.39–4.13) was estimated. This paper informed UK Government policy. Manuscript was subsequently published in Philosophical Transactions of the Royal Society B: Biological Sciences in May 2021.

Read the Pre-print: Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions

Evolutionary phylogenetic analysis of SARS-CoV-2 (then known as Wuhan-Hu-1 virus) showed that it is most closely related to bat coronaviruses in the Betacoronaviruses genera.

It is important to show the relationship between SARS-CoV-2 and other SARS-like viruses, and evidence which indicates that SARS-CoV-2 was not recombinant. This helped debunk the “snake origins” hypothesis which got widespread media coverage at the time.

This Virological thread was valuable for various future pre-prints and papers.

Read the Virological article: 'nCoV’s relationship to bat coronaviruses & recombination signals (no snakes) - no evidence the 2019-nCoV lineage is recombinant

This Facebook Live Q&A event involved a panel, featuring Antonia Ho, who discussed key information and advice for the UofG community, support which was available and what precautions the University was taking at that time.

This event was viewed by over 31 000 people.

Watch here: UofG Coronavirus Q&A

CoV-GLUE is a database of amino acid replacements, insertions and deletions from SARS-CoV-2 sequences sampled. Important for comparisons.

CVR Bioinformatics teams were aware from past experience of the importance of tracking accumulating mutations in new viruses and set this resource up to catalogue these and make them readily accessible to academic and public health researchers.

Visit CoV-GLUE

51-year-old male from Tayside with mild respiratory symptoms.

He had returned from Italy after attending a rugby match.

The sample, named CVR01, was processed by NHSGGC, the West of Scotland Specialist Virology Centre, and sent to CVR Genomics where it was sequenced within 24 hours.

Genomic evidence for early transmission advantage of B lineage mutations refuted using genomic data was posted on Virological. This led to the publication of No evidence for distinct types in the evolution of SARS-CoV-2 in May 2020.

Read the Virological article: On the origin and continuing evolution of SARS-CoV-2

International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) provides a collaborative platform through which global, patient‐oriented clinical studies can be developed, executed and shared.

Visit: ISARIC Website

Submission of the first Scottish COVID-19 sample genome was submitted to GISAID, and the corresponding report was submitted to Virological.

Read the Virological article: First report of COVID-19 in Scotland

Following the establishment of COG-UK, samples were sent from Rory Gunson/WoSSVC to CVR Genomics. The CVR Bioinformatics team assembled data each week. This was a massive effort to get clinical meta-data uploaded on a weekly basis.

The CVR has now contributed >10k sequences to Scotland’s 100K and UK’s >1M genome sequences contributing to key papers.

A short history of the COVID-19 Genomics UK (COG-UK) Consortium

CVR features in ITV news

SARS-CoV-2 and coronavirus toolkit created as an openly available, low-cost set of molecular tools and reagents that would be straightforward for researchers from a variety of scientific backgrounds to utilise, in order to allow them to contribute to SARS-CoV-2 research initiatives.

Read more: MRC PPU: Reverse Genetics Plasmids

Read the relevant blog post: An Openly Available SARS-CoV-2 and Coronavirus Toolkit

Authors analyse data from previous study by Tang et al. and show that the conclusions of this study cannot be substantiated, and advise against overinterpretation of genomic data during the COVID-19 pandemic.

Read No evidence for distinct types in the evolution of SARS-CoV-2

The first description of 20,133 hospitalised COVID-19 patients enrolled in ISARIC4C study published in the British Medical Journal.

The study concluded that mortality in COVID-19 patients was high, and that increasing age, male sex and chronic comorbidity are independent risk factors. This highlights the importance of pandemic preparedness.

Read: Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study

Cat 1 had a tissue sample taken post-mortem on the 22nd April. Cat 2 was swabbed on the 15th May.

The MRC-University of Glasgow Centre for Virus Research (CVR) in partnership with the Veterinary Diagnostic Service (VDS) of the School of Veterinary Medicine identified a cat in the UK that was infected with SARS-CoV-2. It is likely that the infection was transmitted by an infected human.

This led to the publication of "Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission" in April 2021, and the publication of "SARS-CoV-2 and Cats guidelines"

Project aimed to address the question - How effective are infection prevention and control measures that are informed by genetic analysis of coronavirus (rapid and standard) at preventing COVID-19 in NHS hospitals? The project aimed to evaluate the benefit of rapid genomic sequencing of epidemic viruses, alongside standard Infection Prevention Control protocol in hospitals to reduce within hospital infection rates and help identify routes of transmission . The HOCI research project ran from April 2020 to July 2021 and was run from University College London and Glasgow Royal Infirmary was a NHS trial site. Data from the trial showed that the Alpha variant did not cause excess hospital transmission and the Alpha variant was associated with excess disease severity in women but not men.

This research links to publication - The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study

Read the COG-UK blog discussing this project - The COG-UK Project Hospital-Onset COVID-19 Infections (HOCI) Study

ISRCTN registry study infomation - COG-UK Project Hospital-Onset COVID-19 Infections (HOCI) Study

In collaboration with University of Edinburgh, NHS Lothian, NHS Greater Glasgow and Clyde's West of Scotland Specialist Virology Centre, and PHS colleagues, a manuscript was written up to report the first Scottish cases. Manuscript was subsequently published in Nature Microbiology in December 2020.

Read Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

African COVID-19 Preparedness (AFRICO19) is a collaboration between Prof Matthew Cotten (MRC/UVRI and LSHTM Uganda Research Unit), Dr Ke Yuan (UofG), Prof David L Robertson (UofG), Prof James Nokes (KEMRI-Wellcome Trust Research Programme, Kenya), & Prof Martin Antonio (London School of Hygiene and Tropical Medicine).

AFRICO19 aimed to enhance understanding of SARS-CoV-2 in Kenya, The Gambia, Uganda and Globally. A network was created to share knowledge on NGS (inc MinION), coronavirus biology and COVID-19 disease control.

Wellcome grant infomation: African COVID-19 preparedness (AFRICO19)

Dr Janet Scott & Dr Pablo Murcia are members of the expert advisory group who worked on this report. It was submitted to the government and outlines the importance of preparing for a worse-case scenario in the winter of 2020/2021, including a resurgence of COVID-19, major disruptions of health and social care systems and a potential influenza epidemic which would lead to excess respiratory deaths and overwhelming of the test and trace capacity.

Read the report: Preparing for a challenging winter 2020/2021

A key publication from the AFRICO19 project. Authors established rapid local viral sequencing to document genomic diversity of SARS-CoV-2 entering Uganda. This data was important for tracking viral transmission throughout the country and region. They found that virus lineages closely followed the travel origins of infected people.

Read: Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda

Genomic analysis shows that SARS-CoV-2 is not a recombinant of any sarbecoviruses, but it’s receptor binding motif is an ancestral trait shared with bat viruses. Data indicates that the lineage which gave rise to SARS-CoV-2 had been circulating in bat populations for decades prior to the Covid-19 outbreak.

Read: Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Longitudinal cohort study investigating the immunoepidemiology of SARS-CoV-2 in urban and rural Malawi. Collaboration between Prof Mia Crampin, Dr Abena Amoah, Dr Alison Price (MEIRU), Dr Antonia Ho (CVR), Dr Annie Mwale (Public Health Institute of Malawi), Prof Victor Mwapasa, Dr Tonney Nyirenda (KUHeS), Dr Charles Mwansambo (Malawi Ministry of Health), Dr Jonathan Read, Dr Chris Jewell (University of Lancaster), Dr Peter MacPherson (LSTM).

Read more: COVSERO SARS-CoV-2

The podcast is titled ‘Covid-19: what happens when flu season hits?’ Pablo and Ian Sample discuss how respiratory viruses interact on a population level and human scale, and how the 2020 flu season is likely to impact the COVID-19 pandemic.

Listen: Covid-19:what happens when flu season hits?

Using data from 58,000 hospitalised COVID-19 patients enrolled in the CCP-UK study, an easy-to-use risk stratification score based on 8 commonly available parameters at hospital presentation was developed and validated. The 4C Mortality Score categorises hospitalised patients into four risk categories to inform clinical decision making, and out-performed existing scores. The Score has been extensively validated in COVID-19 patient cohorts across the world.

Read: Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score

Written in collaboration with Muge Cevik, a Clinical Lecturer in Infectious Diseases and Medical Virology at the University of St Andrews, the article discusses a publication in The Lancet Microbe which investigated viral load, viral shedding and isolation of the live virus.

The data from this study indicated that infected individuals exhibit an incubation period which lasts approximately 6 days where they show no symptoms but the viral load rapidly increases. Individuals typically start to show symptoms when they have a high viral load and are highly infectious. Periods of infectiousness can last approx. 10 days and PCR tests can show a positive result for approx. 17 days after symptom onset. This highlights the importance of self-isolation after close contact or exposure to COVID-19 to prevent community spread.

The article has reached over 1.8 million reads since publication.

Read the article: COVID-19: when are you most infectious

A combined phylogenetic and epidemiological approach was used to confirm hundreds of introductions of SARS-CoV-2 into Scotland from as early as 19th Feb 2020. The paper discusses details of major community outbreaks such as the international Nike conference, and other key transmission events which occurred 3 weeks before control measures were introduced.

Read: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

This study finds that the 4C Deterioration model has strong potential for clinical utility and generalisability to predict clinical deterioration and inform decision making among adults hospitalised with COVID-19.

Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study

James Shepard, a Clinical Research Fellow discusses how his work involves multiple NHS and academic partners and showed how pathogen genomic sequencing can support and enhance epidemiology and has the potential to inform public health intervention policy.

Listen to the podcast: How did SARS-CoV-2 spread across Scotland?

Watch this news feature on ITV News.

Study involved members of the COG-UK Consortium and ISARIC4C investigators. Data showed that N439K, a mutation of the receptor binding domain of the SARS-CoV-2 Spike protein, enhances the binding affinity to the hACE2 receptor and exhibits resistance to several neutralising monoclonal antibodies. This highlights the importance of molecular surveillance of SARS-CoV-2 mutations for development of vaccines and therapeutics.

Read: Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

G2P studies the effects of emerging mutations in SARS-CoV-2. They work alongside COG-UK and Public Health England. Focus on different elements of new variants such as transmissibility, severity and effectiveness of vaccines and treatments.

Read more about G2P-UK in this UKRI Blog Post.

COG-UK sequenced over 5000 genomes from Scottish Covid-19 cases by August 2020. This genomics data was used to quantify geographical origins of the first wave introductions into Scotland and the spread of these lineages throughout Scotland, as well as to evaluate the effectiveness of the lockdown. Data from the second wave of infections was compared to the first wave and showed that the majority of lineages in circulation during the second wave were different from the first and were introduced from outside the UK. This highlights the importance of restricting travel-associated imports and other public health measures to control outbreaks of infectious disease.

Read: Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

Massimo discusses why viruses such as SARS-CoV-2 mutate and form variants, and why consortiums such as COG-UK and G2P are important to study and monitor variants to help control future outbreaks. Massimo explains the importance of genomic sequencing, how mutations can impact the behaviour of a virus and how vaccines and antiviral drugs are developed.

Read the article: Coronavirus: Rise of the Mutants

A key publication from the AFRICO19 project. Genomic surveillance of SARS-CoV-2 in Uganda has identified a new variant as A.23 has evolved into A.23.1. Changes to the protein coding region resemble changes seen in other Variants of Concern, highlighting that the spread of this new variant should be carefully monitored.

Read: A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic

Toolkit established for studying SARS-CoV-2 in labs. Sequencing of various reverse genetic plasmids, clinical isolates and isolates at different stages of passaging in cells

A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research

Sequence data is available here: Severe acute respiratory syndrome coronavirus 2 Genome sequencing

Read the supporting Contagious Thinking Blog written by Suzannah Rihn: An Openly Available SARS-CoV-2 and Coronavirus Toolkit

Alex Wilson, Steph Rainey, Massimo Palmarini and Emma Thomson were involved in the visit. Emma explains that we have a global responsibility to help other countries to protect them and us

Watch: Covid in Scotland: Inside the Glasgow University lab sequencing the virus

This open-access interface provides information and structural context on mutations and associated variants in the genes encoding SARS-COV-2 proteins that have been identified from the COG-UK genome sequence data set/MRC-CLIMB. SARS-CoV-2 spike gene mutations of importance, based on epidemiological, clinical and/or experimental observations, are the primary focus. Currently features over 1 700 000 genome sequences from the UK.

COG-UK/Mutation Explorer App

COG-UK/ME was based on curated antigenic data from SARS-CoV-2 variants, spike mutations and immune escape

Open-access dashboard was created byCOG-UK

Related COG-UK Blog Post: Introducing Mutation Explorer: An open-access dashboard by COG-UK

To visualise this data in the context of 3D animations, see Sarah Iannucci’s SARS-CoV-2 Spike Protein Mutation Explorer interactive web app SARS-CoV-2 Spike Protein ME App

The UK Government’s Secretary of State for Health and Social Care discusses COVID-19 research with Suzannah Rihn, Massimo Palmarini, Emma Thomson, David L Robertson and Ana da Silva Filipe.

Matt Hancock Visit

Research found limited evidence for selection during zoonosis event immediately before pandemic began, and evidence of strong selection decades ago whilst virus still circulating in bats.

Read: ‘Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

The DeplOyedVaccinE Cohort Study aims to determine the cross-specificity of B and T cell responses in people who have been vaccinated with deployed COVID-19 vaccines. It is a 5 year study which is sponsored by NHS Greater Glasgow and Clyde. Immune cells and immune responses from blood samples of participants will be assayed against a range of SARS-CoV-2 variants to determine immunogenicity.

The DeplOyedVaccinE Cohort Study

This paper investigates the replication kinetics of SARS-CoV-2 in the presence or absence of rhinovirus in the human respiratory epithelium. Data shows that rhinovirus offers an element of protection from SARS-CoV-2 by triggering an IFN response which blocks replication of SARS-CoV-2. This indicates that higher prevalence of rhinovirus in the population is likely to reduce the number of new COVID-19 cases.

Read: Human Rhinovirus Infection Blocks Severe Acute Respiratory Syndrome Coronavirus 2 Replication Within the Respiratory Epithelium: Implications for COVID-19 Epidemiology

Toni explains why it’s important to stick to disease control measures of the past year while vaccines are rolled out.

The Royal College of Pathologists ran this online event which encourages families with young children to explore different elements of virology through colouring and folding. They learned about the appearance of viruses, how they work and how our bodies respond to infection. Dr Toni Ho and Dr Francesca Knapper, Microbiology and Infectious Diseases Speciality Doctor, joined Dr Lizzie Burns, a science-based artist, during the event and discussed their work and their response to the COVID-19 Pandemic.

Viruses and Vaccines: Art-science activity session for families

Start of transfer of knowledge and capacity building from March 2021. Transfer of staff (Ioulia Tsatsani) and honorary appointments of D. L. Robertson and J. Hughes with Public Health Scotland.

This paper uses genetic sequencing to analyse genetic variation within viral populations and within-host mutations after transmission. Data showed that most individuals carried one or two variants, and a small number carried many variants, indicating that purifying selection is taking place. Hence, the transmission bottleneck is narrow and usually only the majority variant is transmitted. However, continued vigilance is essential as some minority variants may escape the immune system and are disseminated widely.

Read: SARS-CoV-2 within-host diversity and transmission

Two cats were swabbed and analysis confirmed that they were carrying SARS-CoV-2. This data confirmed that transmission of SARS-CoV-2 from humans to cats is possible and has occurred during the COVID-19 pandemic. This highlights the importance of monitoring transmission of the virus between humans and cats.

Read: Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission

A key publication from the AFRICO19 project. Genomic epidemiology of the SARS-CoV02 pandemic in Africa. Data showed that most epidemics were initiated from European importantions, but spread of the virus through different African countries led to the emergence of new variants of concern.

Read: A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

One of the largest detailed descriptions of bacterial co-infection and secondary infection, in addition to antimicrobial usage in patients hospitalised with COVID-19 during the first pandemic wave. COVID-19-related bacterial infections were rare; the majority were secondary infections (acquired >48 hours after admission). However, antimicrobial use was high with 85% received one or more antimicrobials during their hospital stay.

Read: Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study

Dr Antonia Ho & Prof David Lowe (UofG) received funding from Public Health Scotland to set up a syndromic surveillance of severe acute respiratory illness in hospitalised adult patients in Greater Glasgow using an NHS-approved digital data collection tool and rapid point-of-care PCR platform for SARS-CoV-2 and influenza.

Sarah Iannucci created this interactive web app as part of MSc in Medical Visualisation and Human Anatomy from the University of Glasgow and the Glasgow School of Art, under the supervision of Dr Ed Hutchinson. The purpose of the app is to provide context for the COG-UK Mutation Explorer dashboard. It shows a 3D model of the SARS-CoV-2 Spike Protein and provides further details about regions of interest and variants of the virus.

Visit the App: SARS-CoV-2 Spike Protein Mutation Explorer Web App

A repeated multi-country survey of the mental wellbeing of >5000 medical doctors from 3 countries at two timepoints during the COVID-19 pandemic. Rates of anxiety and depression were highest in Italy, followed by Catalonia, and lowest in the UK. Across all countries, higher risk of anxiety and depression symptoms were found among women, individuals below 60 years old, those feeling vulnerable/exposed at work, and those reporting normal/below-normal health.

Read: Anxiety and depression among medical doctors in Catalonia, Italy, and the UK during the COVID-19 pandemic

Dr Antonia Ho and Prof Brian Willett, in partnership with Malawi Epidemiology and Intervention Research Unit (MEIRU), Malawi-Liverpool-Wellcome Trust Clinical Research Programme (MLW), Liverpool School of Tropical Medicine (LSTM), and University College London (UCL) received funding from BMGF to develop a national multi-pathogen serosurveillance programme in Malawi

Combined genome sequencing of Omicron, vaccine effectiveness study with G2P, Public Health Scotland & EVADE project. Key publication which shows that Omicron is largely unaffected by the antibodies provided by two doses of the COVID-19 vaccine, but responses are significantly improved by a third dose. This may be linked to Omicron’s change in route of entry into human cells. Additionally, real world infection data confirms that Omicron largely escapes immunity from two vaccine doses, but three doses restores good levels of protection.

Read: The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism

This paper analyses geographical clustering of the earliest known COVID-19 cases and the proximity of positive environmental samples to live-animal vendors suggest that the Huanan Seafood Wholesale Market in Wuhan was the site of origin of the COVID-19 pandemic.

The Huanan market was the epicenter of SARS-CoV-2 emergence

This paper analyses the SARS-CoV-2 outbreak at the University of Glasgow in autumn 2020. Data was compared to data from a previously reorded outbreak at Cambridge University. Differi

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning