n Friday 11 December I was alerted to the fact that a large number of the samples showing positive in our Covid-19 testing laboratory in Birmingham were unusual. Like the other Lighthouse laboratories, dedicated to testing samples from the wider public, we are on the lookout for the presence of three particular genes, with a positive Covid-19 result requiring clean detection of two of the three. That Friday around 25% of all our positives were completely missing one of those genes – the S gene, which encodes the spike protein of the virus and is essential for viral attachment and entry into cells. It is not unusual to see some S gene drop-outs in positive samples, but usually in around 1-2% of them, not in 25%. At the same time this phenomenon was also observed in the Lighthouse lab in Milton Keynes, and communication was instigated with the Covid-19 Genomics UK (CoG) consortium, and our observation was reported to the national testing programme. In under a week it had been confirmed through the CoG genome sequencing data that the observed S gene drop-out was being driven by the emergence of a new variant of Sars-CoV-2, named B117. By Friday 18 December the rapid emergence of this new variant was alarming enough for government to convene an emergency cabinet meeting, announcing on 19 December tier 4 restrictions for the whole of the south-east of England and tougher restrictions on Christmas plans nationally. News of the new variant has led to multiple nations banning travel from the UK, and the closing of our Channel borders. The main question I am being asked now is: is this all commensurate with the threat posed? The B117 lineage is not a new strain of Sars-CoV-2. It is a new variant that has emerged from the virus that has been circulating in the UK. This new variant contains a surprising number of mutations in its genome – mutations arise constantly in viruses as they replicate and move from host to host. Most of these mutations are “silent”, causing no change to the virus structures and proteins they encode, or are damaging to the virus and die quickly. However some mutations result in a slight change to the structures on the virus, possibly making them marginally more efficient at transmitting, or replicating, or attaching to cells. In this case these mutations become advantageous – natural selection will occur for viruses containing these mutations and they will become more successful. In B117, there are an unusual number of these meaningful mutations. Three of the mutations have been observed in the past in many sequenced Sars-CoV-2 genomes, but have now converged to appear together in a single lineage in the S gene. In particular one of the three mutations in this lineage has been implicated in enhancing virus binding to host cells, and another implicated in avoiding antibodies in infections. The mutation implicated in virus binding also affects the ability of the fluorescently labelled probe used in our PCR Covid test to detect the S gene, meaning there is zero S-gene signal in tests positive for B117 variants. It is now clear that the B117 lineage is spreading quickly across the south-east of England, mirroring a stark rise in hospitalisations in the region. There is no evidence to suggest the new lineage causes any more aggressive a type of coronavirus infection, or is even more deadly, but it would seem to be transmitting very efficiently, with modelling suggesting a 65-70% increase in its transmissibility. Once we were clear that our S-gene drop-out test positives were being driven by the new lineage we were able to go back through our entire archive of test data and measure the rise of the new lineage. The resulting graph is worrying, showing an increase from the standard 2% of all positives, to almost 70% within the space of two weeks. This clearly suggests that the new lineage of Covid-19 appears to be able to spread very quickly, though it is not necessarily more deadly. Our lab does not process tests from Birmingham alone: samples are allocated to labs based on demand and capacity at both local and national levels. So we cannot make any inference on whether our data reflects local or national epidemiology, but it is clear that the new B117 lineage is rapidly dominating infections we are detecting in our lab network (the data from Milton Keynes and other Lighthouse labs is identical). We also know that cases of infection caused by the new lineage have been confirmed around the UK. The south-east of England is clearly the epicentre of the new variant of Covid-19 and it is spreading fast across the UK, and possibly abroad, with confirmed cases in Denmark and Italy. Not to act on the data and information currently to hand would be at least negligent – and potentially catastrophic. To wait for confirmation that B117 is more transmissible before implementing control measures would be ethically immoral. As Dr Michael Ryan of the WHO has said many times, to counter Covid-19 you must act fast and you must act decisively. If there is one thing the UK should know better than most, it is the acute cost of failing to heed that advice. Alan McNally is a professor in microbial genomics at the University of Birmingham