Spot the variant—the pursuit of greater vigilance
Authors: None The Lancet Microbe
Journal: The Lancet Microbe (2021)

We knew that the COVID-19 pandemic control measures would focus on vaccine distribution in 2021, with all the challenges related to equitable global access, residual unknowns about the vaccines themselves, and logistical issues. What we hoped would not surface so soon, was the compounding of these challenges by the emergence of highly transmissible SARS-CoV-2 variants. In late 2020, three such SARS-CoV-2 variants were identified: B.1.1.7 in the UK, B.1.135 in South Africa, and P.1 in Brazil. That two of these variants were first identified in the UK and South Africa is notable, as these countries engaged in genomic surveillance of SARS-CoV-2 early in the pandemic by setting up, respectively, the COVID-19 Genomics UK Consortium (COG-UK) and the Network for Genomic Surveillance in South Africa (NGS-SA). Since March, 2020, COG-UK has sequenced over 250 000 SARS-CoV-2 genomes—approximately 5% of all positive COVID-19 cases in the country and more than half of all publicly available sequences. The collected genomic data have been used throughout the pandemic to track transmission of SARS-CoV-2 in the UK (eg, to distinguish local transmission from case importation), to monitor rates of epidemic growth, and to identify genetic mutations of diagnostic, clinical, or epidemiological relevance, such as in the case of the B.1.1.7 variant—information that is regularly fed back to inform policy. NGS-SA operated on a much smaller scale than COG-UK, sequencing 50–100 genomes per month from a random selection of samples across the country. Yet, the approach proved effective in swiftly pinpointing B.1.351 as the variant driving a rapid surge in COVID-19 cases reported in a hospital in the Eastern Cape region in November, 2020. The identification of SARS-CoV-2 variants with increased transmissibility has led many countries to tighten their non-pharmaceutical interventions. Researchers and vaccine manufacturers are investigating the potential effects of the mutations carried by the variants on health outcomes in infected individuals and on natural and vaccine-induced immunity. Preliminary findings (mostly not peer-reviewed) suggest that B.1.1.7 could be associated with an increase in mortality, but reassuringly indicate that the mRNA-based vaccines (Moderna and Pfizer/BioNTech) and the Oxford/AstraZeneca vaccines are likely to retain efficacy against this variant. Despite reduced neutralisation against B.1.351 in the sera of individuals vaccinated with mRNA-based vaccines, titres are thought to be protective. However, findings (not peer-reviewed) that the Oxford/AstraZeneca vaccine provides minimal protection against mild-to-moderate COVID-19 in young adults infected with B.1.351 have prompted South Africa to put on hold the rollout of this vaccine, despite the possibility that efficacy against severe disease might be retained. WHO still recommends the use of this vaccine, even if variants are present in a given country, but emphasises the importance of each country making a risk assessment on the basis of the local epidemiological situation. The emergence of SARS-CoV-2 variants of concern has highlighted the importance of genomic surveillance in the ongoing management of the pandemic. Thus far, global genomic surveillance has been patchy, with most countries sequencing fewer than 5% of SARS-CoV-2-positive samples. Even the USA, which has large sequencing capacity, has sequenced fewer than 1% of its positive cases. However, as the number of infections continues to rise and immunisation potentially limits the spread of more common variants, new variants are likely to be selected for. Such variants need to be identified as soon as possible if containment is to be attempted and if vaccines need to be adapted (already underway for known variants), but uneven surveillance hinders their rapid detection. For variant detection to be timely, genomic surveillance needs to be ramped up globally. The USA is scaling up its surveillance programme, and other countries with available high-throughput sequencing capacity should follow suit. On Jan 26, 2021, the UK launched the New Variant Assessment Platform, by which it will offer genomics expertise and capacity to other countries. This platform is exactly the kind of international cooperation initiative that is needed to support countries that have scarce, if any, sequencing capacity. Just like vaccine distribution, genomic surveillance of SARS-CoV-2 for the identification of biologically relevant variants can only be successful and contribute to overcoming the COVID-19 pandemic if unilateralism is set aside and global, collaborative approaches are implemented.