The latest research from the National Institute of Biological Standards and Control (NIBSC) confirms the increasing frequency of coronavirus Delta sub-variant AY.4.2 found in wastewater samples.
Scientists at the institute have been analysing samples from a London sewage plant since the onset of the pandemic and have previously shown that environmental surveillance can be used to measure levels of virus transmission and proactively identify new variants of concern.
A shift in variant predominance in wastewater samples has been observed through the pandemic closely mirroring sequencing results from clinical samples. The rise of variant D614, which replaced the original Wuhan strain globally during the first few months of the pandemic, was first observed in wastewater samples from March-April 2020. A new more transmissible Alpha variant was first identified in samples on 10 November 2020 and then rapidly increased in frequency to become the dominant variant by the end of January 2021. This Alpha variant was later replaced with a variety of lineages with immune escape properties which led to an increase in virus transmission levels. The Delta variant was the most successful among them and has dominated since early June 2021 (Figure 1A).Figure 1. (A) Fraction of SARS-CoV-2 variants identified in wastewater samples collected in a London sewage plant based on quantification of key spike gene mutations in viral RNA genomes. (B) Fraction of SARS-CoV-2 Delta sub-variant AY.4.2 in wastewater samples (blue line) compared to that in clinical samples (black line) based on quantification of Y145H spike gene mutation in viral RNA genomes. Mean values from replicate sequences (n=12–20) for each sampling date are shown. Error bars indicate standard error of the mean. Data source: NIBSC internal database Oct 2021. Clinical data referred in Fig. 1B were obtained from the UKHSA SARS-CoV-2 variants of concern and variants under investigation in England. Technical briefing 26. Department of Health and Social Care, 2021.
Recent results show that our scientists have been able to detect the most recent Delta sub-variant AY.4.2 present in sewage from early July and then steadily increasing and reaching around 8% of viral sequences in a sample from 21st September 2021 (Figure 1B).
Dr Javier Martin, who led the study, comments:
“Our work further highlights the value of environmental surveillance at detecting changes in trends of different coronavirus variants, including variants of concern that might become dominant in the future. Wastewater sequencing has an advantage over other methods as it is not subject to major surveillance biases, being able to detect all infections in the catchment area and not only those from individuals receiving COVID-19 tests”
It is still unclear what the recent observed rise in frequency of the Delta AY.4.2 sub-variant means in terms of virus transmission and disease, but the UK Health Security Agency has recently designated AY.4.2 as a variant under investigation due to it becoming increasingly common in the UK. Wastewater surveillance, now widely conducted across the UK, will play a critical role in monitoring the spread of this variant and any other variant that might become epidemiologically relevant in the future.