- The Immunology and Genomics group at the IIM (Vigo), led by Antonio Figueras and Beatriz Novoa, has detected, after a year of work using massive sequencing techniques, the SARS-CoV-2 mutations circulating in several Galician towns such as Baiona, Noia and Melide. Taking these results as a reference, the presence of the British variant is confirmed through the detection of exclusive mutations that define it.
- Achieving this milestone in the monitored towns makes it possible to know the pool of viruses circulating in each area and to identify both the most frequent mutations and those associated with risk variants.
Santiago de Compostela, 29 April 2021. Within the framework of the DIMCoVAR project, funded with more than 200,000 euros by the CRUE-Santander Supera COVID Fund, the Spanish National Research Council (CSIC) has achieved the sequencing of the SARS-CoV-2 virus in wastewater samples.
“Since the genetic material of the virus was detected in stool samples from infected patients, there has been international interest in monitoring SARS-CoV-2 in wastewater,” the directors of the Immunology and Genomics group note.
At first, the research group attempted to sequence water samples that had tested positive by PCR and contained a high number of viral gene copies, but because the virus is highly fragmented in wastewater samples, sequencing is not straightforward.
For this reason, since September the group has opted to apply different methodologies for sample sequencing. Now, using more sensitive massive sequencing techniques that require only a small amount of genetic material, it has obtained millions of SARS-CoV-2 sequences.
“This achievement is a great satisfaction for the group, as we have been working on this line for a year. First, within the framework of an agreement with the Xunta de Galicia and with funding from the Supera COVID fund. Being able to detect the mutations circulating in a town is very valuable for identifying variants. It must be taken into account that everything is concentrated in wastewater, even viruses from asymptomatic people who do not go to hospital. That is why it is so important,” says Antonio Figueras.
The CSIC work team, led by Antonio Figueras and Beatriz Novoa and with the participation of Amaro Saco and Magalí Rey, has achieved the sequencing of samples from three of the 15 monitored towns: Baiona, Noia and Melide.
“In Noia and Melide, the mutations detected are compatible with the Spanish and European variants, while in Baiona those compatible with the British, South African and Brazilian variants stand out. Since most of these mutations are in the gene that gives rise to the Spike protein, which interacts with cellular receptors, they are mutations with functional implications for the virus and clinical interest,” says Beatriz Novoa.
“We need to sequence more, but we are already surprised by the number of mutations found in towns such as Baiona, with an overwhelming prevalence of the British variant and unique mutations that define it, as well as mutations shared among several variants of concern, including the British, South African, Brazilian and other variants,” says Antonio Figueras.
The research group has also compared these sequences with 500 SARS-CoV-2 genomes sequenced in Galician clinical patients. This has led to the detection of shared mutations in wastewater samples and COVID-19 patients, as well as others that had not been detected in people affected by the disease since the start of the pandemic. This work could make it possible to detect new potentially “dangerous” mutations earlier.
“All this reaffirms the importance of wastewater monitoring for tracking new virus mutations that may emerge,” CSIC concludes.
The DIMCoVAR project
In addition to CSIC, the project involves the University of Vigo (UVigo) and the company Geseco Aguas. It covers the analysis of the presence of genetic material from SARS-CoV-2 in wastewater from 15 wastewater treatment plants (WWTPs) in Galicia, as well as at the discharge points of WWTPs into the marine environment: Baiona, Nigrán, Gondomar, Cambados, Moraña, Puerto de Son, Muros, Melide, Ares, Cedeira, Noia, Pobra do Caramiñal, Betanzos, Viveiro and Burela.
CSIC’s participation, through the Institute of Marine Research and specifically through the “Immunology and Genomics” and “Process Engineering” research groups, consists mainly of detecting the virus’s genetic material by PCR and developing an epidemiological model based on the results of the analyses. UVigo’s participation corresponds to the “BiotecnIA: Industrial Biotechnology and Environmental Engineering” group.
At the beginning of April, within the framework of this project, it was confirmed that the analyses carried out during this year in 11 of the 15 wastewater treatment plants under study were representative of the evolution of the pandemic in Galicia.