New N501 SARS-CoV-2 mutation may have been circulating in Italy since August 2020

By Dr. Tomislav Meštrović, MD, Ph.D.Jan 13 2021

A recent study published in The Lancet Infectious Diseases journal shows that mutated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains with a substitution at position 501 might have circulated unnoticed even before the end of September 2020, when the rapid emergence of B.1.1.7 lineage (carrying the N501Y mutation) was initially reported.

Study: First detection of SARS-CoV-2 spike protein N501 mutation in Italy in August, 2020. Image Credit: joshimerbin / Shutterstock

On December 14 2020, the authorities of the United Kingdom reported to the World Health Organization (WHO) that a new variant of SARS-CoV-2, a causative agent of an ongoing coronavirus disease 2019 (COVID-19) pandemic, was identified through viral genomic sequencing.

This variant, often referred to as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01), was shown to spread more readily between people, albeit there are no significant associations with symptom severity or vaccine efficacy.

In any case, manifold mutations in the viral spike glycoprotein are characteristic for this variant, with N501Y being a major concern as it involves one of the six key amino acid residues responsible for tight contact between SARS-CoV-2 receptor-binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2) cellular receptor.

Consequently, a group of researchers, led by Dr. Simona Fiorentini from the Department of Molecular and Translational Medicine at the University of Brescia in Italy, conducted detailed metagenomic sequencing and bioinformatic analyses to take a deep look into Italian isolates.

Detailed genetic characterization

In November 2020, a 59-year-old male individual with a history of persistent SARS-CoV-2 infection underwent molecular testing. Upon laboratory confirmation of the infection, genetic characterization of viruses in November sample or MB61-Nov (but also previous sample from August 2020, known as MB61-Aug) was pursued by metagenomic sequencing.

Two complete obtained genomes were subsequently compared with full-length viral genomes freely available on the GISAID platform, which is an open-access source to genomic data of influenza and SARS-CoV-2 viruses.

Strains with the mutation N501Y in the spike RBD, which were recently characterized in Italy and the United Kingdom as incorporated to the quickly emerging B.1.1.7 lineage, were included in the analysis. Finally, sequence alignment and detailed editing was also done to obtain the full picture.

N501T variants present in early August

In short, bioinformatic analyses in this study revealed that the MB61-Aug SARS-CoV-2 isolate had amassed ten amino acid changes compared to early Italian isolates; in addition, three more had appeared along its evolution until the end of November 2020.

It has to be noted that the N501T substitution was found in both MB61-Aug and MB61-Nov SARS-CoV-2 isolates, pointing towards the conclusion that a mutation at the key amino acid residue 501 has already been spreading in Italy since August 2020.

Our time-scaled maximum likelihood tree suggests that these spike N501T variants emerged in early August in northern Italy, and therefore that SARS-CoV-2 strains harboring a substitution at position 501 might have circulated unnoticed even before the end of September 2020, when the rapidly emerging B.1.1.7 lineage (carrying the N501Y mutation) was first reported", say study authors.

The need for a massive research effort

Recent discoveries regarding SARS-CoV-2 evolution, particularly within the RBD, warrant a massive scientific effort in order to pinpoint novel variants with the potential of increased viral spreading, but also with the propensity to show an evasive behavior to infection-derived or vaccine-induced neutralizing immunity.

This study is one step towards that direction, and it also compared Wuhan reference strain with both MB61 variants. The variants actually carried four mutations and one deletion in the spike glycoprotein – two of which were situated within the RBD.

Nonetheless, more complex and lengthy investigations that necessitate collaboration among different research groups will be needed in the future. In that regard, recently established WHO SARS-CoV-2 Virus Evolution Working Group is a way towards improved understanding of this timely issue.