Random variation is an essential component of all living things. It drives diversity, and it is why there are so many different species. Viruses are no exception. Most viruses are experts at changing genomes to adapt to their environment. We now have evidence that the virus that causes Covid, SARS-CoV-2, not only changes but changes in ways that are significant. This is the twenty-fifth part of a series of articles on how the virus changes and what that means for humanity. Read the rest: part one, part two, part three, part four, part five, part six, part seven, part eight, part nine, part ten, part eleven, part twelve, part thirteen, part fourteen, part fifteen, part sixteen, part seventeen, part eighteen, part nineteen, part twenty, part twenty-one,  part twenty-two, part twenty-three, and part twenty-four.

Variants spread rapidly through populations and become the dominant strains, at least locally. There has been an enormous effort to understand the extent, function, and epidemiological consequences of these variants. In the past few months, genome sequencing efforts isolated many SARS-CoV-2 variants throughout the world. Other variants were isolated in laboratories using monoclonal antibodies or pseudotyped viruses, which are virus particles whose envelope proteins can be dictated by researchers to measure antiviral compounds and antibody responses.

Rino Rappuoli and his team of Italian researchers took this one step further. The study, conducted by the Monoclonal Antibody Discovery Lab, among others, aimed to investigate the evolution of SARS-CoV-2 in the immune population. As opposed to many in vitro studies where mutations are artificially created, Rappuoli and his team co-incubated live virus with a highly neutralizing plasma from a patient infected with the wild-type.

After 45 days of exposure, the virus sample developed a deletion to position 140 of the spike protein in the N-terminal domain (NTD). After 73 days, the substitution E484K to the receptor bind domain (RBD) developed, notably observed in the South African, Brazilian, Nigerian, and New York variants. After 80 days, an insertion to the NTD containing rendered the virus entirely resistant for the convalescent plasma sample.

The mutations were remarkably evasive in their own right. The deletion at F140 decreased neutralization titers by four times. The mutation E484K additionally reduced titers four-fold. The insertion in the NTD was able to finish the job, taking neutralization titers from roughly 60 to zero in a matter of days. These mutations developed naturally in conjunction meaning similar mutations could happen in the real world in long-haul Covid-19 infections.

The researchers speculated that the F140 deletion alters the loops in the NTD, depicted in the figure below, which decreases the region’s stability. This, paired with the insertion that remodels part of the region, helps the NTD evade antibodies targeting that specific section of the spike protein. Additionally, E484K swaps the charge at that position and alters antibody binding in the RBD. These three alterations enabled the complete prevention of any antibody neutralization, also shown below.

An unanswered question from this paper is if there were mutations in other protein and non-protein areas of the genome, as there are for naturally occurring variants. Convalescent sera may neutralize through recognition of the envelope, nucleocapsid, or membrane proteins, as well as some of the proteins in the replication complex or elsewhere.

There is a word of caution for this paper. The Italian lab created an immunological escape variant virus capable of infection and transmission. We can only hope that the containment conditions of that laboratory are sufficient so that such a creation never escapes that facility.

How do these results then affect the larger population? A virus aims to survive and spread. It is capable of changing its structure to accomplish this goal. As shown in several long-term immunocompromised Covid-19 patients, such as the Boston, Pittsburgh, and London patients, extended exposure of SARS-CoV-2 to neutralizing antibodies may yield mutations that create a resistant virus. 

These variants are going to continue to pose a challenge to the control of the pandemic through both public health measures and vaccination.