Deborah Carr assesses the onslaught and effects of evolving SARS-CoV-2 variants

Eighteen months into the pandemic, scientists, policy makers and the public at large are concerned about variants of the SARS-CoV-2 virus that have appeared and spread globally. Could these variants pass more easily from person to person, sabotaging any progress made so far in controlling the virus? 

Could the variants make achieving herd immunity, which would at least slow if not stop the virus’s spread through the world’s population, an all but impossible goal? 

We need to take a closer look at what we mean when we say variants, and then focus on three that are the most concerning.

What’s in a name?
Like other RNA viruses, such as influenza and HIV, SARS-CoV-2, the virus that causes Covid-19, naturally changes or mutates over time. Some mutations will disappear as soon as they arise. Others emerge and persist, usually because they have provided the virus with an evolutionary advantage to survive. 

For example, starting in April of 2020 the original strain of SARS-CoV-2 was gradually replaced by a more dominant variant called D614, which research studies indicated was more efficient in reproducing in humans. 

This was thought to be because of its ability to interact more efficiently with the ACE2 receptor (ACE2 is a protein present in the nose, mouth, lungs, and many other tissues of the body), leading to higher amounts of virus in the nasopharyngeal area, where it was just a cough or sneeze away from being expelled into the face of a nearby human.

Genomic sequencing
Changes in the makeup of a virus are detected via genomic sequencing, which involves examining the sequence of nucleotides in genes. Nucleotides function much like letters of the alphabet do in forming words. 

A close comparison of nucleotide sequences can reveal differences between viruses that can either affect the phenotypic (observable) characteristics of a virus or its genotype (genetic material). Such variations may ultimately affect the structure of the proteins forming a virus’s surface, such as the spike proteins of SARS-CoV-2 – which are the ‘fingers’ that the virus uses to reach out to host cells.     

Variant, strain, lineage
When it comes to variants of SARS-CoV-2, terms such as variant, strain, and lineage are used interchangeably. What’s the difference? 

“When specific mutations, or sets of mutations, are selected through numerous rounds of viral replication, a new variant can emerge. If the sequence variation produces a virus with distinctly different phenotypic characteristics, the variant is co-termed a strain. When through genetic sequencing and phylogenic analysis a new variant is detected as a distinct branch on a phylogenic tree, a new lineage is born.”  


Why should we care?
According to public health experts some possible consequences of the new variants are:

  • Ability to spread more easily from person-to-person.
  • More severe disease, increasing the risk of death.
  • Evading detection by current viral diagnostic tests.
  • Therapeutic agents, such as monoclonal antibodies, may be less effective against variants.
  • Evading natural or vaccine-induced immunity.

In Covid-19 Weekly Epidemiological Update, a World Health Organisation report published in February 2021, key characteristics of the three globe-trotting variants that are of highest concern are described. The US CDC’s terminology for naming them is detailed below. 

The WHO recently convened experts to develop a more straightforward naming system for variants that does not use geographic terminology, which can be inaccurate (especially once a virus spreads beyond its point of origin) and inadvertently stigmatise certain countries.

B.1.1.7 Lineage – UK variant
First detected in the UK in autumn 2020, this variant had spread to 106 countries by 2 March 2021, with community transmission reported in 42 of them. On 21 January 2021, the UK’s New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) had released findings that suggested that patients that contracted this variant were at a greater risk of severe disease and death. 

So far antibodies produced either in convalescent serum from an individual who has recovered or acquired from vaccination still appear to be able to neutralise the variant. However, changes in the structure of the variant indicate that monoclonal antibodies (used in certain drug therapies) may be less effective against it.

B.1.351 – South Africa variant
Although the South Africa variant shares some of the same mutations as that of the UK variant, it emerged independently. First appearing in South Africa in early August of 2020, this variant was detected in 56 countries by March 2021, with community transmission reported in eight. 

In several parts of Africa, the variant became present in a high proportion of viral samples from cases. Preliminary evidence suggests that mutations within the variant allow it to evade immune system responses triggered by either previous SARS-CoV-2 infections or by vaccination. 

This could lead to an increased risk of reinfection with SARS-CoV-2, or recently approved vaccines being less effective when used in areas where the variant predominates.

P.1 – Brazil variant
This variant was first identified in routine screening of Japanese travellers returning from Brazil in early January 2021. It was reported in 29 countries, with community transmission reported in three countries. 

In a genomic survey conducted from April to November 2020 in Amazonas State, Brazil, the variant represented 47% of all specimens. In the Amazonas capital, Manaus, cases attributed to the variant were first detected in early December 2020 and by January represented 91% of all cases. 

This led to a surge in new cases after a lull that some thought indicated that city residents had achieved herd immunity against the virus. Some published studies suggest that the new variant can reinfect people who had recovered from SARS-CoV-2, and that a Chinese vaccine currently used in Brazil may be less effective against it.

Faster spread
The one thing that all three variants have in common is that they seem to spread more quickly and easily than other variants. Even if they are not necessarily more severe or deadly, sharp increases in new cases in an area strains healthcare resources, leading to more hospitalisations and possibly more deaths. 

It is also likely that these variants – and more to come – may necessitate modifications being made to current Covid-19 vaccines, similar to what happens every year with seasonal influenza vaccines. However, current non-pharmaceutical interventions such as hand washing, wearing masks, avoiding crowds, and maintaining social distance are equally effective against the variants. Much will depend on how the variants will advance once countries emerge from lockdown.

Although Covid-19 is probably here to stay in some form, there are still effective measures to take to make it a manageable problem, rather than a continuing global pandemic.

Deborah Carr, DVM, MPH currently works for the US Department of Defense.  Her areas of interest include zoonotic diseases, public health, and biosurveillance.

Photo purchased @iStock