New Scientist - USA (2022-04-09)

9 April 2022 | New Scientist | 15

THE recombinant “deltacron”

variants of the coronavirus have

left many people unsure about

the future of the pandemic, amid

fears that they could combine

the delta variant’s virulence

with omicron’s transmissibility.

Recombination, essentially the

viral version of sex, occurs when

a cell is infected with two related

viruses, whose genetic material

could mix as they replicate.

Dozens of potential

recombinant SARS-CoV-2 variants

have been identified in recent

weeks. So, why are these emerging

and how worried should we be?

Recombination can occur

when a viral genome is arranged

in several segments, like that of

a flu virus. When new flu viruses

are assembled, they may take

on some segments from one

variant and other segments from

a second variant if it is present.

In contrast, the genome of

the SARS-CoV-2 virus is composed

of a single strand of RNA. In this

case, recombinants form when

the enzyme that copies the RNA

releases one strand during the

replication process, grabs another

strand and resumes copying.

This can lead to major genetic

mistakes, resulting in viruses that

can’t replicate. It can also generate

recombinant viruses with an

advantageous mix of mutations.

Recombination has been

pivotal in the evolution of

the many coronavirus strains.

In humans, SARS-CoV-

probably began recombining

very early in the pandemic.

When existing variants differ

by just a few mutations, it can

be unclear whether a new variant

with a mix of those mutations

arose via recombination or if the

mutations were independently

acquired. Recombination is

also difficult for sequencing

laboratories to detect. Extra work

is needed to rule out co-infections

and sample contamination.

The arrival of omicron,

which has more than 50 unique

mutations, has made it easier to

spot recombinants. It is like trying

to decipher if two students have

cheated: if they make the same

spelling mistake on one word,

it could be a coincidence, but if

they misspell 10 words in the same

way, someone has been copying.

The first omicron wave, caused

by the BA.1 subvariant of omicron,

began when the delta variant

was still widespread in many

countries. High case numbers

mean many people would have

been infected with delta and BA.

simultaneously, creating more

opportunities for recombination.

Several delta-BA.1 recombinants,

known as “deltacron”, have been

detected, but just two have been

studied sufficiently for researchers

to give them names: XD and XF.

XF hasn’t been sequenced

anywhere in the world since

February and may have quickly

died out. XD is still present in parts

of Europe but is expected to be less

transmissible than the omicron

subvariant BA.2. “I’d be surprised if

it managed to compete with BA.2,”

says Tom Peacock at Imperial

College London.

BA.2 has overtaken BA.1 in

many countries. Along with the

relaxation of restrictions, this has

triggered a second omicron wave.

Many people will therefore be

simultaneously infected with

BA.1 and BA.2. This has created

recombinants, of which seven

have been named: XE, XG, XH,

XJ, XK, XL and XN.

What is the risk?

So how worried should we be?

With flu, recombination can

create more dangerous viruses.

Flu strains from other animals

often kill a large proportion of

the people they infect, but rarely

spread from person to person.

The recombination of human

and animal flu viruses could

produce a strain that readily

spreads between people, while

remaining lethal, potentially

causing a pandemic far worse

than that of covid-19.

By contrast, the SARS-CoV-

virus recombinants that have

been identified so far are mixes

of variants that have already

spread widely in people, many

of whom have some degree

of covid-19 immunity. These

recombinants aren’t expected

to differ considerably from the

variants they evolved from.

A variant with novel mutations

and the ability to evade past

immunity would probably pose a

greater threat than recombinants.

According to the UK’s Scientific

Advisory Group for Emergencies,

the worst-case scenario is a

SARS-CoV-2 variant recombining

with one of the human common

cold coronaviruses, or an

animal coronavirus, to produce

something unexpected

and dangerous.

While that is possible, says

Peacock, it isn’t thought to be

likely to happen. The more

distantly related, the less likely

viruses are to recombine into

a functioning pathogen. ❚

“An entirely new variant
would probably pose
a greater threat than
recombinants”

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Someone with covid-

has dialysis at a hospital

in Liege, Belgium

An artist’s illustration

of the SARS-CoV-2 virus

under a microscope

Analysis Covid-19 recombinants

Should we worry about different variants of the coronavirus merging?

“Deltacron” variants of coronavirus pose a threat, finds Michael Le Page,

but they aren’t the worst-case scenario

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