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NSW Health Pathology researchers have been tracking how the COVID-19 virus mutates in a first-of-its-kind study, revealing patterns that could help predict the emergence of future variants.

In the ear­ly days of the COVID-19 pan­dem­ic, as the world scram­bled to under­stand the fast-mov­ing virus, a team of Aus­tralian researchers set out to study how the virus would evolve long term.

With mil­lions of infec­tions unfold­ing glob­al­ly and new vari­ants rapid­ly emerg­ing, they want­ed to learn how SARS-CoV­‑2 — the virus that caus­es COVID-19 — would evolve in a con­trolled lab set­ting, and if it would weak­en over time.

Fast for­ward more than five years and their find­ings, pub­lished in the Jour­nal of Virol­o­gy, have con­firmed the remark­able adapt­abil­i­ty of the virus, shed­ding light on com­mon muta­tions which emerge repeat­ed­ly and inde­pen­dent­ly in dif­fer­ent strains.

The research, which is the most exten­sive of its kind to date, could help pre­dict the emer­gence of future vari­ants and inform treat­ment and pre­ven­tion design, said first author Dr Charles Fos­ter, from NSW Health Pathology’s Virol­o­gy Research Lab­o­ra­to­ry at Prince of Wales Hos­pi­tal and UNSW’s School of Bio­med­ical Sciences.

“This work could help us antic­i­pate how the virus might evolve next. If we can iden­ti­fy muta­tions that arise repeat­ed­ly —even in a lab setting—it gives us a chance to pre­dict which changes could emerge in the real world, so we can pre­pare for them,” Dr Fos­ter said.

Tracking the virus in a controlled environment

Whole-genome sequenc­ing of COVID-19 cas­es enabled glob­al con­tract trac­ing efforts dur­ing the pan­dem­ic and the iden­ti­fi­ca­tion of muta­tions of con­cern. But fur­ther research was need­ed to under­stand how the virus evolves.

In this mul­ti-year study researchers exam­ined how 11 virus sam­ples from nine dif­fer­ent COVID-19 vari­ants, includ­ing Alpha, Delta, and Omi­cron, mutat­ed over time. The sam­ples were grown in Vero E6 cells – mon­key kid­ney cells com­mon­ly used in virus research which lack a strong immune response.

Using a method called ser­i­al pas­sag­ing, they trans­ferred the virus from one batch of cells to anoth­er repeat­ed­ly, between 33 to 100 times, well above the 15 pas­sages in pre­vi­ous­ly pub­lished research for SARS-CoV­‑2. It’s a method often used to study viral changes, and is used in vac­cine devel­op­ment to atten­u­ate, or weak­en, a virus in a con­trolled way.

“It’s chal­leng­ing to under­stand how COVID-19 adapts only by look­ing at real-world cas­es because there are so many vari­ables at play,” Dr Fos­ter said.

“By grow­ing the virus over many gen­er­a­tions in a con­trolled lab envi­ron­ment, we can observe how it evolves with­out the influ­ence of the immune sys­tem or treat­ments. That gives us a clear­er pic­ture of its nat­ur­al evo­lu­tion­ary pathways.”

The pas­sag­ing was con­duct­ed in a secure lab­o­ra­to­ry and did not aim to increase the trans­mis­si­bil­i­ty or sever­i­ty of the virus sam­ples. The use of Vero E6 cells fur­ther lim­it­ed risks to human health.

How the virus evolved in the lab

The researchers tracked how the virus’s genet­ic code changed dur­ing pas­sag­ing, specif­i­cal­ly, how many muta­tions appeared and whether they stuck around or disappeared.

“One goal of this was to see if muta­tions would devel­op that mir­rored what’s going on in the real world. But on the flip side, we also want­ed to see if new muta­tions would arise that haven’t been seen yet and what impact they might have,” Dr Fos­ter said.

The virus­es con­tin­u­al­ly evolved, even the sam­ple which was put through 100 passages.

“We gave the virus opti­mal con­di­tions to keep devel­op­ing and want­ed to see whether it would even­tu­al­ly attenuate—basically weaken—over time. It didn’t,” Dr Fos­ter said.

“In all cas­es, by the time we stopped, the virus­es were still grow­ing hap­pi­ly and pick­ing up mutations.”

There were new muta­tions which popped up repeat­ed­ly in dif­fer­ent strains – a phe­nom­e­non known as con­ver­gent evo­lu­tion – as well as changes which mir­rored those seen in real world outbreaks.

The sim­i­lar­i­ties sug­gest the virus may be nat­u­ral­ly inclined to devel­op cer­tain changes, regard­less of the envi­ron­ment and exter­nal pres­sures, said senior author Pro­fes­sor William Rawl­in­son, Direc­tor of Micro­bi­ol­o­gy at Prince of Wales Hos­pi­tal and Senior Med­ical Virol­o­gist at NSW Health Pathology.

“Some muta­tions which help the virus adapt may be dri­ven by the make­up of the virus itself, rather than a bid to evade immu­ni­ty,” he said.

“Some of the changes we saw in humans were also hap­pen­ing in vit­ro, which sug­gests it’s not just about trans­mis­si­bil­i­ty or immune evasion—it’s also about the struc­ture and func­tion of the virus itself,” Prof. Rawl­in­son said.

“They could devel­op these impor­tant muta­tions even in the absence of a catalyst.”

While many of the changes occurred in the spike protein—the part of the virus that helps it enter human cells—other parts of the virus also mutat­ed, in some cas­es at even high­er rates. Sev­er­al of the muta­tions are already known to reduce the effec­tive­ness of cer­tain vaccines.

Prof. Rawl­in­son stressed that the research reflect­ed how a virus might evolve in the real world, but did not speed up its evo­lu­tion. He added the risk of the virus devel­op­ing adverse genet­ic changes was low­er in the con­trolled lab envi­ron­ment, than in a real-world set­ting where it would adapt to immune pressures.

Next steps: Sharing data and deepening understanding

Though the research stripped away the com­plex­i­ties of real-world trans­mis­sion, it offers valu­able insights that could help researchers and pub­lic health author­i­ties bet­ter pre­dict how the virus will evolve and inform future treat­ment and pre­ven­tion strategies.

Dr Fos­ter sus­pects the lab find­ings will trans­late to the real world, with the virus to con­tin­ue adapt­ing long term, just sub­ject to more evo­lu­tion­ary pressures.

Fur­ther research will be need­ed, par­tic­u­lar­ly on the repeat muta­tions, to bet­ter under­stand how the virus changes over time and how this com­pares to the real-world infection.

The sequenc­ing data and analy­sis code have been made pub­licly avail­able by the researchers, so it can serve as a resource for oth­er experts.

“We’ve made all of our sequenc­ing data freely avail­able so oth­er researchers can dig into it, com­pare it with clin­i­cal sam­ples, and hope­ful­ly uncov­er even more about how this virus evolves,” Dr Fos­ter said.

(This arti­cle was orig­i­nal­ly pub­lished by the UNSW news­room.)