'Most mutated Covid variant ever' discovered in Indonesia; sparks concerns over immunity and vaccine efficacy

Scientists believe that a Covid variant detected in Indonesia could be the most mutated version of the virus ever recorded. Collected from a patient swab in Jakarta, this morphed version of Delta exhibits 113 unique mutations, with 37 of them affecting the spike protein used by the virus to attach to human cells. To put it into perspective, the infamous Omicron variant carries around 50 mutations. The strain has been labeled by virus-trackers as the "most extreme" they have encountered, though there is no evidence yet that it will become dominant. Top experts are confident that even if it does spread, it won't lead to worldwide lockdowns.

The new variant was submitted to a global Covid genomics database in July and is believed to have emerged from a case of chronic infection. Chronic infections occur when a single patient struggles to defeat the virus within a few weeks, leading to extended infection lasting for months. Such infections often affect individuals with compromised immune systems, such as those with AIDS or undergoing cancer chemotherapy, making them less able to fight off the virus effectively. These prolonged infections are a cause of concern for scientists, as they create conditions that promote virus mutations, potentially enabling it to evade the body's defenses, including immunity from vaccinations.

Of particular worry to experts are mutations on the spike protein, as Covid vaccines are designed based on this portion of the virus. The virologists emphasize that it remains unclear if the newly discovered strain has the potential to spread widely and infect others, and it would need to outcompete existing variants like the descendants of Omicron to establish itself. However, they stress that the greatest fear lies in the emergence of such variants quietly, as some countries have reduced genetic analysis as the pandemic seemed to wane.

Professor Lawrence Young from Warwick University warns against complacency, stating that as the virus continues to mutate and spread, it will cause severe infections in vulnerable individuals and lead to an increased burden of long-term consequences from the infection. He urges more genetic surveillance to detect emerging variants that may be resistant to established immunity and emphasizes the importance of knowing whether new outbreaks are caused by new and potentially more dangerous variants.

"This virus continues to surprise us and being complacent is dangerous," Professor Young said. "This highlights the problem of "living with the virus. As the virus spreads and continues to mutate, it will inevitably result in serious infections in the most vulnerable and it will also increase those suffering the burden of the long-term consequences of infection."

Professor Ian Jones from the University of Reading also highlights the concern over chronic infections, as they can prompt the virus to adapt better to the human immune system, potentially leading to mutations that escape immunity. However, he notes that extended mutations usually come at a cost for the virus itself, meaning the overall risk from such a virus is low.

:The concern over chronic infections is that the virus is mutating in an individual who has already generated immunity," he said. "In other words, the virus almost has to have mutations that can escape that immunity. Such mutations are often offset by a “fitness cost” which means the virus generally doesn’t grow well and overall, the risk from such a virus is low."

He added that, instead of the odd super-mutant strain, we should be more worried about a sudden rise in cases of any Covid type. "What you are really looking for is not the odd, strange sequence here and there but a rapid rise in the frequency of a particular sequence that suggests it is gaining a toehold," he said. "Until then all alarm bells should remain off."

Regarding the patient from whom the variant was collected, specific details about their health, age, and sex have not been disclosed. The strain first came to attention through online Covid variant tracker Ryan Hisner and was later flagged by US virologist Marc Johnson from the University of Missouri.

The article underscores the importance of continued monitoring and analysis of Covid variants, as reducing surveillance could leave countries unaware of changes in virus transmission and the emergence of new variants. Although Delta has faded into obscurity due to being outcompeted by milder variants like Omicron, scientists caution against dismissing the possibility of sudden rises in cases from any Covid type. Vigilance and timely responses remain crucial in the ongoing fight against the virus.

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• Covid
• Indonesia