Full Genome Sequencing of Avian Flu in Cambodia Done Under 24 Hours - medtigo



Full Genome Sequencing of Avian Flu in Cambodia Done Under 24 Hours

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Avian flu, also known as H5N1, is a fatal disease that seldom affects people. As per a report in the Quartz, it has been circulating worldwide for decades, but there have been no instances of human-to-human transmission. Often, human infections occur from encounters with sick birds. When it does infect people, the fatality rate is greater than 50%, which is comparable to ebola and approximately 16 times that of covid.  

In a world suffering from post-pandemic stress, recent outbreaks, particularly those affecting animals like us, are hence cause for alarm. At the start of the year, health officials documented a number of alarming incidents. More than 700 sea lions perished in Peru due to avian influenza, which they likely contracted from pelicans, of which hundreds also perished.  

At a mink farm in Spain, the virus spread throughout the facility’s dense population of mammals (the whole farm contained more than 50,000 mink). The virus that infected the minks has gained at least one mutation that makes it more transmissible across mammals, the most worrying indicator to date that it could trigger epidemics among people.  

Then, on February 23, the infection claimed the life of a Cambodian girl. Her father tested positive, but he did not exhibit any symptoms. The global health community moved swiftly to identify the viral strain and was successful in doing so in record time.  

The World Health Organization (WHO) deemed the Cambodia case “worrisome” in light of the ongoing, widespread global epidemics of avian flu. Bird flu is not new to the United States: According to the WHO, 58 cases have been documented in Cambodia since 2013, resulting in 38 deaths.

However, there was fear that the virus in Cambodia was not local to the region but rather the type responsible for recent outbreaks in Europe and the Americas. This strain, which is odified to pass from mink to mink, is also found in Asia.  

In less than twenty-four hours, a team of scientists led by Erik Karlsson, a virologist who now directs the Institute Pasteur du Cambodge, Cambodia’s chapter of the international French nonprofit that studies diseases and vaccines, sequenced the virus. It was an indigenous strain.  

“When we revealed the data, there was a sense that people were relieved,” Karlsson added. “Alright, this virus has been endemic in Southeast Asia for more than 10 years, the scientific community understood.”  


The detected viral strain has been circulating since 2013, according to Karlsson, and researchers are familiar with its characteristics. “Each time it enters a human or mammal, there’s still a risk it may mutate or become a strain that could spread from person to person,” he adds, “which is why monitoring and sequencing are so crucial—the faster, the better.”  

“The cost of any outbreak increases exponentially with each passing second,” he explained. The rapidity with which Karlsson’s team sequenced the virus in Cambodia exemplifies the lasting influence of pandemic-era investments in surveillance and genomic sequencing, particularly in regions of the world that had previously struggled to access the most modern technologies.  

“Today, instead of spending $150,000 on a sequencer, we can purchase one for about $1,000, and with that, we can sequence the entire genome of an influenza virus for $100 in less than 24 hours,” Karlsson explained.  

The sequencing results have been made accessible to the scientific community at large, for example, through the real-time tracking hosted by Louise Moncla, a professor of pathobiology at the University of Pennsylvania. This is the type of scientific collaboration that led to the development of the covid vaccine, while Karlsson emphasizes that it is in no way a novel strategy; rather, it is one that, in the wake of the covid outbreak, is increasingly recognized as indispensable.  

“It takes a community. You require individuals in the field to conduct interviews. You need individuals to collect samples and analyze them in the laboratory. You need individuals who are constructing these databases for sharing, as well as worldwide infrastructure networks, in order to disseminate these infections,” he explained.  

Beyond the surveillance aspect, sequencing is necessary to make vaccine candidates readily available, as occurred with covid and annually with the seasonal flu. All recognized strains of avian influenza have vaccine candidates; therefore, it would be extremely simple to produce the real vaccine if needed.

The United States also maintains a supply of avian flu vaccinations manufactured by the Australian biotechnology firm CSL Sequerus. Many nations have also long advocated for the United Nations to establish its own supply of avian influenza vaccination. 



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