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Virologist who was first to share COVID genome is shut out of lab in China

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The first person to publicly release the genome sequence of the virus that causes COVID-19 — virologist Zhang Yongzhen — appears to have resolved a public dispute with the Shanghai Public Health Clinical Center (SPHCC), Fudan University, that erupted last week.

Zhang had been photographed camping outside his laboratory since Sunday, after the SPHCC closed the lab.

The SPHCC did not respond to Nature’s request to comment but has released public statements saying the laboratory was one of several that needed renovations — and that it provided Zhang’s team with an alternative space.

According to social media posts on Zhang’s personal Weibo account, the institute gave the research team two days to leave but the SPHCC did not initially specify where they should relocate. Later, Zhang said officials told his team to move to a lab that did not have the necessary biosafety conditions to store their samples, which contain unknown pathogens. Zhang’s lab is a biosafety level 3 laboratory.

Zhang said he had been sleeping outside his laboratory since Sunday night, even in the rain. The social media posts include photos of him lying under blankets.

Zhang told Nature on Monday that his situation was “terrible”.

“You don’t know what I have experienced,” he said, but declined to comment further.

According to the social media account of Chen Yanmei, a virologist at the SPHCC, and a member of Zhang’s team, their students’ incomplete experiments were now “impossible to save”. Chen said she was also camping out, inside the lab. Chen also declined to be interviewed by Nature.

But by late Tuesday night, Zhang said in a post that a tentative agreement had been reached with the SPHCC to resume normal research activity in the laboratory. The post states that Zhang will work with the centre to relocate the laboratory and restart research.

Virus sequence

In 2020, Zhang was the first scientist — together with Edward Holmes, a virologist at the University of Sydney in Australia — to share the genome of SARS-CoV-2 with the world on the website virological.org. That act is widely credited as a key factor enabling the swift development of vaccines against COVID-19.

Since 2020, Zhang has received international acclaim. That year, Zhang featured in Nature’s 10 — an annual list of people behind key developments in science, and in 2022 he was awarded the Mohammad bin Rashid Al Maktoum Knowledge Award, which carries a US$1 million bursary.

But Holmes, a long-time collaborator of Zhang’s, says that since 2020, Zhang’s research output has dwindled. Before 2020, Zhang had an extensive research network and would collect samples of animals and people to study viral evolution, says Holmes. But since 2020, Zhang’s work has largely involved analysing previously collected samples and Holmes’s own collaboration with Zhang is less prolific. “He drove that collaboration but there is nothing to collaborate on now; he hasn’t been able to get any data,” says Holmes. “All I can do is offer support from afar.”

According to the Dimensions database, Zhang co-authored 5 research articles in 2018, 9 in 2019 and 18 in 2020. But that growing publication rate dropped to 3 in 2021 and 4 in 2022. Zhang co-authored 6 articles in 2023, none of which contained original data.

Holmes believes the lab closure is part of an effort to sideline Zhang for unauthorized sharing of data. “It is heartbreaking to watch,” he says. “It is unfathomable to me to have a scientist of that calibre sleeping outside his lab.”

International star

But Yanzhong Huang, a specialist in Chinese health policy at the Council on Foreign Relations in New York City, says the true nature of the dispute and protest are “shrouded in mystery”.

Fan Xiaohong, a physician who heads the SPHCC told reporters for Chinese newspaper Southern Weekly that Zhang’s contract had expired, but he had refused to leave. A post on Zhang’s social media said that although his own contract with SPHCC had formally ended in 2023, members of his team had renewed their contracts with the hospital, and the laboratory is still owed funding.

Even without clarity on the details of the dispute, Dali Yang, a researcher who studies politics in China at the University of Chicago, says it’s concerning that Zhang is sleeping outside his lab. “Many people who know about him are aghast because he is truly an international star,” says Yang.

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Ancient malaria genome from Roman skeleton hints at disease’s history

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A coloured transmission electron micrograph showing a blue and green cell with several organelles inside a red cell.

The malaria parasite Plasmodium falciparum infecting a red blood cell.Credit: Dennis Kunkel Microscopy/Science Photo Library

Researchers have sequenced the mitochondrial genome of the deadliest form of malaria from an ancient Roman skeleton. They say the results could help to untangle the history of the disease in Europe.

It’s difficult to find signs of malaria in ancient human remains, and DNA from the malaria-causing parasite Plasmodium rarely shows up in them. As a result, there had never been a complete genomic sequence of the deadliest species, Plasmodium falciparum, from before the twentieth century — until now. “P. falciparum was eliminated in Europe a half century ago, and genetic data from European parasites — ancient or recent — has been an elusive piece in the puzzle of understanding how humans have moved parasites around the globe,” says Daniel Neafsey, who studies the genomics of malaria parasites and mosquito vectors at the Harvard T.H. Chan School of Public Health in Boston, Massachusetts.

Malaria has long been a leading cause of human deaths. “With the development of treatments such as quinine in the last hundreds of years, it seems clear [humans and malaria] are co-evolving,” says Carles Lalueza Fox, a palaeogenomicist at the Institute of Evolutionary Biology in Barcelona, Spain. “Discovering the genomes of the ancient, pre-quinine plasmodia will likely reveal information about how they have adapted to the different anti-malarial drugs.”

Ancient pathogen

There are five malaria-causing species of Plasmodium, which are thought to have arisen in Africa between 50,000 and 60,000 years ago, and then spread worldwide. Most researchers agree that they reached Europe at least 2,000 years ago, by the time of the Roman Empire.

Plasmodium falciparum “has significantly impacted human history and evolution”, says Neafsey. “So, that makes it particularly important to discover how long different societies have had to deal with [it], and how human migration and trade activities spread it.”

Researchers can glean valuable information about the origin, evolution and virulence of the parasite from DNA extracted from the ancient remains of infected people. But it is difficult to know where to look: it is not always obvious whether a person was infected with Plasmodium, and whether DNA can be recovered depends on how well it has been preserved.

In a preprint posted on the server bioRxiv1, a team of researchers led by a group at the University of Vienna identified the first complete mitochondrial genome sequence of P. falciparum from the bones of a Roman who lived in Italy in the second century ad, known as Velia-186.

Plasmodium falciparum had been detected in Velia-186 in a previous study2. The authors of the latest preprint extracted the parasite’s DNA from the body’s teeth, and were able to identify 5,458 pieces of unique genetic information that they combined to get a sequence covering 99.1% of the mitochondrial genome. They also used software to compare the genome with modern samples, and found that the Velia-186 sequence is closely related to a group of present-day strains found in India.

Carried by migration

The researchers say their findings support a hypothesis that P. falciparum spread to Europe from Asia around at least 2,000 years ago3. The Indian strains “were already present in Europe [then]; thus, a potential arrival with globalization episodes such as the Hellenistic period — when it is first described by Greeks — seems plausible”, says Lalueza Fox.

Neafsey says the work is a “technical tour de force” and an interesting addition to the limited field of ancient malaria genomics. But he adds that the results should be interpreted with caution because there are only a few samples, and points out that a genome sequence from DNA in the parasite’s cell nuclei, rather than its mitochondria, “might indicate a more complex story of parasite movement among ancient human populations”.

Lalueza Fox suggests exploring other potential sources of Plasmodium DNA, such as old bones, antique medical equipment and even mosquito specimens in museums. “The integration of genetic data from these heterogeneous sources will provide a nuanced view of this disease,” he says. “It would be interesting to see what lessons we can learn from the past on the strains and dispersals of this pathogen.”

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