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Daily briefing: Hard numbers reveal risk of death from coronavirus

Age is the biggest predictor of who will die from COVID-19. Plus: A checklist for reproducible code and Africa is declared free from wild polio.

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NICEF health consultant Hadiza Waya tries to immunise a child during vaccination campaign against polio, Nigeria.

A health worker immunizes a child during a polio vaccination campaign in northwest Nigeria in 2017.Credit: Pius Utomi Ekpei/AFP/Getty

Africa declared free from wild polio

The World Health Organization has declared Africa free of wild polio. The continent’s last case of wild polio was recorded four years ago in northeast Nigeria. There are now just just two countries on Earth where the virus remains endemic: Afghanistan and Pakistan. Africa’s fight against polio isn’t over: in rare cases, infections can be caused by the oral polio vaccine. These vaccine-derived polio strains can spread in areas where many children have not been immunized, so vaccination must continue.

Nature | 3 min read

Anti-dengue mosquito trial success

Cases of dengue fever plummeted by a “staggering” 77% after researchers released mosquitoes that were modified to be resistant to the virus. These mosquitoes carry dengue-blocking Wolbachia bacteria, which then spread through local mosquito populations. Wolbachia-carrying mosquitoes were released over a six-month period in randomly designated parts of Yogyakarta in Indonesia, starting in 2016. The results have been reported in press releases, and the full data are yet to be published.

Nature | 6 min read

Reference: University of California Berkeley press release

COVID-19 coronavirus update

Medical staff wearing protective clothing and a ventilator looking at a computer monitor in a hospital intensive care unit

A health-care worker checks data on a computer before treating a person infected with COVID-19 in April at the Veteran Affairs Medical Center in New York City.Credit: Robert Nickelsberg/Getty

Why the United States is having a data crisis

Political meddling, disorganization and years of neglect of the management of public-health data mean that the United States is flying blind when it comes to coronavirus. Compared with leading countries such as Korea, Singapore and New Zealand, the country offers vanishingly few details on how the disease is spreading, even as lockdown measures ease. Scientists are frustrated that the pandemic has become so politically charged that they can’t get the data they need to help authorities to save lives.

Nature | 8 min read

Monkey shortage hampers US drug efforts

Testing in monkeys is a crucial final step before starting human trials of COVID-19 drugs and vaccines, but in the United States the well has run dry. Testing of these drugs and vaccines has increased global demand, and China, which supplied 60% of the nearly 35,000 monkeys imported for research in the United States last year, stopped exporting them. US researchers are left vying for permission to do monkey testing at primate research centers run by the National Institutes of Health, but most are turned down. “I have to tell them, ‘I’m sorry, we are not allowed to start your research,’” says infectious-disease researcher Koen Van Rompay, who runs one of the centers.

The Atlantic | 8 minutes

Age is the biggest predictor of who will die

Four studies (three of which have not yet been peer-reviewed) from Spain, England, Italy and Geneva, Switzerland, pinpoint the infection fatality ratio (IFR), which is the proportion of people infected with the virus, including those who didn’t get tested or show symptoms, who will die as a result. All found that the IFR was close to zero in younger people and rose steeply from around the age of 50. For every 1,000 people in their mid-seventies or older who are infected, around 116 will die. Men are also almost twice as likely as women to die from the disease.

Nature | 6 min read

Read more: Scientific American digs in to why age and sex raise the risk of getting very ill — as well as the influence of other factors, such as underlying conditions and social inequality. (14 min read, from 20 August)

Reference: medRxiv preprint 1, medRxiv preprint 2, medRxiv preprint 3 & The Lancet Infectious Diseases paper

Source: Ref. 4; Ref. 1; Nature analysis based on Ref. 2

Notable quotable

“There is a fascination with death, but COVID-19 appears to cause a substantial amount of long-term illness.”

Although fatality estimates are important for understanding the risk of viral spread to people in different age groups, they don’t tell the full story of the toll COVID-19 takes, says infectious-disease researcher Marm Kilpatrick. (Nature)

Features & opinion

The market is killing new antibiotics

Antibiotics are one of the world’s most desperately needed classes of drug. Yet many of the companies developing them are struggling to survive. In the last 2 years, the companies that made 5 of the 15 antibiotics approved by the US Food and Drug Administration since 2010 have declared bankruptcy or put themselves up for sale. Nature investigates the bitter paradox that is hobbling efforts to solve one of humanity’s greatest challenges.

Nature | 13 min read

Would your ten-year-old code still run?

The Ten Years Reproducibility Challenge dares scientists to find and re-execute old code, to reproduce computationally driven papers that they had published ten or more years earlier. Extinct hardware and dead programming languages are among the hurdles for researchers taking it on in a bid to illuminate how code can be made more resilient to change. “Ten years is a very, very, very, very long time in the software world,” says Victoria Stodden, who studies computational reproducibility. “Roughly equivalent in the software world to infinity”.

Nature | 12 min read

Code reproducibility tips

Although it’s impossible to guarantee computational reproducibility over time, these strategies can maximize your chances.

Code Workflows based on point-and-click interfaces, such as Excel, are not reproducible. Enshrine your computations and data manipulation in code.

Document Use comments, computational notebooks and README files to explain how your code works, and to define the expected parameters and the computational environment required.

Record Make a note of key parameters, such as the ‘seed’ values used to start a random-number generator. Such records allow you to reproduce runs, track down bugs and follow up on unexpected results.

Test Create a suite of test functions. Use positive and negative control data sets to ensure you get the expected results, and run those tests throughout development to squash bugs as they arise.

Guide Create a master script (for example, a ‘run.sh’ file) that downloads required data sets and variables, executes your workflow and provides an obvious entry point to the code.

Archive GitHub is a popular but impermanent online repository. Archiving services such as Zenodo, Figshare and Software Heritage promise long-term stability.

Track Use version-control tools such as Git to record your project’s history. Note which version you used to create each result.

Package Create ready-to-use computational environments using containerization tools (for example, Docker, Singularity), web services (Code Ocean, Gigantum, Binder) or virtual-environment managers (Conda).

Automate Use continuous-integration services (for example, Travis CI) to automatically test your code over time, and in various computational environments.

Simplify Avoid niche or hard-to-install third-party code libraries that can complicate reuse.

Verify Check your code’s portability by running it in a range of computing environments.

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Quote of the day

“Honestly, hope is not going to get us there… I’m just like, where’s the plan? Where’s the strategy? What are we going to do that we don’t need hope?”

Go beyond hope to save what we have left from climate change, says marine biologist Ayana Elizabeth Johnson, co-editor of a new book of essays about tackling the crisis. (The Washington Post)

It’s fantastic to be back at Briefing towers (my attic) after two rejuvenating weeks in the woods. In case you missed it, here’s one more chance to enjoy our very special ‘find the penguin’. Leif Penguinson, Passepartout, Heidi, Guino the pinguino and Bosworth the Buoyant are frolicking in Fantasy Canyon, Utah. Can you find all five penguins? When you’re ready — here’s the answer.

Flora Graham, senior editor, Nature Briefing

With contributions by Nicky Phillips and David Cyranoski

Updates & Corrections

  • Clarification 04 September 2020: The heading of the code reproducibility tips entry has been changed to reflect the general nature of the advice.

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