Covid-19 came to Cambodia a year ago, on January 23rd, when a Chinese national flew in from Wuhan, the city where the disease was first discovered, and soon fell ill with a fever. A PCR test to detect the genetic material of SARS-CoV-2, the coronavirus that causes Covid-19, turned out positive. With this news, the disease had officially pierced another nation’s borders.
For Cambodia, a developing country with a rudimentary health system and several direct flights from Wuhan, the new disease appeared to pose a particularly high risk.
Dr. Jessica Manning, a public health researcher at the National Institute for Allergies and Infectious Diseases who has worked in Cambodia for years, also saw an opportunity: she helped the country join the global effort to find new diseases.
Dr. Manning passed nasal and oral samples from the patient through a genetic sequencer, a device that reads the letters that make up an organism’s genome. The sequencer was recently accepted into her laboratory in the parasitology department of the Cambodian government in Phnom Penh. “I couldn’t wait for the sequences to come from the sequencer,” recalled Dr. Manning. “It was sheer dizzying excitement.”
The sequencer uploaded the raw data to an online software package called IDseq, which can be used to assemble the genomes in the sample and compare them to other known organisms. The system confirmed without any advice from Dr. Manning’s group said the sample might contain that it contained a virus with a genome practically identical to that of the new coronavirus identified in Wuhan. Of the approximately 30,000 letters in the virus’ genome, only one differed between the two sequences.
In those early days of Covid-19, researchers did not know how accurate the PCR tests were or whether the virus was creating new strains with potentially different properties. The Cambodian report confirmed the accuracy of the PCR test and found that there were only minor changes in the sequences. The virus didn’t seem to mutate significantly – an indication that the disease would be easier to test, treat, and vaccinate.
For Dr. Manning, the exercise was proof that even a small research outpost in developing countries could successfully identify new or unexpected pathogens and extract vital information about them from their genome. As such, your lab and others who like it could serve as an early warning system for the next potential pandemic.
Open the black box
The 40-year-old Dr. Manning began her career by studying not new but known diseases, which particularly affected the developing world.
In 2008, while studying medicine at Emory University, she went to Mali to study and treat malaria as part of a project at the University of Bamako. “I lived in the bush for six months collecting samples,” she said. “Serious malaria cases come at night that no one has told me. I haven’t slept really well in months. It was terrible because a lot of the kids would die just as we were judging them, 10 seconds inside the doorway entrance. “
The first time she remembered giving a young, critically ill patient a new antimalarial drug called artesunate. “She was almost dead and two days later she was fine,” said Dr. Manning. “It was like Lazarus.” Dr. Manning holds a photo of himself with the patient, a girl named Fatoumata, in her office.
She liked the way the work combined research and treatment of patients. “It brings this whole new dimension when you are by the bed and on the bench,” she said, referring to the laboratory. “When you work like this, all your senses are attacked. It’s overwhelming. But that’s where we should work. “
Following public health projects in Haiti, Malawi and Rwanda, Dr. Manning received a master’s degree in epidemiology in 2014 and then took a position as a medical researcher at the National Institute for Allergies and Infectious Diseases under the direction of Dr. Anthony S to Fauci.
At the institute, she was trying to figure out how to develop a universal mosquito vaccine that would protect people from the many diseases that mosquitoes transmit. The vaccine would trigger an immune response in the mosquito’s saliva and prevent pathogens in the mosquito from infecting the person bitten. Dr. Manning started a survey in Cambodia to study how immune markers change in humans when exposed to mosquito saliva and related diseases. So far, the project has found five molecules that could help develop a vaccine against mosquito saliva.
The survey also found that many diseases in Cambodia remained a mystery. “Diagnosing is difficult, and some errors are more difficult to diagnose than others,” said Dr. Manning. “We tend to focus on the big ones like malaria. We use malaria as a trash can diagnosis when a patient is very feverish. “When doctors aren’t sure what is going on, they often treat patients with a bag of antibiotics and anti-malarial drugs.
In 2018, Dr. Manning, of the Bill and Melinda Gates Foundation, of a global major challenge that gave researchers grants to use genomics to learn more about infectious diseases in developing countries. Dr. Manning saw it as a way to “find out what is going on in this black box in Cambodia” – to find out exactly which pathogens have caused the many unexplained diseases.
Apr. 16, 2021, 5:42 pm ET
In 2019, Dr. Manning received one of the scholarships and soon flew with three colleagues to the Chan Zuckerberg Biohub, a research center in San Francisco, where they learned how to use tools that can be used to open the black box.
“Like a giant puzzle”
To identify unknown pathogens, Dr. Manning’s project uses an approach known as metagenomic sequencing. More traditional techniques of genome diagnosis, such as the PCR tests commonly used to detect coronavirus, look for the characteristic genetic sequence of an individual pathogen. These tests are accurate, quick, and relatively cheap – but they can only find a pathogen that you already know you are looking for.
Instead, metagenomic sequencing reads all of the genomic material in a sample and identifies all of the organisms present: helpful bacteria, common pathogens, microbes that have never been discovered before. “Metagenomics can show what we don’t know what we don’t know,” said Dr. Manning, paraphrasing a popular quote from former US Secretary of Defense Donald H. Rumsfeld.
However, identifying the unknown unknowns is complicated. Common sequencing machines break down DNA and RNA molecules into short segments, each with tens to hundreds of genetic building blocks, and read the block sequences in each. This creates billions of short sequences with no information on how they were originally arranged.
To understand all of this data, Dr. Mannings Labor IDseq, a free, online, open source software package that reverse engineered how any short segments can fit together to form any number of genomes and compares them to known genomes in public databases.
“It’s like a giant puzzle,” said Joseph DeRisi, a biochemist at the University of California at San Francisco and lead developer of IDseq. “Where the edges of the pieces match, you can snap them together and put together a picture of the genome.” This analysis is computationally intensive and is based on hundreds or thousands of powerful processors. However, IDseq runs on servers in the cloud, so researchers in developing countries can perform the analysis remotely for free.
After completing their training in metagenomics, Dr. Manning and her colleagues returned to Cambodia and started a sequencing project at a hospital in the city of Chbar Mon. Now when patients come to the hospital with an unexplained fever, the workers take blood samples and send them to Dr. Manning at the Cambodian government’s parasitology department in Phnom Penh, where researchers are performing metagenomic analysis to find out what exactly is making the patient sick.
One such patient appeared in May. Phoun Phalla, 13, had had sporadic fever, pain, and chills for the last eight months, and no one was entirely sure what was wrong with her.
After Phalla’s parents gave her permission to take part in the metagenomics study, medical staff drew her blood and had it delivered by car to the laboratory in Phnom Penh. There the technicians ran their samples through the sequencer and uploaded the data to IDseq.
The scan showed that phallas carried a form of malaria that could lurk in a patient’s liver and then flood into the bloodstream, causing fever, fatigue, and headaches. Standard anti-malarial drugs are of limited use. The parasite withdraws into the liver and flares up again weeks or months later.
With a firm diagnosis in hand, the hospital prescribed primaquine, one of the few drugs that can kill malaria parasites hidden in the liver. Phalla soon recovered, cooked and played with her young relatives. “The people here feel that they have been taken care of,” said her mother. “I’m very relieved that she is better.”
An early warning system
The search for novel pathogens in Southeast Asia has recently become an important part of the global effort to understand the Covid-19 pandemic and stop the next one before it occurs. In late January, a group of researchers, mostly at the Pasteur Institute in Cambodia, announced that they had used metagenomic sequencing to discover a coronavirus closely related to SARS-CoV-2 in a bat that was caught in Cambodia in 2010 Southeast Asia is an important area to consider in the ongoing search for the origins of SARS-CoV-2 and future coronavirus surveillance, ”the researchers write.
“This is what we were looking for and we found it,” said Dr. Veasna Duong, who led the study, told Nature in November. “It was exciting and surprising at the same time.”
This finding has caught the attention of researchers who want to better understand how and when viruses cross species.
Dr. In particular, Duong is studying places where humans come near fruit bats. “This type of exposure could allow the virus to mutate, which could lead to a pandemic,” he told the BBC last month.
Dr. Manning plans to work with Cambodia’s Communicable Disease Center and use metagenomics to monitor animals in two local wetland markets where pathogens could make the leap to humans. And her group recently expanded their fever monitoring project to two hospitals in Phnom Penh to provide early warning of the spread of new and undiagnosed diseases.
A small Cambodian laboratory on its own is unlikely to set off the next potential pandemic, but it has strong proof of concept for Dr. Manning’s approach delivered.
“The Cambodia-based project really showed the value of metagenomic sequencing,” said Dr. Farhad Imam, a genomics expert and program officer at the Gates Foundation who helped select the proposal from Dr. Manning for a grant.
“You can practically set up an early detection network for the next outbreak,” he said. “The faster we find out what it is, the faster we can build the tools to defeat it.”
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