COVID-19: Genetic network analysis provides 'snapshot' of pandemic origins

9-Apr-2020 2:30 PM EDT, by University of Cambridge

Newswise — Researchers from Cambridge, UK, and Germany have reconstructed the early "evolutionary paths" of COVID-19 in humans - as infection spread from Wuhan out to Europe and North America - using genetic network techniques.

By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.

"There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously," said geneticist Dr Peter Forster, lead author from the University of Cambridge.

"These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is the first time they have been used to trace the infection routes of a coronavirus like COVID-19."

The team used data from virus genomes sampled from across the world between 24 December 2019 and 4 March 2020. The research revealed three distinct "variants" of COVID-19, consisting of clusters of closely related lineages, which they label 'A', 'B' and 'C'.

Forster and colleagues found that the closest type of COVID-19 to the one discovered in bats - type 'A', the "original human virus genome" - was present in Wuhan, but surprisingly was not the city's predominant virus type.

Mutated versions of 'A' were seen in Americans reported to have lived in Wuhan, and a large number of A-type viruses were found in patients from the US and Australia.

Wuhan's major virus type, 'B', was prevalent in patients from across East Asia. However, the variant didn't travel much beyond the region without further mutations - implying a "founder event" in Wuhan, or "resistance" against this type of COVID-19 outside East Asia, say researchers.

The 'C' variant is the major European type, found in early patients from France, Italy, Sweden and England. It is absent from the study's Chinese mainland sample, but seen in Singapore, Hong Kong and South Korea.

The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on January 27, and that another early Italian infection route was related to a "Singapore cluster".

Importantly, the researchers say that their genetic networking techniques accurately traced established infection routes: the mutations and viral lineages joined the dots between known cases.

As such, the scientists argue that these "phylogenetic" methods could be applied to the very latest coronavirus genome sequencing to help predict future global hot spots of disease transmission and surge.

"Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources, which can then be quarantined to contain further spread of the disease worldwide," said Forster, a fellow of the McDonald Institute of Archaeological Research at Cambridge, as well as the University's Institute of Continuing Education.

The findings are published today in the journal Proceedings of the National Academy of Sciences (PNAS). The software used in the study, as well as classifications for over 1,000 coronavirus genomes and counting, is available free at http://www.fluxus-technology.com.

Variant 'A', most closely related to the virus found in both bats and pangolins, is described as "the root of the outbreak" by researchers. Type 'B' is derived from 'A', separated by two mutations, then 'C' is in turn a "daughter" of 'B'.

Researchers say the localisation of the 'B' variant to East Asia could result from a "founder effect": a genetic bottleneck that occurs when, in the case of a virus, a new type is established from a small, isolated group of infections.

Forster argues that there is another explanation worth considering. "The Wuhan B-type virus could be immunologically or environmentally adapted to a large section of the East Asian population. It may need to mutate to overcome resistance outside East Asia. We seem to see a slower mutation rate in East Asia than elsewhere, in this initial phase."

He added: "The viral network we have detailed is a snapshot of the early stages of an epidemic, before the evolutionary paths of COVID-19 become obscured by vast numbers of mutations. It's like catching an incipient supernova in the act."

Since today's PNAS study was conducted, the research team has extended its analysis to 1,001 viral genomes. While yet to be peer-reviewed, Forster says the latest work suggests that the first infection and spread among humans of COVID-19 occurred between mid-September and early December.

The phylogenetic network methods used by researchers - allowing the visualisation of hundreds of evolutionary trees simultaneously in one simple graph - were pioneered in New Zealand in 1979, then developed by German mathematicians in the 1990s.

These techniques came to the attention of archaeologist Professor Colin Renfrew, a co-author of the new PNAS study, in 1998. Renfrew went on to establish one of the first archaeogenetics research groups in the world at the University of Cambridge.

###




Filters close

Showing results

110 of 2528
Released: 10-Jul-2020 3:05 PM EDT
Simple blood test can predict severity of COVID-19 for some patients
University of Texas Health Science Center at Houston

An early prognosis factor that could be a key to determining who will suffer greater effects from COVID-19, and help clinicians better prepare for these patients, may have been uncovered by researchers at The University of Texas Health Science Center at Houston (UTHealth). Results of the findings were published today in the International Journal of Laboratory Hematology.

Released: 10-Jul-2020 12:50 PM EDT
Genetic ‘fingerprints’ of first COVID-19 cases help manage pandemic
University of Sydney

A new study published in the world-leading journal Nature Medicine, reveals how genomic sequencing and mathematical modelling gave important insights into the ‘parentage’ of cases and likely spread of the disease in New South Wales.

Released: 10-Jul-2020 12:35 PM EDT
Our itch to share helps spread COVID-19 misinformation
Massachusetts Institute of Technology (MIT)

To stay current about the Covid-19 pandemic, people need to process health information when they read the news. Inevitably, that means people will be exposed to health misinformation, too, in the form of false content, often found online, about the illness.

Newswise: Pandemic Inspires Framework for Enhanced Care in Nursing Homes
Released: 10-Jul-2020 12:25 PM EDT
Pandemic Inspires Framework for Enhanced Care in Nursing Homes
University of Pennsylvania School of Nursing

As of May 2020, nursing home residents account for a staggering one-third of the more than 80,000 deaths due to COVID-19 in the U.S. This pandemic has resulted in unprecedented threats—like reduced access to resources needed to contain and eliminate the spread of the virus—to achieving and sustaining care quality even in the best nursing homes. Active engagement of nursing home leaders in developing solutions responsive to the unprecedented threats to quality standards of care delivery is required.

Newswise: General Electric Healthcare Chooses UH to Clinically 
Evaluate First-of-its-kind Imaging System
Released: 10-Jul-2020 12:15 PM EDT
General Electric Healthcare Chooses UH to Clinically Evaluate First-of-its-kind Imaging System
University Hospitals Cleveland Medical Center

University Hospitals Cleveland Medical Center physicians completed evaluation for the GE Healthcare Critical Care Suite, and the technology is now in daily clinical practice – flagging between seven to 15 collapsed lungs per day within the hospital. No one on the team could have predicted the onset of the COVID-19 pandemic, but this technology and future research with GEHC may enhance the capability to improve care for COVID-19 patients in the ICU. Critical Care Suite is now assisting in COVID and non-COVID patient care as the AMX 240 travels to intensive care units within the hospital.

Released: 10-Jul-2020 11:50 AM EDT
COVID-19 Can Be Transmitted in the Womb, Reports Pediatric Infectious Disease Journal
Wolters Kluwer Health: Lippincott Williams and Wilkins

A baby girl in Texas – born prematurely to a mother with COVID-19 – is the strongest evidence to date that intrauterine (in the womb) transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can occur, reports The Pediatric Infectious Disease Journal, the official journal of The European Society for Paediatric Infectious Diseases. The journal is published in the Lippincott portfolio by Wolters Kluwer.

Released: 10-Jul-2020 9:45 AM EDT
How COVID-19 Shifted Inpatient Imaging Utilization
Harvey L. Neiman Health Policy Institute

As medical resources shifted away from elective and non-urgent procedures toward emergent and critical care of COVID-19 patients, departments were forced to reconfigure their personnel and resources. In particular, many Radiology practices rescheduled non-urgent and routine imaging according to recommendations from the American College of Radiology (ACR). This new Harvey L. Neiman Health Policy Institute study, published online in the Journal of American College of Radiology (JACR), evaluates the change in the inpatient imaging volumes and composition mix during the COVID-19 pandemic within a large healthcare system.

access_time Embargo lifts in 2 days
Embargo will expire: 12-Jul-2020 7:00 PM EDT Released to reporters: 10-Jul-2020 9:00 AM EDT

A reporter's PressPass is required to access this story until the embargo expires on 12-Jul-2020 7:00 PM EDT The Newswise PressPass gives verified journalists access to embargoed stories. Please log in to complete a presspass application. If you have not yet registered, please Register. When you fill out the registration form, please identify yourself as a reporter in order to advance to the presspass application form.

Released: 10-Jul-2020 9:00 AM EDT
Team is first in Texas to investigate convalescent plasma for prevention of COVID-19 onset and progression
University of Texas Health Science Center at Houston

A research team is the first in Texas to investigate whether plasma from COVID-19 survivors can be used in outpatient settings to prevent the onset and progression of the virus in two new clinical trials at UTHealth.


Showing results

110 of 2528

close
0.82248