News Scan for Oct 13, 2020

News brief

$100 million next-generation genomics initiative begins in Africa

A group led by the African Commission through the Africa Centres for Disease Control and Prevention (Africa CDC), yesterday launched the Africa Pathogen Genomics Initiative (Africa PGI), a $100 million, 4-year partnership to expand and integrate next-generation genomic sequencing (NGS) capabilities across the continent to improve health surveillance and lab networks and better tackle antimicrobial resistance (AMR).

"The Africa PGI will help Member States build their capacities to operate strong surveillance and laboratory networks supported by advanced technologies to reduce the burden of disease and respond to outbreaks quickly and effectively," Africa CDC Director John Nkengasong, PhD, MS said in a press release.

While some institutions in Africa already have access to NGS technology, the necessary finances, training, and database infrastructure has not been in place for widespread use. To address this, critical partners in the effort include Illumina and Oxford Nanopore, which are providing NGS machines and training; the Bill and Melinda Gates Foundation and the US Centers for Disease Control and Prevention, which are providing funding and technological assistance such as the Advanced Molecular Detection program; and Microsoft, which will be working with Africa PGI on its digital architecture and more.

Africa PGI hopes to create systems to better prevent, track, and control the approximately 140 infectious disease outbreaks that the continent sees each year as well as problems due to AMR. Besides creating a real-time, shared database, the initiative will also establish a training program for pathogen genomics and connect participants with international research opportunities.
Oct 12 Africa CDC press release

French Guiana reports first Oropouche fever outbreak

The World Health Organization (WHO) today detailed the first detection of Oropouche fever, a vector-borne illness that has symptoms similar to dengue and similar diseases—in French Guiana, the latest country in the Americas to report the virus.

In a statement, the WHO said French Guiana health officials identified seven lab-confirmed cases in Saul, following a probe into a number of dengue-type infections in the remote village that is surrounded by the Amazon rain forest.

The area is a popular hiking destination, but the population is currently low due to pandemic-related travel restrictions, and the attack rate appears to be as high as 70%. Of 37 suspected cases, most involved men, with a median age of 36 years.

Public health investigations are under way, including a mission to explore vector sources, which could include midges or mosquito species known to spread the virus in the Americas.

Earlier Oropouche outbreaks have been reported in both rural and urban settings in a number of other countries in the Americas region, including Brazil and Peru.
Oct 13 WHO statement

COVID-19 Scan for Oct 13, 2020

News brief

COVID-19 passed from humans to large cats at Bronx Zoo, study suggests

The first SARS-CoV-2 infections in US animals were confirmed in large cats at the Bronx Zoo in March during the height of the local COVID-19 outbreak. An American Society for Microbiology study today details the genomic characteristics of viruses that infected zookeepers, four tigers, and three African lions, supporting a human-to-animal transmission pathway.

SARS-CoV-2—the virus that causes COVID-19—has a suspected zoonotic origin, meaning it arose in animals. Genome sequencing of SARS-CoV-2 shows a close relationship with bat coronaviruses. Natural SARS-CoV-2 infections in animals have been reported in dogs, cats, and farmed mink, and in ferrets and fruit bats in the lab.

"Identifying susceptible animal species, reservoirs, and transmission routes between species is a topic of global scientific and public interest," the authors wrote.

The study examined respiratory and fecal virus samples from two Malayan tigers, two Amur tigers, three African lions, and respiratory samples from animal keepers at the Wildlife Conservation Society's Bronx Zoo in New York City. The study authors found close evolutionary relationships between human and cat viral strains, with genetically identical viral strains for one tiger and keeper.

The concurrent community outbreak, similarities in viral sequence, and lack of new animal introductions during the study period support a human-to-animal transmission pathway, but the mechanism of transmission is yet unclear. The study authors call for further transmission mechanism research as well as more conservative protocols in settings with close human-animal contact, including the use of personal protective equipment.

"As long as anthropogenic development and population growth bring humans and wildlife into increasing proximity, legal and illegal harvesting persists, and consumption of wildlife and wildlife products exists, there will be continued and significant risk of pandemic viral emergence with devastating global impact on human and animal health, economies, food security, and biodiversity," the authors warn.
Oct 13 mBio study

US pandemic costs may total $16 trillion—or 90% of annual GNP

A JAMA commentary yesterday by Harvard University experts estimated US COVID-19–related economic costs at more than $16 trillion, or about 90% of the annual gross domestic product over the course of the pandemic.

Economic impacts represent a loss of nearly $200,000 for a family of four due to lost income and shorter, less healthy lives. The experts analyzed mortality, morbidity, mental health impacts, and direct economic losses, assuming that the pandemic will be contained by fall 2021. Unemployment insurance claims total more than 60 million to date. Lost output due to unemployment suggests a loss of $7.6 trillion over the next decade.

Deaths and reduced quality of life represent another significant COVID-19–related economic loss. With approximately 5,000 US deaths per week, projections point to another 250,000 deaths in the next year in addition to increased deaths from other causes, totaling 625,000 cumulative deaths and $4.4 trillion in expenses.

Significant long-term complications occur in roughly a third of those who survive severe or critical disease. With seven times as many survivors as deaths, long-term impairment might affect twice as many people as the number of deaths. Respiratory problems similar to moderate chronic obstructive pulmonary disease—estimated to reduce quality of life by 25% to 35%—may be characteristic of this group, leading to an estimated $2.6 trillion loss through 2021.

Mental health impacts are also consequential, with 40% of US adults reporting symptoms of anxiety and depression, compared with a rate of 11% in 2019. Projections suggest an additional 80 million individuals with mental health conditions and total losses of about $1.6 trillion.

The authors highlight the potential for pandemic mitigation policies to dramatically reduce economic costs, especially wide-scale population testing, contact tracing, and isolation. A $6 million investment to test 100,000 individuals shows a projected savings of $176 million, without considering probable reduction in future cases.

"The immense financial loss from COVID-19 suggests a fundamental rethinking of government's role in pandemic preparation," the authors wrote. "As the nation struggles to recover from COVID-19, investments that are made in testing, contact tracing, and isolation should be established permanently and not dismantled when the concerns about COVID-19 begin to recede."
Oct 12 JAMA commentary