NIH: Ebola Virus More Stable Than Previous Study Suggested

Credit CDC PHIL

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Last August, while Ebola was still accelerating in West Africa, we saw a study warning that the Ebola Virus Is Rapidly Evolving.  Specifically, that 99 Ebola viruses taken from 78 people from Sierra Leone during the month of June, and found that the virus is showing a marked propensity to accumulate `interhost and intrahost genetic variation’ as it passages through the population.

This led to media reports such as Ebola virus mutating rapidly as it spreads from Nature News, and  Ebola Is Rapidly Mutating As It Spreads Across West Africa via NPR’s Goats & Soda Blog.

As I noted at the time,  while scientists have the ability to sequence and compare these variant viruses, they don’t necessarily know what these individual mutations (or their aggregate) means to the virus, or how it might change its behavior.

 

Still, this study raised the level of concern over how this virus was evolving, and what changes in its behavior that might eventually bring.

 

Yesterday the NIH announced a far more reassuring survey of the Ebola virus’s evolution, which found a far less aggressive rate of change in the virus than previously announced.  First the NIH announcement, followed by a link to the study, then I’ll be back with a bit more.

 

NIH study finds no evidence of accelerated Ebola virus evolution in West Africa

 

The Ebola virus circulating in humans in West Africa is undergoing relatively few mutations, none of which suggest that it is becoming more severe or transmissible, according to a National Institutes of Health study in Science. The study compares virus sequencing data from samples taken from patients in Guinea (March 2014), Sierra Leone (June 2014) and Mali (November 2014).

 

“The Ebola virus in the ongoing West African outbreak appears to be stable—that is, it does not appear to be mutating more rapidly than viruses in previous Ebola outbreaks, and that is reassuring,” said Anthony S. Fauci, director of the National Institute of Allergy and Infectious Diseases (NIAID), part of NIH. “We look forward to additional information to validate this finding, because understanding and tracking Ebola virus evolution are critical to ensuring that our scientific and public health response keeps pace.”

Obtaining virus samples for analysis was challenging for researchers during the outbreak. The NIAID study published today relies on data from the Guinea and Sierra Leone cases as well as samples from two case clusters in Mali obtained from the International Center for Excellence in Research (ICER) located in Bamako. NIAID and the Malian government have been partners in the ICER since 2002. The Mali case clusters originated from people who became infected in Guinea and traveled to Mali, where they were diagnosed.

Today’s study, from NIAID’s Rocky Mountain Laboratories, finds that there appear to be no genetic changes that would increase the virulence or change the transmissibility of the circulating Ebola virus, and that despite extensive human-to-human transmission during the outbreak, the virus is not mutating at a rate beyond what is expected. Further, they say, based on their data it is unlikely that the types of genetic changes thus far observed would impair diagnostic measures, or affect the efficacy of candidate vaccines or potential virus-specific treatments.

As of March 11, the World Health Organization listed more than 24,000 confirmed, suspected or probable cases of Ebola virus disease in West Africa, with about 10,000 deaths.

 

Mutation rate and genotype variation of Ebola virus from Mali case sequences

T. Hoenen¹,*, D. Safronetz¹,*, A. Groseth¹,*,  K. R. Wollenberg²,*, O. A. Koita³,  B. Diarra³, I. S. Fall⁴, F. C. Haidara⁵, F. Diallo⁵, M. Sanogo³, Y. S. Sarro³, A. Kone³, A. C. G. Togo³, A. Traore⁵, M. Kodio⁵, A. Dosseh⁶, K. Rosenke¹, E. de Wit¹, F. Feldmann⁷, H. Ebihara¹, V. J. Munster¹, K. C. Zoon⁸, H. Feldmann¹,†,‡, S. Sow⁵,†,‡

 

The occurrence of Ebola virus (EBOV) in West Africa during 2013–2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (9.6 × 10^–4 substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns.

 

 

Last night Lisa Schnirring of CIDRAP News reviewed these findings, and looked at reports of two new Ebola cases in Liberia, an update on the American being treated at the NIH, and news on one of the candidate vaccines in:

 

Gene study finds no worrisome changes in Ebola virus

Lisa Schnirring | Staff Writer | CIDRAP News

A genetic analysis published today of Ebola virus samples over the course of the outbreak found few changes and noted that the virus is apparently more stable than a study back in August had suggested.

(Continue . .. )

Study: Ebola Virus Is Rapidly Evolving

Credit CDC PHIL

 

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One of the concerns we have when any zoonotic virus spills over into the human population is that over time, as it passes from one person to the next, it could pick up host adaptations – mutations – that could make the virus a greater threat over time.

 

In the laboratory, researchers will often conduct serial passage experiments (see Serial Passage Of H5N2 In Mice) to observe these evolutionary changes, and try to figure out what they mean.

 

Often, these genetic changes are of little or no effect, and can sometimes even be detrimental to the `biological fitness’ of the virus. Those that favor replication in the new found host, however, tend to carry on to produce more progeny, advancing their new lineage forward,  drowning out the earlier `wild type’ virus in the host.

 

A recent concern has been that Ebola - which up until now has never really spread in kind of long chains of human cases that we are seeing now – could better adapt to human physiology over time.

 

Today we’ve a study appearing in the Journal Science where scientists sequenced 99 Ebola viruses taken from 78 people from Sierra Leone during the month of June, and found that the virus is showing a marked propensity to accumulate `interhost and intrahost genetic variation’ as it passages through the population.

 

First a bit from the study, then I’ll be back with more.

Published Online August 28 2014

Science DOI: 10.1126/science.1259657

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

Stephen K. Gire¹,²,*, Augustine Goba³,*,†, Kristian G. Andersen¹,²,*,†, Rachel S. G. Sealfon²,⁴,*, Daniel J. Park²,*, Lansana Kanneh³, Simbirie Jalloh³, Mambu Momoh³,⁵, Mohamed Fullah³,⁵,‡, Gytis Dudas⁶, Shirlee Wohl¹,²,⁷, Lina M. Moses⁸, Nathan L. Yozwiak¹,², Sarah Winnicki¹,², Christian B. Matranga², Christine M. Malboeuf², James Qu², Adrianne D. Gladden², Stephen F. Schaffner¹,², Xiao Yang², Pan-Pan Jiang¹,², Mahan Nekoui¹,², Andres Colubri¹, Moinya Ruth Coomber³, Mbalu Fonnie³,‡, Alex Moigboi³,‡, Michael Gbakie³, Fatima K. Kamara³, Veronica Tucker³, Edwin Konuwa³, Sidiki Saffa³, Josephine Sellu³, Abdul Azziz Jalloh³, Alice Kovoma³,‡, James Koninga³, Ibrahim Mustapha³, Kandeh Kargbo³, Momoh Foday³, Mohamed Yillah³, Franklyn Kanneh³, Willie Robert³, James L. B. Massally³, Sinéad B. Chapman², James Bochicchio², Cheryl Murphy², Chad Nusbaum², Sarah Young², Bruce W. Birren², Donald S. Grant³, John S. Scheiffelin⁸, Eric S. Lander²,⁷,⁹, Christian Happi¹⁰, Sahr M. Gevao¹¹, Andreas Gnirke²,§, Andrew Rambaut⁶,¹²,¹³,§, Robert F. Garry⁸,§, S. Humarr Khan³,‡§, Pardis C. Sabeti¹,²,†§

 

In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2,000x coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from Middle African lineages ~2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Since many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.

• In Depth Infectious Disease Genomes reveal start of Ebola outbreak

  • Gretchen Vogel
  Science 29 August 2014: 989-990.
  • Summary
  • Full Text
  • Full Text (PDF)

These researchers found that the virus had evolved into three distinct lineages in Sierra Leone during the month of June (one of which appears to have died out), along with accumulating scores of amino acid changes to its genome.

 

It should be noted that while scientists have the ability to sequence and compare these variant viruses, they don’t necessarily know what these individual mutations (or their aggregate) means to the virus, or how it might change its behavior. 

 

Based on the location of some these changes, there are concerns that the PCR primers currently used to detect it patients may need adjusting, and that some of the antiviral drugs being developed could be impacted as well. 

 

And while it is theoretically possible that changes to the genome could affect the transmissibility of the virus, we haven’t seen any evidence of that happening.

 

Unknown at this time are what genetic changes might be occurring in the virus in Liberia and Guinea, or even Nigeria. The bottom line, however, is that the longer this virus circulates in humans, the better chance it has of producing a mutation we really don’t want to see.

 

For some more coverage on this report, NPR’s Goats & Soda Blog has:

 

Ebola Is Rapidly Mutating As It Spreads Across West Africa

by Michaeleen Doucleff

 

 

This from Scientific American:

 

Patient Zero Believed to be Sole Source of Ebola Outbreak

By pinpointing the virus’s source, a new report validates steps health care workers are taking to battle the disease

Aug 28, 2014 |By Dina Fine Maron

And this from Nature News. 

 

Ebola virus mutating rapidly as it spreads

Outbreak likely originated with a single animal-to-human transmission.

EID Journal: Deep Sequencing and Phylogenetic Analysis of NCoV

 

Coronavirus – Credit CDC PHIL

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Like police detectives on the trail of a shadowy killer, epidemiologists, virologists, and microbiologists are using every scientific tool in their arsenal to profile, identify, and (with luck) halt the transmission of the novel coronavirus (NCoV) that has recently emerged in a handful of patients in the Middle East.

 

Some of these efforts involve old fashioned shoe-leather detective work; conducting patient interviews and contact tracing.

 

Other disease detectives concentrate primarily on the physical evidence, conducting experiments in the lab.

 

The result is, practically every day, new clues are revealed, and new avenues of investigation are opened.  

 

This week alone we’ve seen reports on NCoV’s receptor binding (see Nature: Receptor For NCoV Found) and a detailed epidemiological investigation into last month’s family cluster (see Eurosurveillance: H2H Transmission of NCoV In UK Family Cluster).

 

Yesterday, the CDC’s EID Journal added a fairly technical report to NCoV’s dossier entitled:

 

Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus

 Matthew Cotten, Tommy T. Lam, Simon J. Watson, Anne L. Palser, Velislava Petrova, Paul Grant, Oliver G. Pybus, Andrew Rambaut, Yi Guan, Deenan Pillay, Paul Kellam , and Eleni

Abstract

A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East. We report the deep genome sequencing of the virus directly from a patient’s sputum sample.

 

Our high-throughput sequencing yielded a substantial depth of genome sequence assembly and showed the minority viral variants in the specimen. Detailed phylogenetic analysis of the virus genome (England/Qatar/2012) revealed its close relationship to European bat coronaviruses circulating among the bat species of the Vespertilionidae family.

 

Molecular clock analysis showed that the 2 human infections of this betacoronavirus in June 2012 (EMC/2012) and September 2012 (England/Qatar/2012) share a common virus ancestor most likely considerably before early 2012, suggesting the human diversity is the result of multiple zoonotic events.

 

 

Since it was first proposed by Pauling and Zuckerkandl in 1962 ("Molecular disease, evolution, and genetic heterogeneity"), molecular biologists have been refining the Molecular Clock Hypothesis (MCH). 

 

One that proposes the speed of evolutionary change in different organisms is reasonably constant, can be measured, and can be used to extrapolate (roughly) how long it has been since two or more related organisms diverged from a common ancestor.

 

What is called their tMRCA  (Time To Most Recent Common Ancestor).

 

You can read a nice history and explanation of this hypothesis in:

 

The Molecular Clock and Estimating Species Divergence

By: Simon Ho, Ph.D. (Australia National University) © 2008 Nature Education

 

 

The problem is calibration, as individual species mutate at vastly different rates.

 

Fortunately, scientists are getting much better at determining how fast many different organism’s genetic clock runs, and research since the 2003 SARS outbreak has helped to quantify the approximate speed of change among human coronaviruses.

 

Using this information, and comparing the whole genome of two novel human NCoVs samples taken from patients last summer (England/Qatar/2012 & EMC/2012), their analysis has led to two possible scenarios.

 

From the discussion portion of this paper:

 

In the interest of public health, it is critical to determine whether these CoV infections in humans are the consequence of a single zoonotic event followed by ongoing human-to-human transmissions or whether the 3 geographic sites of infection (Jordan, Saudi Arabia, and Qatar) represent independent transmissions from a common nonhuman reservoir.

 

The large genetic diversity of CoV maintained in animal reservoirs suggests that viruses that independently moved to humans from animals at different times and places are likely to be reasonably dissimilar in their genomes, possibly making the multiple transmission events model less likely.

Further information is needed to confirm this point because the currently available data are limited.

 

If we calibrate our molecular clock analysis using the evolutionary rate of Zhao et al. (20) estimated for SARS-CoV, we dated the tMRCA of EMC/2012 and England/Qatar/2012 viruses to early 2011.

 

Therefore, if both sequenced viruses and the other cases descended from a single zoonotic event, then this tMRCA suggests that the novel virus has been circulating in human population for >1 year without detection and would suggest most infections were mild or asymptomatic.The rate would have to be considerably faster, of a magnitude observed for human influenza A virus, for the tMRCA to be compatible with the earliest known cases in April 2012.

 

Perhaps more probable, therefore, is that the 13 known cases of this disease represent >1 independent zoonotic transmission from an unknown source.

 

Viral sequence data from other patients infected with this novel human betaCoV will help to more accurately estimate the estimate a genomic evolutionary rate specific to this virus, which will then yield a tMRCA estimate closer to the actual time.

 

 

So while the authors admit it is possible that these two cases are linked by a largely mild or asymptomatic chain of undetected human transmission, they believe it is more probable that NCoV has spilled over from more than one zoonotic sources over the past year in the Middle East.

 

Probabilities aside, determining which of these two scenarios is correct remains the top priority of epidemiologists investigating this virus.

 

The authors conclude by writing:

 

Precise identification of the origin of this virus, defining its mode of evolution, and determining the mechanisms of viral pathogenesis will require full-genome sequences from all cases of human infection and substantially more sampling and sequencing from Vespertilionidae bats and other related animals.

 

The sequencing method reported here markedly shortens the time required to process the clinical sample to genome assembly to 1 week and will provide a useful tool to study this novel virus.