[D66] The origins and evolution of the SARS-CoV-2 virus

[R.O.]

wsws.org:

The origins and evolution of the SARS-CoV-2 virus
By Frank Gaglioti
24 August 2020

The SARS-CoV-2 virus that causes the disease COVID-19 is nimbly and 
stealthily racing through community after community devastating the 
world’s population. Over 23 million people have contracted the virus 
worldwide and 810,000 have died. It is critical to review the 
evolutionary history of this particular virus to provide necessary 
insights into how the pandemic can be brought under control.

Researchers worldwide are working arduously to trace the virus globally 
by studying samples obtained from various nations looking for subtle 
mutations that it undergoes as it infects, replicates and multiplies, 
providing them clues to the source and route of spread.

COVID-19 is caused by a type of coronavirus known as SARS-CoV-2, named 
for its similarity to the coronavirus that caused SARS. The virus is 
called a coronavirus because it is covered by club-like structures that 
give the virus a similar look to the sun’s corona in electron micrographs.

The SARS-CoV-2 virus is part of a family of organisms that are known to 
infect mammals and birds. The Coronaviridae family are made up of a 
positive-sense single-stranded RNA completely enveloped in a complex 
protein and bilipid shell. These viruses are relatively large, 
consisting of 26 to 32 kilobase pairs. RNA or ribonucleic acid is a 
nucleic acid that is essential for all reproductive processes and like DNA.

The first known scientific encounter with this family of virus is 
thought to be when veterinarians puzzled over bronchial infections 
afflicting cats, pigs, and chickens in the early 20th century.

Study of disease afflicting and damaging tobacco crops in the late 19th 
century led some thoughtful scientists like Dimitri Ivanovsky to 
conjecture the existence of non-bacterial infectious agents causing the 
“tobacco mosaic disease.” It would take another 50 years to capture the 
first images of the Tobacco Mosaic Virus. The invention of the electron 
microscope in 1931 enabled scientists to observe viruses more closely, 
allowing a more extensive and direct study of these micro-organisms. 
Virology as a field began to flourish.

Human coronaviruses were first identified in the 1960s. Seven species of 
coronavirus are known to afflict humans. Four result in relatively mild 
upper respiratory tract conditions, including the virus 229E that causes 
the common cold, along with NL63, OC43 and HKU1.

The other three strains, SARS, MERS, and SARS-CoV-2, are far more 
virulent. All these viruses were new to human populations when they 
first arose in the 21st century. A feature of SARS, MERS and COVID-19 is 
that they had a zoonotic origin, that is they originated in animal 
populations and then jumped into humans. The SARS outbreak in 2002, with 
a case fatality rate of 11 percent, showed the world the deadly 
potential of coronaviruses, but this was a warning that was mostly 
ignored. There had only been 8,422 cases and since 2004 no SARS-CoV has 
been reported worldwide. One advantage for public health responses to 
SARS was that it had an incubation period of 4 to 6 days and patients 
presented with symptoms prior to becoming infectious.

In their extensive investigations, the World Health Organisation (WHO) 
concluded that the SARS virus originated in bat populations, but the 
exact species remains unknown. Work commenced on the development of a 
SARS vaccine with testing on animals. The vaccine resulted in protective 
immunity but produced an immune mediated hypersensitivity as an adverse 
effect. The SARS threat, for unknown reasons, expired after six months 
though limited outbreaks did occur later.

With the threat of a pandemic having ended after six months, so did any 
interest in funding a vaccine, as pharmaceutical companies saw no profit 
in funding or exploring such research. The co-director of the Center for 
Vaccine Development at Texas Children’s Hospital and dean of the 
National School of Tropical Medicine at the Baylor College of Medicine 
in Houston, Dr. Peter Hotez, had been attempting to develop a SARS 
vaccine in 2016 but couldn’t get funding for his work. “We tried like 
heck to see if we could get investors or grants to move this into the 
clinic ... But we just could not generate much interest,” he said.

“We could have had this ready to go and been testing the vaccine’s 
efficacy at the start of this new outbreak in China (COVID-19) … There 
is a problem with the ecosystem in vaccine development, and we’ve got to 
fix this,” Hotez said.

The genomic sequence of the SARS virus was published in August 2003 by 
Chinese scientists in Beijing. In actuality, when the cause of the 
pneumonia-like illness was first identified in Wuhan, some believed this 
was a new outbreak of the SARS virus. SARS-CoV-2 and SARS share a 
genomic sequence that is approximately an 80 percent match.

Middle East Respiratory Syndrome, or MERS, emerged in Saudi Arabia in 
2012 and had a zoonotic origin in bats and was spread to humans through 
contact with dromedary camels. The virus produced symptoms similar to 
SARS but it had a low infectivity though highly lethal. Of the reported 
2,500 cases, 35 percent died from the disease.

With limited capacity to spread from human to human, it was mainly 
passed through contact with infected people in hospitals. In the main it 
was concentrated in the Arabian Peninsula, although there were further 
outbreaks in South Korea in 2015 and Saudi Arabia in 2018. It continues 
to smoulder in the Middle East.

When the SARS CoV-2 virus emerged in late 2019, the world was totally 
unprepared. Health systems internationally had been systematically run 
down and were ill-equipped to respond. The warnings from WHO of the 
dangerous potential of the virus were largely ignored or belittled. The 
murderous government policies that dominated have been described as 
malign neglect or herd immunity.

SARS CoV-2 arose in Wuhan in December 2019. The virus is thought to have 
originated from bats and to have transferred to humans through an 
intermediary species. The exact origins of the virus may never be known. 
“It is quite possible we won’t find it (the species). In fact, it would 
be exceptionally lucky if we land on something,” a geneticist from 
University College London, Lucy van Dorp, told Nature .

Back in 2013, the Wuhan Institute of Virology had investigated the 
coronavirus genome from the horseshoe bat ( Rhinolophus affinis ). The 
viruses named RATG13 and SARS-CoV-2 were found to be 96 percent 
genetically similar. There are, however, subtle molecular changes that 
continue to be investigated that contribute to selection pressures that 
drive the virulence, pathogenicity, and immunogenic qualities of the virus.

In their detailed analysis of the origin of the SARS-CoV-2 virus, 
Andersen et al., 2020, offered three possible explanations: 1) natural 
selection in an animal host before jumping into humans, 2) natural 
selection in humans after the virus transferred into human hosts, and 3) 
the product of artificial manipulation, which has been refuted by 
several virologists. According to Van Dorp, “… the 4% difference between 
the genomes of SARS-CoV-2 and RATG13 still represents some 50 years 
since they last shared a common ancestor.”

It was thought that pangolins ( Manis javanica ), a scaly ant-eating 
mammal, may be the intermediate host between bats and humans, but 
genetic studies indicate that as unlikely. However, some scientists 
think that because coronavirus-like SARS-CoV-2 cases have been found in 
pangolins, that species cannot be ruled out as the intermediary source.

Scientists are currently examining species of animals that were kept and 
sold in the live markets in Wuhan where bats may have been in the 
buildings’ roof near animals and humans. Presently a team of experts 
from the WHO are working with their Chinese counterparts to answer this 
pressing question.

“The opportunities for these viruses to spill over across a very active 
wildlife-livestock-human interface is clear and obvious,” the president 
of the EcoHealth Alliance in New York City, Peter Daszak, told Nature. 
The complex evolutionary history of SARS-CoV-2 disproves President 
Donald Trump’s ignorant claims (which have a political purpose) that the 
virus came out of a Chinese laboratory. “Whether they [China] made a 
mistake, or whether it started off as a mistake and then they made 
another one, or did somebody do something on purpose?” Trump said.

In a recent paper published in Nature Microbiology —“Evolutionary 
origins of the SARS-CoV-2 sarbecovirus lineage responsible for the 
covid-19 pandemic,” led by Maciej F Boni from the Center for Infectious 
Disease Dynamics at Pennsylvania State University—found that the lineage 
of SARS-CoV-2 had been circulating in bat populations for decades. “If 
these viruses have been around for decades that means that they’ve had 
lots of opportunity to find new host species, including humans,” said 
Professor David Robertson from the University of Glasgow.

Scientists have carefully examined the Receptor Binding Domain (RBD) of 
the genetic sequence that codes for the spike protein, the necessary 
structure on the virus’ exterior shell that is used to bind and 
penetrate the human cell. The spike protein has been compared to a 
grappling hook that grips the host cell, then creates a cleavage site 
that enables the opening and penetration into the host cell.

This means that the SARS-CoV-2 spike proteins had evolved to target a 
feature of human cells known as angiotensin converting enzyme 2 receptor 
(ACE2) which are well known to assist in regulating blood pressure.

Andersen et al ., remark that the RBD is the critical component of the 
spike protein that allows it to bind to ACE2 receptors. SARS-CoV-2 
appears to bind with great affinity to the human ACE2 receptors, but 
computational analysis predicted that the interaction is not ideal. 
According to the New York Times, “the authors indicate that the 
high-affinity bindings of the virus’ spike protein to human ACE2 is most 
likely a by-product of natural selection that has permitted another 
‘optimal binding solution to arise.’ They then conclude that this is 
strong evidence that SARS-CoV-2 is not a product of genetic 
reconstruction or tampering.”

“These two features of the virus, the mutations in the RBD portion of 
the spike protein and its distinct backbone, rule out laboratory 
manipulation as a potential origin for SARS-CoV-2,” wrote Kristian 
Andersen, associate professor of immunology and microbiology at Scripps 
Research, and co-leader of the study.

With SARS-CoV-2 virus proliferating around the world, the opportunity 
arises for further mutations and the emergence of new strains of the 
virus. This can mean that new virus strains may develop in the future 
not treatable by possible vaccines that were originally made to treat 
older strains.

According to Assistant Teaching Professor of Computer Science and 
Technology Niema Moshiri, COVID-19’s mutation rate is lower than 
seasonal influenza. The SARS-CoV-2 genome has a limited repair function 
that edits out most mutations. This has meant the virus has remained 
relatively uniform.

“What we are finding is that the SARS-CoV-2 virus appears to be mutating 
more slowly than the seasonal flu which may allow scientists to develop 
a vaccine,” Moshiri wrote on LiveScience. Despite this, variations do 
occur, and virologists are constantly looking at the variants to 
determine if a more virulent strain may be emerging or if the virus is 
losing its potency.

Scientists are collecting virus sequences and storing them in a globally 
available database. This is used to determine the rate of mutation and 
where in the virus genome mutations are occurring. Such mutations can 
affect the virulence and how effectively the virus can infect human host 
cells. The existence of different viral strains can be used to trace 
outbreaks.

Analysis of the SARS-CoV-2 virus from different countries has shown that 
the virus has undergone several predicted but insignificant mutations 
already. Scientists led by Peter Forster, along with researchers based 
in the UK and Germany, traced 160 COVID-19 genomes from China, Europe, 
and the US. They identified three strains of the virus called A, B and 
C. Type A is considered to be the original Chinese “ancestral type.” 
Type B is found in Asia, Europe and the US and has diverged from A with 
2 mutations. Type C differs from type B at one site and is mostly 
confined to Europe and mostly absent from China.

More recently, researchers have alerted that a new strain, D614G, has 
become dominant in many countries. “The D614G variant first came to our 
attention in early April, as we had observed a strikingly repetitive 
pattern. All over the world, even when local epidemics had many cases of 
the original form circulating, soon after the D614G variant was 
introduced into a region it became the prevalent form,” wrote 
theoretical biologist at Los Alamos National Laboratory Bette Korber, in 
the journal Cell .

“This mutation is present in roughly two third of all global strains,” 
according to Associate Professor Denis Bauer, transformational 
bioinformatics team leader at CSIRO’s Australian e-Health Research 
Centre. The mutation that originated in the virus’ spike protein (not 
the RBD section) is thought to make it more contagious, but speculation 
that the virus is more virulent is extremely difficult to prove.

Scientists from the Department of Epidemiology of Microbial Diseases at 
the Yale School of Public Health led by Nathan D. Grubaugh published a 
paper in Cell titled “Making Sense of Mutation: What D614G Means for the 
COVID-19 Pandemic Remains Unclear.” The paper examines whether the 
strain is more transmissible, infectious, or deadly, but concludes that 
“these data do not prove that G614 is more infectious or transmissible 
than viruses containing D614.” They conclude there is no evidence that 
the virus strain leads “to more severe disease.”

The history of human populations and coronaviruses indicate a possible 
course for the current pandemic. For instance, the virus OC43 is 
responsible for the common cold, but a study by researchers from the 
University of Leuven in Belgium suggest it may have been responsible for 
a pandemic in 1889 that killed more than 1 million people 
internationally. They speculate that humans eventually developed 
immunity against the virus, making future infections more benign.

The course of this pandemic is on par with one of history’s most severe 
health crisis in modern times. For humanity to develop herd immunity to 
SARS-CoV-2 would imply untold millions of deaths and incompletely 
understood chronic health morbidities. Yet, in the 21st century, where 
scientific knowledge is capable with confronting the threat, capitalism 
enchains humanity’s ability to respond in kind.