Questions on the origins of the SARS virus

The excerpt below comes from an essay published recently by the Institute of Science in Society.

SARS and Genetic Engineering?

The complete sequence of the SARS virus is now available, confirming it is a new coronavirus unrelated to any previously
known. Has genetic engineering contributed to creating it? Dr. Mae-Wan Ho and Prof. Joe Cummins call for an investigation.

The World Health Organisation, which played the key role in coordinating the research, formally announced on 16 April that a
new pathogen, a member of the coronavirus family never before seen in humans, is the cause of Severe Acute Respiratory
Syndrome (SARS).

"The pace of SARS research has been astounding," said Dr. David Heymann, Executive Director, WHO Communicable Diseases
programmes. "Because of an extraordinary collaboration among laboratories from countries around the world, we now know with
certainty what causes SARS."

But there is no sign that the epidemic has run its course. By 21 April, at least 3 800 have been infected in 25 countries with
more than 200 dead. The worst hit are China, with 1 814 infected and 79 dead, Hong Kong, 1 380 infected and 94 dead, and
Toronto, 306 infected, 14 dead.

A cluster of SARS patients in Hong Kong with unusual symptoms has raised fears that the virus may be mutating, making the
disease more severe. According to microbiologist Yuen Kwok-yung, at the University of Hong Kong, the 300 patients from a
SARS hot spot, the Amoy Gardens apartment complex, were more seriously ill than other patients: three times as likely to suffer
early diarrhoea, twice as likely to need intensive care and less likely to respond to a cocktail of anti-viral drugs and steroids.
Even the medical staff infected by the Amoy Gardens patients were more seriously ill.

John Tam, a microbiologist at the Chinese University of Hong Kong studying the gene sequences from these and other patients
suspects a mutation leading to an altered tissue preference of the virus, so it can attack the gut as well as the lungs.

The molecular phylogenies published 10 April in the New England Journal of Medicine were based on small fragments from the
polymerase gene (ORF 1b) (see Box), and have placed the SARS virus in a separate group somewhere between groups 2 and 3.
However, antibodies to the SARS virus cross react with FIPV, HuCV229E and TGEV, all in Group 1. Furthermore, the SARS virus
can grow in Vero green monkey kidney cells, which no other coronavirus can, with the exception of porcine epidemic diarrhea
virus, also in Group 1.

Coronaviruses

Coronaviruses are spherical, enveloped viruses infecting numerous species of mammals and birds. They contain a set of
four essential structural proteins: the membrane (M) protein, the small envelope (E) protein, the spike (S) glycoprotein,
and the nucleocapside (N) protein. The N protein wraps the RNA genome into a ‘nucleocapsid’ that’s surrounded by a
lipid membrane containing the S, M, and E proteins. The M and E proteins are essential and sufficient for viral envelope
formation. The M protein also interacts with the N protein, presumably to assemble the nucleocapsid into the virus.
Trimers (3 subunits) of the S protein form the characteristic spikes that protrude from the virus membrane. The spikes
are responsible for attaching to specific host cell receptors and for causing infected cells to fuse together.

The coronavirus genome is a an infectious, positive-stranded RNA (a strand that’s directly translated into protein) of
about 30 kilobases, and is the largest of all known RNA viral genomes. The beginning two-thirds of the genome contain
two open reading frames ORFs, 1a and 1b, coding for two polyproteins that are cleaved into proteins that enable the
virus to replicate and to transcribe. Downstream of ORF 1b are a number of genes that encode the structural and
several non-structural proteins.

Known coronaviruses are placed in three groups based on similarities in their genomes. Group 1 contains the porcine
epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCV), feline
infectious peritonitis virus (FIPV) and human coronovirus 229E (HuCV229E); Group 2 contains the avian infectious
bronchitis virus (AIBV) and turkey coronavirus; while Group 3 contains the murine hepatitis virus (MHV) bovine
coronavirus (BCV), human coronavirus OC43, rat sialodacryoadenitis virus, and porcine hemagglutinating
encephomyelitis virus.


Where does the SARS virus come from? The obvious answer is recombination, which can readily occur when two strains of
viruses infect a cell at the same time. But neither of the two progenitor strains is known, says Luis Enjuanes from the
Universidad Autonoma in Madrid, Spain, one of the world leaders in the genetic manipulation of coronaviruses.

Although parts of the sequence appeared most similar to the bovine coronavirus (BCV) and the avian infectious bronchitis virus
(AIBV) (see "Bio-Terrorism & SARS", this series), the rest of the genome appear quite different.

Could genetic engineering have contributed inadvertently to creating the SARS virus? This point was not even considered by
the expert coronavirologists called in to help handle the crisis, now being feted and woed by pharmaceutical companies eager to
develop vaccines.

A research team in Genomics Sciences Centre in Vancouver, Canada, has sequenced the entire virus and posted it online 12
April. The sequence information should now be used to investigate the possibility that genetic engineering may have contributed
to creating the SARS virus.

If the SARS virus has arisen through recombined from a number of different viruses, then different parts of it would show
divergent phylogenetic relationships. These relationships could be obscured somewhat by the random errors that an extensively
manipulated sequence would accumulate, as the enzymes used in genetic manipulation, such as reverse transcriptase and other
polymerases are well-known to introduce random errors, but the telltale signs would still be a mosaic of conflicting phylogenetic
relationships, from which its history of recombination may be reconstructed. This could then be compared with the kinds of
genetic manipulations that have been carried out in the different laboratories around the world, preferably with the
recombinants held in the laboratories.