SARS & Beta2c nCoV Similar Histories

SARS & Beta2c nCoV Similar Histories 
Recombinomics Commentary 20:00
March 8, 2013

This recent cluster provides the first clear evidence of human-to-human transmission of this novel coronavirus, coinfection of this novel coronavirus with another pathogen (influenza A), and a case of mild illness associated with this novel coronavirus infection. In light of these developments, updated guidance has been posted on the CDC coronavirus website
The above comments in a CDC early release MMWR describe the recent beta2c novel coronavirus cluster in the UK.  The difference between the above cluster and earlier clusters in Jordan and Saudi Arabia is one of circumstances. In the UK cluster the index case developed symptoms while performing Umrah in Saudi Arabia, while family members developed symptoms in the UK.  Since the family members had no recent travel outside of the UK, H2H transmission was demonstrated. However, the earlier cluster in Jordan had more symptomatic cases and the number of confirmed/probable cases was 12, which included two confirmed deaths. That cluster was largely composed of health care workers (7 nurses and 2 doctors) from the same ICU, and the deaths were one nurse (45F) and one doctor/intern (25M). Although disease onset dates were not released, the dates of death were 1 week apart, and family members of the HCWs were also symptomatic.  The other cluster was a familial cluster in Riyadh involving 4 cases.  Two died and were confirmed as was a survivor. The 4th case was classified as probable and disease onset dates fully supported H2H transmission in the family.

Thus, although clear evidence existed for H2H transmission in the clusters, the circumstances unique to the UK cluster clearly demonstrated the transmission as well as the import of the virus into the UK via commercial airline, followed by clear transmission, which was a hallmark of the SARS CoV international spread in 2003.  Moreover, the SARS spread in 2003 was similar to the Jordan cluster, which involved a large number of HCW’s who developed severe pneumonia leading to the death of two relatively young HCWs (45F and 25M).  In 2003 a high percentage of HCWs were infected because SARS CoV grew well in the lower respiratory tract, so transmission was limited, but dramatic in “super spreaders” which frequently caused HCW infections.

This effect was clearly seen in the 2002/2003 SARS spread.  Initially the virus was largely confined to Guangdong Province, adjacent to Hong Kong.  Reports of a “mystery disease” were being cited by ProMED, which also noted the associate with severe pneumonia and death.  However, details were sketchy and China insisted that the situation was resolving, which dramatically changed in March, due to events in February.  A physician treated patients travelled to Hong Kong for a wedding and checked into room 911 at the Metropole Hotel for a 1 night stay on February 21.  There was at least one super spreading event (vomiting in hall on the 9th floor) which led to the infection of at least a dozen guests with rooms on the 9th floor.  At least four of these infections led to super spreading events involving health care workers in Hong Kong, Singapore, Hanoi, and Toronto.

This international spread led to significant scientific cooperation, as well as media coverage, because the infections were killing middle age patients and infecting large numbers of HCWs and the etiological agent was still a mystery.  However, the agent was quickly identified as a novel coronavirus that was in group 2 (betacornavirus), but distinct from the only known human betacornavirus, OC43, which had been identified decades earlier as a human cold virus (in addition to a group 1, alphacornavirus, which had also been identified decades earlier, 229E, and also caused human colds. 
 The novel virus was called SARS (Sudden Acute Respiratory Syndrome), and was subsequently classified as 2b.  SARS was most easily identified in samples from the lower respiratory tract, which were readily available in the severe and fatal cases.  The SARS outbreak also gave rise to a sequence database of bat coronaviruses, because the sequences from exotic animals found in live markets in Guangdong Province and Hong Kong had sequences which were virtually identical to each other and the early human cases. 
 The search for a natural reservoir (which used the same PCR primer set used to identify the first two human nCoV cases) found that bats were frequently infected with a wide range of coronaviruses (which were in guano and easily accumulated in bat caves), which included beta2a sequences related to SARS CoV, as well as other beta sub-clades designated as beta2c and beta 2d.

In the fall of 2012 a fatal case (60M) from Bisha, Saudi Arabia, presented with SARS-like symptoms (at a hospital in Jeddah) and died.  Testing for SARS and other human respiratory viruses was negative, which led to testing using the set of universal coronavirus primers, which produced a positive (designated EMC/2012 for the Emaras Medical Center, which generated the sequence).  Sequencing led to the identification of a novel coronavirus, which had not been previously reported in humans and was most closely related to the bat beta2c sequences from Guangdong Province (series HKU4 and HKU5).  Those primers were then used samples from a case from Qatar (49M) who had been transported by air ambulance to the UK for treatment with SARS-like symptoms.  He also tested positive, and the 206 BP insert was sequenced and found to differ from EMC/2012 at only one position (99.5% identity). 
 In contrast, the closet bat sequence had 35 differences (82.5% identity) clearly demonstrating that the two human cases were infected with a novel human virus.  A short partial sequence from a 2008 collection from a bat in the Netherlands was somewhat higher, so samples collected from bats in Europe and Africa were retested with probes targeting beta2c, which confirmed that European bats had an identity of 89% (using a conserver region of the polymerase gene), which was closer than bat sequences from Asia or Africa, but well short of the identities in the human sequences.  A full sequence from the Qatar case (designated England 1since it was generated by the Health Protection Agency, HPA, in London) showed that the full sequence (over 30,000 BP) was also 99.5% identical to EMC/2012. 
 The HPA also released the full sequence for the index case (60M) for the UK cluster.  That sequence, England 2, allowed for the generation of a consensus sequence for the full beta2c genome (30,118 BP), which showed that England 1 only had 17 differences, in addition to a 6 BP deletion.  Similarly, England 2 only had 23 differences, indicating each sequence was more than 99.9% identical to the consensus, while the identity for EMC/2012 was just under 99.8%.  In contrast, the most closely related bat sequence had an identity of 89% for a highly conserved region of the polymerase gene.  Partial sequences for the first case from Riyadh (45M) were identical to the consensus, while the two sequences for the Qatari treated in Germany (Essen) had no differences for one region and only one difference for the other, clearly demonstrating that all five patients had sequences virtually identical to each other and easily distinguished from all bat sequences.

The sequences allowed for PCR testing that would specifically identify the novel beta2c sequence s in clinical samples.  However, the low level of RNA in the upper respiratory tract produces false negatives, which grossly under estimate the transmission of the novel beta2c coronavirus.