Full genome sequence of novel coronavirus expected shortly

Sep 27, 2012 (CIDRAP News) – British health officials said today that a Rotterdam lab that first characterized the novel coronavirus linked recently to two severe illnesses hopes to publish the whole genome in the next 24 to 48 hours, and the UK's Health Protection Agency (HPA) launched guidance to help clinicians investigate and manage possible cases.

The HPA said in an update that the full genome sequence will be published by Ron Fouchier, PhD, based at Erasmus University in the Netherlands. The sequence will be based on cultured virus that has been at the lab since early July.

Yesterday the agency gave the same time frame for release of the full sequence and did not change the estimate in today's update.

The HPA had earlier released the partial sequence for the virus's polymerase gene, obtained from an infected patient undergoing treatment in London, which enabled scientists to compare it with others and determine that the new virus is related to bat coronaviruses. The HPA said it doesn't yet have a viral isolate, but clinical material from the patient is being cultured to make isolates.

Also, the HPA shared new details about molecular diagnostics for identifying the new virus. It said pan-coronavirus primers described by an international group of researchers in 2003 and in a 2008 report from Belgian researchers should both be useful. However, the clinical material the HPA has does not react with specific assays it has for OC23, 229E, NL64, or SARS. It said it welcomed offers of reagents and information from scientists who specialize in the area.

In other developments, the HPA published some clinical tools to help clinicians manage suspected and confirmed cases along with close contacts. The tools include an algorithm for investigating and managing possible cases; it describes the testing process, protective actions to take if an infection is confirmed, and the next steps to take for sample collection and data reporting.

Another algorithm walks clinicians through investigating close contacts of patients with confirmed novel coronavirus infections. For contacts who don't have clinical symptoms during the initial visit, the HPA recommends that baseline clotted blood samples be taken as soon as possible, ideally no later than 7 days after exposure. The algorithm recommends that follow-up samples be taken at least 14 days after baseline or 28 days after exposure if a sample couldn't be taken when the case-patient was asymptomatic. It says a contact form should be completed 10 days after the initial data is collected.

The HPA also issued a nine-page infection control resource for handling confirmed and suspected cases. It noted that coronaviruses are mainly transmitted by large respiratory droplets and direct or indirect contact with secretions. The agency also said the viruses can be detected in feces and urine and in some instances can be transmitted by aerosolized respiratory droplets and feces. It detailed steps to take in addition to standard precautions, such as what type of respirator and personal protective equipment (PPE) to use.

In developments elsewhere, Hong Kong's Centre for Health Protection (CHP) said today that the process to make novel coronavirus infection a notifiable disease is under way. It said a legislative amendment will be recorded tomorrow, taking effect immediately. Health practitioners will be required to notify the CHP's director of health if they suspect the disease, and labs will be required to report virus leaks that may pose a public health risk.

No new infections involving the novel coronavirus have been detected beyond the Qatari man hospitalized with a severe respiratory illness and renal failure in a London intensive care unit and a 60-year-old Saudi Arabian man who was infected with a virtually identical virus who died in June.

The identification of a new coronavirus has raised global health worries, because a then-novel one in 2003 caused the SARS epidemic that sickened 8,422 people, killing 916 of them. Health officials have said the new virus is clearly different than the one that caused SARS, and some have said that an animal source can't be excluded.

See also:

Sep 27 HPA update

Sep 27 CHP statement

Sep 26 HPA algorithm for investigating possible novel coronavirus infections

Sep 26 HPA algorithm for investigating close contacts of confirmed cases

Sep 26 HPA infection control advice

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