New human coronavirus reported

Mar 23, 2004 (CIDRAP News) – Dutch researchers report that they have discovered a new human coronavirus—a close relative of the agent of severe acute respiratory syndrome (SARS)—that causes respiratory illness in infants and immunocompromised adults.

Writing in an early online edition of Nature Medicine, the researchers report that they used a new technique to isolate and identify the virus from a 7-month-old infant suffering from a respiratory illness. In screening samples from several hundred more patients over a 9-month period, they found the virus in seven more patients, suggesting it is widespread.

The researchers, Lia van der Hoek and colleagues from the University of Amsterdam and other centers in Amsterdam, sought to identify the cause of coryza, conjunctivitis, and fever in a 7-month-old baby who was hospitalized in January 2003. Clinical samples tested negative for numerous viruses, including the two human coronaviruses known at the time—HCoV-229E and HCoV-OC43, both of which cause the common cold. (The SARS-associated coronavirus was identified in March 2003.)

The investigators then placed clinical samples in several cell cultures, including human fetal lung fibroblasts and monkey kidney cells, according to the report. Cell damage was seen only in one line of monkey kidney cells, so the kidney cell culture was analyzed further. After further tests for known viruses were negative, the researchers developed a new virus discovery method.

The article explains that identifying unknown pathogens is difficult because polymerase chain reaction (PCR) testing relies on the use of primers consisting of nucleic-acid sequences from known organisms. The researchers developed a method they call Virus-Discovery-cDNA AFLP (amplified restriction fragment–length polymorphism), or VIDISCA. The technique involves several steps for filtering components other than viral nucleic acids out of a sample and then using enzymes to cut remaining strands of DNA into shorter fragments.

Applying this technique to the infected monkey cells and to uninfected cells, the researchers found unique DNA fragments only in the infected sample, the article says. Thirteen of 16 fragments were similar to known coronaviruses, but significant differences in all the fragments pointed to a new coronavirus. The investigators used the fragments to design a PCR test for the virus, which they named HCoV-NL63. The test confirmed the presence of the virus in another sample from the sick child.

To determine if the new virus was circulating in humans, the authors then used two diagnostic PCR assays to analyze respiratory specimens collected from patients over a 9-month period. In tests of about 500 samples, they found the new virus in seven more patients, all of whom were ill in the winter. At least five of these had respiratory tract illnesses; no clinical data were available for the other two.

Of the eight patients including the index patient, five were infants less than a year old and three were adults, the report says. Two of the adults probably had suppressed immune systems, because of bone-marrow transplantation and AIDS; clinical data for the third adult was unavailable. The coronavirus was the only respiratory agent found in six of the eight patients, suggesting that it was the cause of their symptoms.

The authors say that no known virus is identified in about 20% to 30% of respiratory disease cases. "Our results indicate that HCoV-NL63 is present in a significant number of respiratory tract illnesses of unknown etiology," they conclude. They predict that further research will yield a clearer picture of the virus's prevalence and its association with disease.

Van der Hoek L, Pyrc K, Jebbink MF, et al. Identification of a new human coronavirus. Nature Med 2004; advance online publication [Abstract]

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