Common colds. These are probably most frequently caused by rhinoviruses but both enterovirus and coronavirus infections may cause a similar symptomatology. Respiratory syncytial virus (RSV) and parainfluenza virus infections may manifest themselves as common colds in adults but create more significant problems in the young age group.​​

Infections of the pharynx. A red, sore throat is one of the most common clinical signs of viral infection. Gingivostomatitis and tonsillitis may both have viral etiology. The herpes viruses may cause enanthems, with eruptions of the mucous membrane of the pharynx. Vesicular gingivostomatitis may result from both primary and recurrent herpes simplex infections. Herpangina with a few small blisters on the soft palate and the posterior wall of the throat or the tongue is seen in children or adolescents. Tonsillitis with a badly smelling greyish exudate covering the tonsils is seen in at least 50 per cent of cases of EBV induced infectious mononucleosis (IM). This is not a feature of CMV-induced IM. Tonsillitis may also occur in HSV induced gingivostomatitis. Tender, swollen tonsils may represent a lymphoid reaction of many virus infections and is a common finding in adenovirus infections. Possible, common viral agents are listed below. 

Common viral causes of upper respiratory tract infections and their laboratory diagnosis.

• A nasopharyngeal washing (NPW) or even throat swabs are appropriate specimens. If refrigerated and collected in virus transport medium, HSV retains infectivity for a few days, whereas entero and adenoviruses survive prolonged transportation times. The likely hood of virus particles to remain infective, and thus grow when cultured in the laboratory, is greatly increased if the specimen is collected in virus culture medium, which contains antibiotics, which will suppress bacterial contaminants.
• Some enteroviruses will not grow in culture and their detection may require PCR. This is particularly important in patients with neurological symptoms, if severe enterovirus infection of the newborn is suspected, or in the case of nosocomial transmission.
• In children, polioviruses are occasionally cultured from NPWs or stool samples. Most often, this represents a recent oral poliovirus vaccination. In these cases it is obviously important to review the vaccination history.
• Enteroviruses are present in the gut for prolonged periods of time and virus culture or PCR of stool specimens may therefore be helpful for the diagnosis when the patient is first seen long after onset of disease.
• Measles or rubella infections are best diagnosed by virus serology. Virus serology requires a tube of clotted blood (red top) with no additives. Generally, the presence of virus specific IgM antibodies indicates recent or current infection. VZV and HIV infections are best diagnosed by serology in combination with PCR.

 Infectious mononucleosis (IM) syndrome.

The most common cause of infectious mononucleosis (IM) syndrome is the Epstein Barr virus (EBV), but several other causative agents, in order of importance, are CMV, HHV6 and Toxoplasma gondii.

Laboratory diagnosis - Infectious mononucleosis (IM) syndrome.

• Heterophile antibodies, resulting in a positive monospot test are present in 80-90 per cent of adolescent cases. If the adolescent patient presents with the clinical syndrome of IM but is monospot negative, specific EBV serology should be performed.
• The monospot test is not helpful in children younger than four or five, since the majority of primary pediatric EBV infections are monospot negative.

 Pattern of serological markers in EBV infection.

Lower respiratory tract infections.

All of the respiratory viruses can be associated with a common cold in adults and children, but infants and toddlers are more likely to develop severe respiratory syndromes including croup, bronchiolitis and pneumonia. These conditions represent a major admitting diagnosis during the winter period in temperate climates, and RSV remains the single most important respiratory virus and represents 70 per cent of all admitted respiratory viral illness. Acute laryngotracheitis and croup are primarily associated with parainfluenza virus type 1, whereas RSV primarily causes bronchiolitis. Viral pneumonia can be caused by any of the agents in Table 5 and is a special concern in patients with underlying pulmonary of cardiovascular disorders and in immuno-compromised children.

Important pediatric respiratory pathogens

• Respiratory syncytial virus (RSV)
• Parainfluenza virus 1,2,3 (PIV 1,2,3)
• Influenzavirus A,B
• Adenovirus

 Laboratory diagnosis - Viral lower respiratory tract infections.

The appropriate specimen is nasopharyngeal washing. A nasopharyngeal swab is the second best choice. A throat or a nose swab is not appropriate. Most respiratory viruses with the exception of adenoviruses and rhinoviruses are labile, and will be inactivated if the transport of the specimen exceeds one day. If an overnight transportation is necessary, it is wise to collect the specimen in virus transport medium (can be obtained beforehand from the virus laboratory). With the rapid diagnostic tests currently available, transportation of specimens has become less of an issue, but expedient transport results in expedient diagnosis. 

Once in the laboratory, we can make the diagnosis of RSV within the hour, using rapid tests. We also offer rapid tests for influenza, parainfluenza and adenoviruses. The current techniques used usually have an excellent specificity, meaning that a positive result is reliable, however the sensitivity of the tests may vary and is dependent on a multitude of factors, meaning that a negative rapid test result does not exclude the presence of the virus. Therefore, we recommend that virus culture be set up in important cases, since although lengthy (more than 10 days) it is still, if appropriately performed on fresh specimens, the gold standard.