Friday, June 19, 2009

Influenza A (H1n1) - Worldwide : Other Viral Infections


A ProMED-mail post
ProMED-mail is a program of the International Society for Infectious Diseases

Date: Thu 18 Jun 2009
Source: Eurosurveillance, Volume 14, Issue 24, 18 Jun 2009 [edited]

A variety of respiratory viruses found in symptomatic travellers returning from countries with ongoing spread of the new influenza A(H1N1)v virus strain

By: P Follin[1], A Lindqvist1, K Nystrom1, M Lindh [2]

    1. Department of Communicable Disease Prevention and Control, Region Vastra Gotaland, Sweden,
    2. Department of Virology, Sahlgrenska University Hospital, Gothenburg, Sweden

Clinical specimens from 79 symptomatic individuals with a recent history of travel to countries with verified transmission of influenza A(H1N1) virus (North America) were tested with a multiple real-time PCR targeting a broad range of agents that may cause acute respiratory infection. This analysis revealed that besides 4 cases of influenza A(H1N1) virus, other respiratory viruses were diagnosed in almost 60 percent of the samples. These observations are a reminder that many different viral transmissions occur simultaneously in countries with ongoing spread of influenza A(H1N1) virus. The findings demonstrate that the definition of suspected cases by clinical and epidemiological criteria has only a poor capacity for discriminating influenza A(H1N1)v from other viral infections.


A new influenza A(H1N1) virus variant has spread globally since its 1st appearance in April 2009 [1,2] and as of 17 Jun 2009, there were 39 620 cases reported by the World Health Organization (WHO) [3]. On 30 Apr 2009, the European Commission suggested a case definition [4], which has been adopted and modified by most authorities in the European Union Member States. In agreement with this recommendation, testing for influenza A was recommended in Sweden for cases with a clinical presentation including respiratory symptoms and fever above 38 C and epidemiological circumstances such as recent travel (within 7 days) to areas where the new influenza has been observed [5] or close contact with confirmed cases.

The regular sentinel surveillance for seasonal influenza has been extended and now focuses on identification of imported cases with influenza A(H1N1) virus, and on preventing secondary transmission by contact tracing and antiviral medication in an attempt to delay sustained community transmission. In order to provide a better basis for the decision whether or not to initiate preventive measures, expanded testing, targeting a broad range of respiratory agents has been applied to specimens from all suspected cases in the region Vastra Gotaland (1.5 million inhabitants). We report here the results of this expanded testing.

Material and methods

This report includes samples of patients who, during the period from 24 Apr to 10 Jun 2009 presented with influenza-like symptoms and a history of recent travel to the United States or Mexico, and therefore were recommended for examination and sampling. This clinical examination was performed by infectious disease clinicians on call at Sahlgrenska University Hostpital/Östra in Gothenburg, and our report is based on their evaluation and laboratory results. In summary, of all 79 patients included with a travel history, 90 percent presented with respiratory symptoms, 5 percent without respiratory symptoms, and for the remaining 5 percent this information is not documented. 66 percent had fever above 38 C, 29 percent had no fever; information on fever was missing for 5 percent. Nasopharyngeal swabs were sent to the molecular diagnostic unit at the virological laboratory at Sahlgrenska University Hospital for testing by a multiple real-time PCR targeting 13 viruses and 2 bacteria, ! run in 6 parallel multiplex PCRs on an ABI 7500 instrument [6]. Samples that were reactive for the influenza A component (matrix protein target, [7]) of this PCR were subtyped by an additional real-time PCR targeting the haemagglutinin gene, run in 3 parallel reactions specific for the H3N2 and H1N1 subtypes that have been circulating for a long time, as well as for the new H1N1v strain. [Readers requiring information on the primers and probes used in the real-time PCR are referred to a Table in the original text].

Results and discussion

In total, samples from 79 patients were tested (42 males, 37 females; median age 30 years, range 1-75 years), with between 10 and 16 samples on average each week and most of them taken from patients with respiratory symptoms and a history of recent travel to North America. Four cases with the new influenza A (H1N1)v variant were diagnosed. Interestingly, in 56 percent of the cases, other aetiologies were identified (Table).

Table. Viral aetiologies for the patients fulfilling definition of suspected cases of influenza A(H1N1)v, Region Vastra Gotaland, Sweden, Apr-Jun 2009 (n=79)

Viral aetiology / Number / Percentage

Rhinovirus / 28 / 34
Coronavirus / 8 / 10
Influenza B virus / 3 / 4
Human parainfluenza virus types 1-3 / 3 / 3 / 4
Adenovirus / 2 / 2
Influenza A (H1N1) virus / 4 / 5
Metapneumovirus / 1 / 1
Enterovirus / 1 / 1
Respiratory syncytial virus / 0 / 0
Mycoplasma pneumoniae, Chlamydia pneumoniae / 0 / 0
Negative / 32 / 39

Total number / 82 / 100

(Note: 3 patients had double infections with rhinovirus, together with enterovirus, metapneumovirus or adenovirus.)

The most common finding was rhinovirus, observed in 28 of 82 cases (34 percent), and 3 of these patients also had a 2nd viral infection (enterovirus, metapneumovirus and adenovirus). The frequent identification of rhinovirus and other viruses demonstrates that the criteria for suspected cases of influenza A(H1N1)v are relevant as indicators of a viral infection, but not specific for influenza A. On the other hand, applying more restrictive criteria would probably have excluded most infections with the new A(H1N1) virus strain, considering that their clinical presentation has been reported to be relatively mild. This illustrates a dilemma with surveillance actions aiming at revealing the spread of new respiratory infections. If the applied criteria are too strict (for example fever above 39 C, cough and muscle pain), the epidemic is likely to be underestimated, because only the severe cases are identified. If on the other hand the criteria are liberal, as illustrated by the cur! rent epidemic, most of the cases will probably have other aetiologies. The positive predictive value of clinical criteria for identification of influenza A is particularly low in the early phase of an epidemic, when the incidence of influenza A is low, but will become relatively high during the peak when a large proportion of respiratory infections will be due to influenza A virus. The value of broad virology testing decreases in the course of an influenza epidemic, when the detection rate of other aetiologies may decrease from above 50 percent as observed in this report to below 10 percent during the influenza peak (unpublished observations from our laboratory).

The cases with influenza A were analysed further by a typing PCR that within 4-5 hours could identify whether the strain was a traditional H1N1 or H3N2 virus, or the new H1N1 variant. This typing system targets specific regions of the haemagglutinin gene and has been developed in our laboratory (unpublished). It has proved to have a good sensitivity, as illustrated by cycle threshold (Ct) values that are typically lower than those obtained in the general PCR for influenza A, which targets a conserved region of the matrix protein gene.

The results of the multiple PCR used in our setting were available within 24 hours after sampling and served at the same time as confirmation for the result of the 1st, general influenza A PCR. In cases that presented with typical influenza-like symptoms but were negative for influenza A in the 1st PCR, the finding of an alternative aetiology was helpful for the decision to refrain from preventive measures. Such measures include oseltamivir treatment of patients and influenza testing and prophylactic treatment of their close contacts. The clinical practice was not always different, but in some cases, the identification of an alternative aetiology such as rhinovirus was helpful for the decision not to treat the patient of contacts, even when the patient had symptoms clearly indicative of possible influenza. From this experience, we therefore conclude that a broad diagnostic test is a valuable tool in the early investigation of a new emerging respiratory virus like the new influ! enza A(H1N1)v.

[Note added in proof: On 17 Jun 2009, Sweden changed to a stricter case definition for suspected cases. It now requires more than 2 symptoms besides epidemiology and fever.]


1. Centers for Disease Control and Prevention (CDC). Swine influenza A (H1N1) infection in 2 children--Southern California, Mar-Apr 2009. MMWR Morb Mortal Wkly Rep. 2009;58(15):400-2.

2. Novel Swine-Origin Influenza A (H1N1) Virus Investigation Team. Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans. N Engl J Med. 2009 Jun 3. [Epub ahead of print].

3. World Health Organization (WHO). Influenza A(H1N1) - update 50. Jun 17, 2009. Available from: <>.

4. Commission Decision of 30 Apr 2009 amending Decision 2002/253/ EC laying down case definitions for reporting communicable diseases to the Community network under Decision n 21/19/98/EC. 2009/363/EC. Official Journal L 110/58. 01.05.2009. Available from: <>.

5. World Health Organization (WHO). Influenza A(H1N1) - update 2. Apr 26, 2009. Available from: <>

6. Brittain-Long R, Nord S, Olofsson S, Westin J, Anderson LM, Lindh M. Multiplex real-time PCR for detection of respiratory tract infections. J Clin Virol. 2008;41(1):53-.

7. Ward CL, Dempsey MH, Ring CJ, Kempson RE, Zhang L, Gor D, et al. Design and performance testing of quantitative real time PCR assays for influenza A and B viral load measurement. J Clin Virol. 2004;29(3): 179-88.

Communicated by:ProMED-mail

[These data among other things reveal that the positive predictive value of clinical criteria for identification of influenza A is low in the early phase of an epidemic, when the incidence of influenza A is low, but will become relatively higher during the peak, when a large proportion of respiratory infections will be due to influenza A virus. Among the viruses detected, rhinoviruses and coronaviruses predominated in this survey. - Mod.CP]


John Glenn, MBCI
Enterprise Risk Management
John.GlennMBCI at gmail dot com
Fort Lauderdale FL

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