Getting to know the flu pandemic

It has been the big medical story of the year, dominating headlines and overrunning diagnostic labs – here we get the inside story on H1N1, find out how it came to be and why it isn’t really swine flu at all…

SINCE late April, 2008, laboratories worldwide have experienced unprecedented volumes of respiratory samples. While most western scientists were waiting for the impending new pandemic of influenza to spread to the world from Asia and considered Avian influenza and related strains to be the top contenders, it appears that the next great wave of worldwide influenza developed in our own backyard. 

A rapid increase in influenza cases reported near Mexico City beginning in March, 2008, was quickly followed by unusual influenza activity in the US. California noted cases starting in late March and confirmed in April to be the same H1N1 strain as that seen in the Mexican outbreak1. As can be seen from the graph based on data reported by the World Health Organization (WHO) and National Respiratory and Enteric Virus Surveillance System (NREVSS) (Figure 1), almost all of the following influenza isolates identified were a previously unknown strain, now designated 2009 influenza A (H1N1), also known as “novel H1N1” because it differed in several genetic ways from the already circulating influenza A (H1N1). 

The virus seems to have been generated by a unique combination of six genes from influenza A strains of both human and avian origins that had managed to meet and recombine their RNA genetic elements in swine (hence the early designation of “swine flu,” an unfortunate choice of names that suggested that pigs were a potential source of the infection and sent pork demand tumbling unnecessarily), and from there move into humans. In fact, some reports have suggested that the basis for this apparent “genetic promiscuity” may have originated in US-based industrial pig farms in the late 1990’s11. The genes included existing H1N1 matrix, neuraminidase, and hemagglutinin gene segments from Eurasian swine,  neuraminidase and hemagglutinin genes from H3N1 and H3N2 segments circulating in birds, nucleoprotein and viral matrix genes from classic swine influenza H3N2, polymerase protein genes from avian and swine strains H1N1 and H3N3, and nonstructural protein genes from H1N12.

This virus is unusual in a number of aspects. Its appearance in laboratories has continued rather steadily since this spring, whereas in previous years the “flu season” usually ended around May. In fact, in the second week of September of this year, 99% of all viruses typed by the reporting laboratories were 2009 influenza A (H1N1) (http://www.cdc.gov/flu/weekly/). Surprisingly, the disease in most patients seems to be less severe than disease caused by the previously circulating influenza strains - Influenza A (H1N1) and (H3N2) - although certainly there are sporadic reports of severe cases and even deaths. However, the virus appears to be unusually contagious, spreading rapidly among family members or close contacts. Even during the summer months, when most influenza virus activity in the temperate US almost disappears, this virus has continued to proliferate and cause disease (Figure 1). Because of the rapidly changing influenza pandemic situation, many sources for this information were only accessible on-line, and not yet available in formal publications. 

Since the beginning of the epidemic in March, the World Health Organization has reported that >60,000 specimens have tested positive for influenza, as reported on FluNet, the international web-based database (http://gamapserver.who.int/GlobalAtlas/home.asp). Of these, almost 60% were determined to be the novel strain, although that number is an underestimate as not all strains were typed (WHO Weekly Epidemiological Record, September 4, 2009; http://www.who.int/wer/). Of the >8,000 samples received for influenza testing by participating laboratories, 76% were positive and more than half of those harbored the new 2009 influenza A strain. In the world at large, parts of Asia and Africa still showed a large percentage of cases that were caused by subtypes other than 2009 influenza A (H1N1) but the western hemisphere and Europe had much less diversity (http://www.cdc.gov/h1n1flu/updates/international/map.htm).

The 'genetic promiscuity' leading to the rise of HINI

Patients who are experiencing influenza-like-illness (ILI), and often those with simple upper respiratory symptoms not likely to represent influenza, have presented themselves for testing in doctors’ offices, emergency departments, and outpatient clinics in record numbers. The constellation of symptoms associated with influenza disease includes fever, headache, fatigue, cough, sore throat, runny or stuffy nose, body aches, and gastrointestinal symptoms such as diarrhea (more common in children). These symptoms are not different from seasonal influenza, but the patient groups at highest risk for novel H1N1 are slightly different this year. Older adults (>65) are not at higher risk as they are for seasonal influenza, but when they do become ill, their disease can be serious. The groups at higher risk this flu season include young children < 5 years, pregnant women, particularly those carrying multiple fetuses, diabetics, obese people, and those with asthma or other respiratory problems5. Laboratories that usually stopped testing around May have been forced to continue to test for influenza all summer, causing havoc with summer vacation plans and laboratory workload. 

Why is it important to know if a patient’s influenza-like-illness is caused by the previously circulating influenza A strains or the 2009 novel influenza A H1N1 strain?  There are two good reasons, firstly antiviral treatment recommendations are based on the infection strain and secondly patients in the higher risk groups infected with novel 2009 H1N1 should be managed more aggressively. The novel 2009 H1N1, now the dominant strain in the US, is resistant to amantidine and rimantidine, but still primarily susceptible to oseltamivir, although there are now several reports documenting the isolation of resistant strains (http://www.who.int/csr/disease/swineflu/notes/h1n1_antiviral_use_20090925/en/index.html). It has been suggested that widespread use of oseltamivir prophylaxis in the absence of disease is more likely to result in development of antiviral resistance (http://www.cdc.gov/h1n1flu/recommendations.htm) . In contrast, the previously circulating seasonal influenza A (H1N1) strains were resistant to oseltamivir but remained susceptible to an older oral drug class, the adamantanes. Both versions of influenza A are susceptible to zanamivir (Relenza), but because zanamivir must be administered as an aerosol, it may not be appropriate for some severely ill patients.  For current treatment and prophylaxis guidelines, which are changing rapidly, consult the CDC website http://www.cdc.gov/h1n1flu/recommendations.htm. 

Despite the need for rapid information based on diagnostic test results, there are currently no diagnostic tests that are both reliable and rapid. Types of assays available include rapid antigen tests appropriate for point-of-care testing, both membrane enzyme immunoassays (MEIAs) and immunochromatographic tests (ICTs), the most commonly used tests worldwide. Although performance, especially sensitivity, in the past was not ideal, the rapid availability of positive results was thought to be helpful for clinical decisions. A recent paper evaluating 20 rapid antigen tests with culture-obtained viruses (unfortunately the novel influenza A H1N1 strain was not tested) showed widely variable sensitivity among the tests, with the most sensitive test requiring 3 times the initial volume as some other tests10. With regard to this year’s circulating strain of H1N1 novel 2009, the problem appears to have intensified; the rapid tests’ sensitivities range from 10-70%3, a sensitivity so low that many clinicians and microbiologists are choosing not to offer the test. Although positive results may still be helpful (even though false positives are relatively common), especially in low-prevalence areas, negative result cannot be used to rule out infection. With the advent of 2009 influenza A H1N1, recent studies have shown that individuals who test negative with these assays can still be infectious and should not be encouraged to reenter public settings such as schools, churches or hospitals without confirmation from more sensitive tests. The CDC’s recent interim guideline on rapid tests (http://www.cdc.gov/h1n1flu/guidance/rapid_testing.htm) suggests that laboratories add a statement about the limitations of the tests and not make infection control decisions on the basis of these tests.

Aside from the rapid antigen tests, all other available assay types are high complexity. Culture has always been quite sensitive, but its turnaround time is too slow for clinical use9. Direct fluorescent antibody testing of respiratory secretions is specific, but its sensitivity is dependent on the expertise of the laboratory performing the test. A recent study showed poor sensitivity in one laboratory but good sensitivity has been seen in other settings4,9. The current gold standard for testing is use of a molecular diagnostic method for detection of viral nucleic acids4,6. Of the commercial molecular assays currently available, only the Focus assay is FDA-cleared for specific identification of novel 2009 H1N1, although other platforms (Prodesse ProFlu+ and Luminex xTag) do detect the novel strains along with other influenza A strains, so it would not be missed.  A number of laboratories have developed their own in-house molecular tests on varying platforms, based on sequences or procedures published by CDC or others, available on the WHO website (http://www.who.int/csr/resources/publications/swineflu/CDCrealtimeRTPCRprotocol_20090428.pdf)7,8.