World Health Organization Global Influenza Surveillance Research Articles

Alarming case of avian influenza A (H5) in humans: call for urgent action in Ecuador

Alarming case of avian influenza A (H5) in humans: call for urgent action in Ecuador

Results from the WHO external quality assessment for the respiratory syncytial virus pilot, 2016-17.

BackgroundExternal quality assessments (EQAs) for the molecular detection of respiratory syncytial virus (RSV) are necessary to ensure the provision of reliable and accurate results. One of the objectives of the pilot of the World Health Organization (WHO) Global RSV Surveillance, 2016‐2017, was to evaluate and standardize RSV molecular tests used by participating countries. This paper describes the first WHO RSV EQA for the molecular detection of RSV.MethodsThe WHO implemented the pilot of Global RSV Surveillance based on the WHO Global Influenza Surveillance and Response System (GISRS) from 2016 to 2018 in 14 countries. To ensure standardization of tests, 13 participating laboratories were required to complete a 12 panel RSV EQA prepared and distributed by the Centers for Disease Control and Prevention (CDC), USA. The 14th laboratory joined the pilot late and participated in a separate EQA. Laboratories evaluated a RSV rRT‐PCR assay developed by CDC and compared where applicable, other Laboratory Developed Tests (LDTs) or commercial assays already in use at their laboratories.ResultsLaboratories performed well using the CDC RSV rRT‐PCR in comparison with LDTs and commercial assays. Using the CDC assay, 11 of 13 laboratories reported correct results. Two laboratories each reported one false‐positive finding. Of the laboratories using LDTs or commercial assays, results as assessed by Ct values were 100% correct for 1/5 (20%). With corrective actions, all laboratories achieved satisfactory outputs.ConclusionsThese findings indicate that reliable results can be expected from this pilot. Continued participation in EQAs for the molecular detection of RSV is recommended.

Access by Design, Benefits if Convenient: A Closer Look at the Pandemic Influenza Preparedness Framework's Standard Material Transfer Agreements.

The World Health Organization (WHO) adopted the Pandemic Influenza Preparedness Framework (PIP Framework) after being forced to grapple with the demands of developing countries for the fairer distribution of vaccines and antivirals created using influenza viruses isolated from within their territories. Though adopted as a nonbinding resolution, the PIP Framework has been praised for its novel legal approach to access and benefit-sharing (ABS), using Standard Material Transfer Agreements (SMTAs) to create binding terms and conditions on both providers and users of PIP biological materials. The PIP Framework's SMTA1 regulates the movement of influenza viruses with human pandemic potential through the WHO's Global Influenza Surveillance and Response System (GISRS) as it operates to monitor the spread of seasonal influenza and detect the emergence of pandemic strains. Member States give consent to the WHO to transfer their materials to third parties under the terms of a negotiated SMTA2. The SMTA2 details benefits such as vaccines and antivirals to be made available to the WHO for distribution in the event of an influenza pandemic. I analyzed the PIP Framework, its SMTAs, and secondary sources to determine whether the PIP Framework will effectively function as an ABS instrument during an influenza pandemic. The SMTAs do not create any direct or binding agreements between Member States and third-party recipients of influenza viruses. In the lead-up to and during a pandemic, the SMTA1 secures access to influenza viruses for the WHO, and the SMTA2 secures access for commercial users of virus samples, but the SMTA2 may be ineffective in securing tangible benefits for the sovereign providers of those materials. As the international community starts to consider how to best regulate access to nonpandemic influenza pathogen samples, it is imperative that we first address the shortcomings of the only pathogen-specific international ABS instrument available, and we should do so before it is put to the ultimate test.

Laboratory preparedness in EU/EEA countries for detection of novel avian influenza A(H7N9) virus, May 2013

Following human infections with novel avian influenza A(H7N9) viruses in China, the European Centre for Disease Prevention and Control, the World Health Organization (WHO) Regional Office for Europe and the European Reference Laboratory Network for Human Influenza (ERLI-Net) rapidly posted relevant information, including real-time RT-PCR protocols. An influenza RNA sequence-based computational assessment of detection capabilities for this virus was conducted in 32 national influenza reference laboratories in 29 countries, mostly WHO National Influenza Centres participating in the WHO Global Influenza Surveillance and Response System (GISRS). Twenty-seven countries considered their generic influenza A virus detection assay to be appropriate for the novel A(H7N9) viruses. Twenty-two countries reported having containment facilities suitable for its isolation and propagation. Laboratories in 27 countries had applied specific H7 real-time RT-PCR assays and 20 countries had N9 assays in place. Positive control virus RNA was provided by the WHO Collaborating Centre in London to 34 laboratories in 22 countries to allow evaluation of their assays. Performance of the generic influenza A virus detection and H7 and N9 subtyping assays was good in 24 laboratories in 19 countries. The survey showed that ERLI-Net laboratories had rapidly developed and verified good capability to detect the novel A(H7N9) influenza viruses.

Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity

BackgroundThe World Health Organization (WHO) organizes consultations in February and September of each year, spearheaded by an advisory group of experts to analyze influenza surveillance data generated by the WHO Global Influenza Surveillance and Response System (GISRS). The purpose of these consultations is to recommend the composition on influenza virus vaccines for the northern and southern hemispheres, respectively. The latest news of influenza viruses is made available to the public and updated on the WHO website. Although WHO discloses the manner in which it has made the recommendation, usually by considering epidemiological and clinical information to analyze the antigenic and genetic characteristics of seasonal influenza viruses, most individuals do not possess an understanding of antigenic drift and when it occurs.FindingsWe have constructed a web server, named Fluctrl, and implemented a pipeline whereby HA sequence data is downloaded from the Influenza Virus Resource at NCBI along with their isolation information including isolation year and location, which are parsed and managed in MySQL database. By analyzing the frequency of each amino acid residue of the HA1 domain expressed by the viruses on annual basis, users are able to obtain evolutionary dynamics of human influenza viruses corresponding with epidemics. Users are able to upload and analyze their HA1 sequences for generating evolutionary dynamics. In addition, a distribution of amino acid residues at a particular site is represented geographically to trace the location where antigenic variants are seeded.ConclusionsFluctrl is constructed for monitoring the antigenic evolution of human influenza A viruses. This tool is intended to inform the general public how and when influenza viruses evade the human body's immunity. Furthermore, leveraging the geographic information, the original locations of emerging influenza viruses can be traced. Fluctrl is freely accessible at http://sb.nhri.org.tw/fluctrl.

Influenza A(H1N1)pdm09 virus: viral characteristics and genetic evolution

From April 2009 to the present, the influenza A(H1N1)pdm09 virus has been evolving continuously, acquiring new amino acid changes that may alter its antigenic characteristics, virulence, and its antiviral drug susceptibility. Phylogenetic analysis of the hemagglutinin (HA) gene of A(H1N1)pdm09 viruses showed that it clustered into 8 genetic groups relative to A/California/7/2009, in addition to others reported by regional influenza surveillance networks. However, none were considered antigenically distinct from the vaccine virus A/California/7/2009, which was recommended for use during the 2012–2013 influenza season in the Northern Hemisphere. Amino acid substitution D222G in the HA1 subunit of HA was the first potential virulence marker of the influenza A(H1N1)pdm09 virus that was associated with severe clinical outcomes. The vast majority of influenza A(H1N1)pdm2009 viruses tested by the WHO-GISRS (World Health Organization-Global Influenza Surveillance and Response System) laboratories were sensitive to neuraminidase inhibitor (NAI) drugs, and during the 2011–2012 influenza season the resistance prevalence was low (1%) or undetectable in the United States and Europe. Resistance to NAIs was detected predominantly in patients with severe conditions, most of whom were immunosuppressed. The resistance was usually associated with the H275Y mutation in the NA protein sequence, although other amino acid substitutions were also reported to confer resistance or decreased susceptibility to 1 or more NAIs. Global virological surveillance should be strengthened for new influenza variants carrying new mutations or reassorted segments that may affect viral features such as virulence, transmission, or antiviral susceptibility.

Symposium on viral respiratory disease surveillance

Recognition of the need for respiratory disease surveillance for informing prevention strategies dates back to the late 1940’s. Sir Christopher Andrews realized that the development of a successful influenza vaccination programme would be hindered by the unpredictable nature of the influenza virus and proposed the formation of a world influenza centre and a network of linked national laboratories which tracked influenza epidemics, to the World Health Organization (WHO). This network, now the WHO Global Influenza Surveillance Network (GISN) remains in place today and, although it’s primary goal is still to inform seasonal influenza vaccine strain selection, it has had to widen its activities to address emerging public health needs. There has been a renewed focus on understanding the overall burden of disease caused by influenza, especially in countries with no seasonal influenza prevention programmes, as a strategy to increase influenza awareness. While the zoonotic and pandemic threats from the highly pathogenic avian influenza (HPAI) H5N1 and H7N7 viruses and the realization that pandemic influenza arises from avian influenza viruses have stimulated global and national pandemic preparedness activities. Nevertheless, improved surveillance systems for both animal (avian and pig) and human influenza viruses are needed for informing and refining prevention strategies. Although the public health focus globally has been on influenza, the burden of disease caused by other respiratory viruses is also substantial and is largely under-recognised. A range of respiratory viruses are implicated in pneumonia, a disease recognised as a major killer of young children in developing countries and of the elderly in developed countries. There is also evidence that some respiratory viruses may be evolving allowing virulent variants to cause outbreaks in certain at-risk populations presenting another possible pandemic risk, highlighting the need to monitor unusual outbreaks of respiratory disease and the importance of the surveillance of respiratory viruses in general. Overall, prevention strategies for respiratory viruses other than influenza are less well defined, undoubtedly contributing to their perceived lower public health priority. Major advances in the diagnosis of respiratory virus infections have been made through the wider use of molecular diagnostic techniques which are now enabling rapid and sensitive respiratory pathogen surveillance. It is now possible to identify a wide range of respiratory pathogens in a higher proportion of respiratory infections, along with multiple pathogen infections. The application of these molecular techniques has also lead to the discovery of a number of new respiratory viruses; the clinical importance of the human metapneumovirus (hMPV) is now well established, while with others such as the human bocavirus (HBoV) and human rhinovirus type C (HRV-C), their clinical correlates are only just being elucidated. The knowledge base on these viruses urgently needs expanding through well designed controlled studies and other activities, including widened surveillance. The future challenge is to build on what has been achieved for the global surveillance of influenza by establishing standardized surveillance protocols which incorporate a widening range of respiratory viruses. The purpose being to inform and refine respiratory disease prevention strategies. These strategies must then be communicated to governments and public health messages developed for the education of the general public. DOI:10.1111/j.1750-2659.2010.00140.x www.influenzajournal.com

Vaccines against Influenza A (H1N1) Pandemic

The World Health Organization (WHO) has reported, as of September 2009, that the influenza A (H1N1) influenza pandemic has originated >300,000 laboratory-confirmed cases and 3917 deaths in 191 countries. It is recognized that pandemic vaccines have their greatest impact as a preventive strategy when administered before or near the peak incidence of cases in an outbreak. Therefore, vaccination campaigns should be in place when influenza A (H1N1) 2009 vaccines are available. We undertook this study to provide updated information on clinical evaluation of influenza A (H1N1) vaccines and review recommendations for influenza A (H1N1) vaccination campaigns and public health policy. The following methods were used: 1) review of registry at ClinicalTrials.gov. 2) search of PubMed Central (PMC) for influenza A (H1N1) vaccine. 3) review of recommendations of WHO, Mexican Health Secretariat (SSA) and Advisory Committee on Immunization Practices (ACIP) on influenza A (H1N1) vaccination campaigns. Until October 1, 2009 there were 11 available influenza A (H1N1) candidate strains provided by WHO Global Influenza Surveillance Network. ClinicalTrials.gov registers 45 phase I and II clinical trials evaluating immunogenicity and safety of influenza A (H1N1) vaccines. Preliminary results support administration of a single dose and use of adjuvants. Main recommendations of WHO, SSA and ACIP include epidemiologic considerations, objectives, definition of target groups and reinforcement of other mitigation measures. The present pandemic of influenza A (H1N1) has shown mild to moderate severity. Vaccination strategies in Mexico will have the objective of decreasing severe outcomes, slowing transmission, protecting groups at increased risk of infection, complications, or death, and preventing overload of health services. Control of the pandemic should include reinforcement of other non-pharmacologic measures of mitigation and, importantly, an adequate strategy of social communication.

Diagnostic Assay Recommended by the World Health Organization for Swine Origin Influenza A (H1N1) Virus Cross-Reacts with H5N1 Influenza Virus

Pandemic influenza poses a significant risk to global human health. The unpredictable nature of the influenza virus necessitates accurate, reliable, and rapid diagnostic assays for the detection of, and characterization of the current pandemic caused by, swine origin influenza virus (SOIV) in order to better understand the nature of the pandemic and implement appropriate health interventions. SOIV emerged in mid-April 2009 (1), leaving laboratories around the world scrambling to establish a diagnostic test to detect this novel influenza virus. The World Health Organization (WHO) responded with remarkable speed by releasing guidelines and protocols for a real-time reverse transcription (RT)-PCR assay 15 days after the reported identification of SOIV (2). This provided a rapid and sensitive assay for the detection of SOIV that was critical for the determination of the spread and extent of SOIV infections. These guidelines recommend three primer-and-probe sets: InfA, amplifying a conserved region of the matrix gene from all influenza A viruses; SW H1, designed to specifically detect the hemagglutinin gene segment (subtype H1) from SOIV; and SW InfA, designed to specifically detect the nucleoprotein (NP) gene segment from all swine influenza viruses. As part of the WHO Global Influenza Surveillance Network, the New Zealand National Influenza Centre regularly participates in WHO external quality assurance panels of 10 RNA samples that are H1N1, H3N2, or H5N1 influenza A virus or, recently, SOIV. In following the WHO recommended guidelines exactly, it was found that the SW InfA primer-and-probe set amplified all six H5N1 RNA samples. This is clinically relevant, as the proficiency panel RNA returned threshold cycle (CT) values (InfA assay, 23.44 to 28.67) well within the range of what we regularly observe with clinical samples. In addition, the SW InfA primer-and-probe set detected two additional H5N1 viruses not provided in the proficiency panel, the human H5N1 strain A/Vietnam/3028/2004 and an avian H5N1 strain, A/Mallard/New Zealand/272-73/2008. The efficiency of this reaction was 79% (three replicates) compared to 94% (five replicates) for the amplification of SOIV RNA, suggesting that mismatches within the primer target region reduced assay efficiency. To prove that the H5N1 NP gene sequence was amplified by the SOIV SW InfA assay, all real-time RT-PCR amplicons were sequenced. The two SOIV RNA samples from the proficiency panel and SOIV-positive control showed 100% identity to the consensus sequence of 394 NP full-length gene segments available as of 29 July 2009. In contrast, all H5N1 RNA samples from the proficiency panel contained at least 31 nucleotide differences from the SOIV consensus sequence but showed between 93.3% and 96.8% identity to A/Vietnam/1203/2004. Alignment of all SOIV and human H5N1 NP gene segments available in GenBank showed that 391 SOIV viruses have one mismatch in the SW InfA forward primer (Table ​(Table1).1). The remaining three SOIV sequences have a further mismatch in either the forward primer or the probe. The majority (74.6%, or 91 sequences) of available human H5N1 sequences are identical within the SW InfA primer-and-probe regions, having two mismatches in the forward primer, two in the probe, and four in the reverse primer region. None of the mismatches occurred within 9 nucleotides of the 3′ end, an important determinant for primer specificity. TABLE 1. Comparison of SOIV and human H5N1 NP gene sequences with SW infA primer and probe sequences The speed at which these assays were developed and deployed to the WHO Global Influenza Surveillance Network was remarkable, particularly with the limited SOIV sequence information available at the time of development. Other factors which constrained the development of RT-PCR primer targets include the origin and genetic rate of change for each gene segment; only five of the eight gene segments are of swine origin (3), while the rapidly evolving HA and NA genes have a propensity to drift at a much higher rate than conserved segments such as NP (5). This report demonstrates that the SW InfA assay is not specific to SOIV and is able to detect both human and avian (H5N1) influenza A viruses and so there is the potential for misidentification. Following WHO guidelines, the utilization of all primer-and-probe sets for the detection of SOIV should provide an accurate diagnosis. However, we have observed that for the same SOIV RNA sample, the SW InfA assay consistently returns lower CT values than the SW H1 assay and so clinical samples with higher CT values can yield an SW H1-negative, SW InfA-positive result. In these cases, we suggest sequencing of real-time SW InfA PCR amplicons to ensure the amplification of SOIV (4). Alternatively, and especially for countries in which H5N1 is endemic, an H5N1-specific assay could be performed to exclude this diagnosis. However, a negative H5N1 result would not exclude other influenza virus subtypes that may cross-react with the SOIV assay.

Widespread Oseltamivir Resistance in Influenza A Viruses (H1N1), South Africa

To the Editor: Oseltamivir is the most widely used antiviral drug for influenza; it is a potent inhibitor of influenza virus neuraminidase (NA) protein (1). Until recently, oseltamivir resistance occurred in <1% of circulating viruses globally. An increased number of influenza A viruses (H1N1) with resistance to oseltamivir was first reported to the World Health Organization (WHO) by Norway in late January 2008. The viruses carried a specific histidine-to-tyrosine mutation at position 274 (H274Y; H275Y in N1 numbering system) in the NA protein that confers high-level resistance to oseltamivir (2). Further surveillance by the European Surveillance Network for Vigilance against Viral Resistance and the WHO Global Influenza Surveillance Network (GISN) showed that 16% of community isolates (0%–67% by country) of influenza A viruses (H1N1) circulating in the 2007–08 season in several other countries were also oseltamivir resistant (3). The predominant influenza subtype circulating in South Africa this winter season is H1N1. To determine whether oseltamivir-resistant viruses have spread to South Africa, we examined influenza A (H1N1) isolated during the 2008 winter season for resistance to this antiviral compound. Specimens were obtained mainly from the National Institute of Communicable Diseases (NICD) active sentinel surveillance program in all 9 provinces. Throat or nasopharyngeal swabs were taken from patients within 48–72 hours of onset of symptoms and sent to NICD laboratories for virus isolation as described (4). Of the H1N1 subtype viruses isolated in May and June, 23 were sent to the WHO Collaborating Centers for Reference and Research on Influenza in London and Melbourne for resistance testing (5,6). Forty-five of the viruses, which included viruses isolated in July, were tested at NICD by using a modified amplification refractory mutation system PCR (ARMS-PCR) (7). This method can simultaneously detect wild-type or mutant virus with the 274 mutation in a single PCR. Partial sequencing of the NA and hemagglutinin (HA) genes was performed to confirm the NA H274Y resistance mutation and to determine genetic drift in HA from the A/Brisbane/59/2007 virus recommended for the Northern Hemisphere 2007–08 vaccine. At the time of resistance testing, 92 H1N1 subtype viruses had been isolated. The 23 virus isolates sent to the WHO Collaborating Centers were highly resistant to oseltamivir by the NA inhibition enzyme assay, with 50% inhibitory concentration values of 554 nM to 1,485 nM (A. Hay, I. Barr, pers. comm.). All 45 isolates tested locally were positive by ARMS-PCR for oseltamivir resistance at position 274. The H274Y mutation was confirmed by sequence analysis of the N1 genes. The N1 sequences were closely related to those isolated in Europe and elsewhere in the 2007–08 winter season. However, the presence of 1 or 2 aa mutations in viruses from South Africa (M23L and N73K in the stalk region) compared with resistant European isolates indicated that some genetic drift of N1 from the older strains had occurred. Although most 2008 isolates were closely related to the A/Brisbane/59/2007 strain, several of the isolates from South Africa had mutations in an additional 2 or 3 aa residues at positions 183, 185, and 189, which mapped close to the receptor binding site of HA. (GenBank accession numbers for nucleotide sequences obtained in this study are {type:entrez-nucleotide-range,attrs:{text:EU914901-EU914916,start_term:EU914901,end_term:EU914916,start_term_id:195661082,end_term_id:195661112}}EU914901-EU914916.) Before the 2007–08 Northern Hemisphere winter, surveillance by GISN laboratories showed that oseltamivir-resistant H1N1 subtype viruses were extremely rare. Low numbers of drug-resistant viruses carrying the H274Y mutation usually followed oseltamivir treatment and showed reduced fitness with poor transmission (8). Consequently, fitter nonresistant viruses appear to have predominated. In contrast, no evidence indicated that persons from whom resistant viruses were isolated during the European 2007–08 winter season had either been treated or been in close contact with another person who had been treated with oseltamivir (2,8). We report oseltamivir-resistant H1N1 subtype viruses in Africa and the Southern Hemisphere. It appears that resistant viruses have spread from the Northern Hemisphere and have undergone extensive transmission within the population. These viruses may soon appear in other countries in the Southern Hemisphere. Ongoing monitoring is needed to understand the further evolution of oseltamivir resistance. Clinical symptoms of all patients in this study suggest an illness similar to that generally associated with seasonal influenza A virus (H1N1); no complications were reported. This finding is not unexpected because all isolates tested in the study were from outpatients. The policy in South Africa for use of oseltamivir for treatment of severe influenza remains unchanged because 2008 H3N2 subtype viruses are still drug sensitive.

William Graeme Laver PhD, FRS (1929–2008)

William Graeme Laver PhD, FRS (1929–2008)

The WHO Global Influenza Program and its Animal Influenza Network.

The World Health Organization (WHO) Global Influenza Program makes annual recommendations on influenza vaccine formulation and related activities. This results in 230 million annual doses of vaccine produced for human use. The success of this program is based on the collection and genetic and antigenic analyses of influenza viruses collected by the WHO Global Influenza Surveillance Program. New programs focus on pandemic preparedness and include development and distribution of testing reagents for emerging or potentially emerging human influenza viruses. WHO Animal Influenza Network focuses on aspects of ecology and molecular biology of animal influenza viruses in the context of human health.

Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection

In recent years, collaborations often between mathematical and computational biologists and scientists in the World Health Organization (WHO) global influenza surveillance network, have resulted in a number of mathematical and computational advances including: increasing the resolution at which antigenic surveillance data can be analyzed, providing methods for genetic analysis and prediction, and an increased understanding of the determinants of repeated influenza vaccination. These advances increase the information extracted from influenza surveillance and increase the quantitative data available for the vaccine strain selection process. This mathematical and computational work is possible because of the wealth of information collected over many years by the WHO global influenza surveillance network, and further advances will be greatly facilitated by implementation of the proposed strengthening of virological and epidemiological surveillance in the WHO global agenda on influenza surveillance and control.