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      Global Infections—Avian Influenza and Other Significant Emerging Pathogens: An Overview

      review-article
      , DO, MPH, FACPM
      Disease-a-Month
      Mosby

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          Abstract

          The single greatest threat to man’s continued existence on earth is the virus. Joshua Lederberg, Nobel Laureate Infections remain a leading cause of death worldwide.1, 2, 3, 4, 5, 6, 7 Although the United States has been able to significantly control many of the infectious diseases that continue to afflict much of the rest of the world, these pathogens remain a threat to us nevertheless.2, 3 Control of emerging infectious diseases can be a daunting task given the large number of disease-causing organisms and the opportunity for adaptation, evolution of antimicrobial resistance, and host factors.1, 2, 3, 4, 5, 6, 7 Also, newer pathogens are emerging, such as metapneumovirus. 8 Other new viruses, often from East Asia, nosocomial infections continue to be a persistent cause of preventable death in U.S. hospitals, and mutations of existing pathogens into highly virulent strains is likely to continue.1, 5 In addition to the natural evolution of pathogens, global modernization and development are increasingly placing people into new regions and environments and thus new exposures. Bioterrorism represents another risk of exposure to emerging diseases through the intentional use of biological agents—military grade and adapted naturally found pathogens.1, 4 As such, there are numerous emerging infectious threats that are suitable for an entire edition of Disease-a-Month to address. Global travel, immigration into the U.S. from countries with endemic illnesses not commonly found in North America, and societal factors (domestic and international) that include poverty, homelessness, institutionalization, overcrowding, and lack of access to health care set the stage to create conditions that facilitate the emergence and spread of previously unknown, little recognized, or emerging illnesses that are endemic to or novel strains in foreign lands that can become very quickly clinical realities to the United States.1, 2, 3, 4, 5, 6, 7 Although the scope of this edition focuses on avian influenza, it is important to recognize that preparedness efforts as a response to a potential pandemic can also enhance awareness, diagnostic, and treatment capabilities toward other significant infectious diseases worldwide and underscore the importance of continued vigilance for and training about these pathogens.1, 4, 5, 7 The following are pathogens that have the potential to cause outbreaks and remain significant public health problems. Tuberculosis (Mycobacterium tuberculosis; TB) is the second most common cause of death in the world, resulting in 3-4 million deaths annually and 8 million new cases a year. It is also the most common opportunistic infection associated with HIV. 9 This is not just a global threat, but a domestic one, with drug- and multidrug-resistant TB continuing as a significant public health concern. Of concern, extremely drug-resistant TB (XDR-TB) is emerging. TB is often problematic to treat in the most common form; a strain that is resistant to most of the first- and second-line treatments could be devastating if allowed to go unchecked. Infection such as measles is a virus long viewed as both a childhood disease and one that has been controlled in the U.S. This notwithstanding, measles is still the cause of severe illness worldwide. Moreover, there continue to be outbreaks in the U.S. among unimmunized or inadequately immunized individuals. In 2006, a computer programmer from India infected with measles arrived in Boston, Massachusetts. 10 In response to his infecting several individuals, 23,000 doses of measles vaccine were ordered and/or distributed in anticipation of the potential for a significant public health crisis. Only 56% of infants in India are vaccinated against this potentially lethal pathogen, whereas 93% of U.S. children are. Measles is one of the top 5 causes of death worldwide for children. Clearly, global travel can bring infections from far-off lands into our waiting rooms and communities with relative ease! Malaria remains a significant global health problem and is vector borne. How many of us or our colleagues have seen or treated a case, yet it is one of the leading causes of death for children and adults worldwide. Plague remains a significant public health problem in selected nations worldwide, with sporadic cases occurring in the U.S., sometimes being diagnosed long distances away from where the infection occurred. Recall the couple visiting New York City who fell ill, only to be diagnosed with Yersinia pestis (plague), which they were exposed to from rodent excreta at the Southwest home. Unexpected pathogens in the 1990s, such as West Nile Virus (WNV), have become almost household words by 2007. In fact, WNV has become almost synonymous with mosquito-borne illness, yet worldwide Dengue is the most common mosquito-borne infection and is quickly becoming a global public health concern, given that 2.5 billion people live in areas where dengue viruses can be transmitted! The geographical spread of both the mosquito vector and dengue viruses has led to a global resurgence of both dengue fever and dengue hemorrhagic viruses. 7 How many clinicians have seen a case or could readily recognize dengue or other hemorrhagic fever viruses in a patient? It is important to note that servicemen and servicewomen returning from the Middle East and other foreign lands may harbor endemic illnesses that U.S. physicians may be unaware of or unaccustomed to treating. In anticipation of veterans returning from the Persian Gulf and other places across the globe, it is important to familiarize ourselves with pathogens that are likely to infect them. During the 20th century there were several major influenza outbreaks and three pandemics occurring in 1918, 1957, and 1968. The most important was the Spanish Flu global epidemic of 1918 that resulted in 50 million deaths, although some estimates suggest an even higher loss of life.6, 11 This does not reflect the full toll that such outbreaks inflict upon a society, which includes economic, emotional with the loss of loved ones, and of course illness that does not result in death. Experts express concern that it is only a matter of time until the next pandemic occurs; it’s not “if” but “when” an influenza virus mutates into a highly virulent, contagious strain. In 1997 the world was introduced to a likely candidate to create such a pandemic: highly pathogenic avian influenza HPA H5N1. 6 H5N1 is a particularly worrisome strain of influenza virus not only because it mutates rapidly and has a tendency to acquire genes from other strains of influenza viruses that may concomitantly be infecting other animal species, but because it has demonstrated several of the characteristics necessary for a pathogen to cause a pandemic: ability to cause severe disease and death in humans against a backdrop of a population with little to no inherent immunity for which no widely available vaccine exists and capable of person-to-person transmission. Evidence from subsequent outbreaks of H5N1 in Vietnam suggest changes in the virus consistent with this possibility. Of the latter two, the FDA recently approved an H5N1 vaccine, and H5N1 remains at the present inefficient at person-to-person transmission, albeit it is likely to acquire that ability given the adaptability of this virus. During that year, several persons became infected with an avian influenza strain that resulted in significant illness in chickens and resulted in the almost total destruction of Hong Kong poultry flocks in an attempt to contain the disease. It was a successful strategy, for the moment. In 2002 an antigenically distinct strain of avian influenza emerged in the same location in China, and by 2005, was infecting humans subsequently as well as spreading to numerous species of birds and resulting in the deaths of hundreds of millions of birds and almost 200 people. A new Euro-African lineage of H5N1 has resulted in several fatal human infections in Egypt by 2007.11, 12 Genetically the virus is becoming more antigenically diverse and forming distinguishable groupings. Genome analysis has shown that H5N1 now has 3 distinct lineages (clades) with sublineages and reassortment occurring. This is worrisome as it demonstrates the virus persisting and evolving. 12 In 2003 another pathogen became recognized as a global threat by the World Health Organization (WHO) with the potential to become a global pandemic—a novel coronavirus, Severe Acute Respiratory Syndrome (SARS), or SARS CoV. 13 The first known cases of SARS occurred in Guangdong province, China in November 2002. SARS CoV is believed to be an animal virus that crossed the species barrier to humans, perhaps as a result of ecological changes or human behaviors that placed people in greater proximity to coronavirus that lead to viral adaptation and subsequent human to human transmission. By July 2003, SARS CoV spread internationally and resulted in over 8000 cases in 26 countries with 774 deaths reported. 13 Although WHO considers the world to be in an inter-epidemic period, it remains difficult to predict when or if another SARS will emerge, let alone cause another outbreak, especially given that the natural reservoir of SARS CoV has not been identified or contained. In terms of birds infected and killed across several continents, avian influenza has already caused a global pandemic. Will the next human pandemic be the result of avian influenza? We hope this issue of Disease-a-Month will assist the reader in understanding the highly pathogenic avian influenza H5N1 and enhance your preparedness efforts.

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          Most cited references8

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          Characterization of the 1918 influenza virus polymerase genes.

          The influenza A viral heterotrimeric polymerase complex (PA, PB1, PB2) is known to be involved in many aspects of viral replication and to interact with host factors, thereby having a role in host specificity. The polymerase protein sequences from the 1918 human influenza virus differ from avian consensus sequences at only a small number of amino acids, consistent with the hypothesis that they were derived from an avian source shortly before the pandemic. However, when compared to avian sequences, the nucleotide sequences of the 1918 polymerase genes have more synonymous differences than expected, suggesting evolutionary distance from known avian strains. Here we present sequence and phylogenetic analyses of the complete genome of the 1918 influenza virus, and propose that the 1918 virus was not a reassortant virus (like those of the 1957 and 1968 pandemics), but more likely an entirely avian-like virus that adapted to humans. These data support prior phylogenetic studies suggesting that the 1918 virus was derived from an avian source. A total of ten amino acid changes in the polymerase proteins consistently differentiate the 1918 and subsequent human influenza virus sequences from avian virus sequences. Notably, a number of the same changes have been found in recently circulating, highly pathogenic H5N1 viruses that have caused illness and death in humans and are feared to be the precursors of a new influenza pandemic. The sequence changes identified here may be important in the adaptation of influenza viruses to humans.
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            Infectious diseases: considerations for the 21st century.

            A Fauci (2001)
            The discipline of infectious diseases will assume added prominence in the 21st century in both developed and developing nations. To an unprecedented extent, issues related to infectious diseases in the context of global health are on the agendas of world leaders, health policymakers, and philanthropies. This attention has focused both on scientific challenges such as vaccine development and on the deleterious effects of infectious diseases on economic development and political stability. Interest in global health has led to increasing levels of financial support, which, combined with recent technological advances, provide extraordinary opportunities for infectious disease research in the 21st century. The sequencing of human and microbial genomes and advances in functional genomics will underpin significant progress in many areas, including understanding human predisposition and susceptibility to disease, microbial pathogenesis, and the development new diagnostics, vaccines, and therapies. Increasingly, infectious disease research will be linked to the development of the medical infrastructure and training needed in developing countries to translate scientific advances into operational reality.
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              Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses

              The first cases of human infection with highly pathogenic avian influenza (HPAI) strain H5N1 occurred in Hong Kong in 1997; it was brought under control by massive culling of the chicken population ( 1 , 2 ). An antigenically distinct strain emerged in 2002, in the same location, and has since spread to hundreds of millions of birds ( 3 , 4 ). More alarming has been the growing number of human influenza (H5N1) infections; by September 2006, 251 human cases had been reported, resulting in 148 deaths ( 2 ). From late 2005 to early 2006, HPAI (H5N1) was detected for the first time in birds in eastern Europe, the Middle East, and northern Africa, indications that the virus was spreading, possibly aided by wild bird migration. Human cases were reported beginning in January 2006 in Egypt, Iraq, Turkey, Djibouti, and Azerbaijan. Methods We sequenced and analyzed the genomes of 36 recent isolates of highly pathogenic influenza (H5N1) viruses collected from Europe, northern Africa, the Middle East, and Asia. We used high-throughput methods described previously ( 5 ). Sample Collection Samples primarily consisting of pooled trachea and lung tissue, pooled intestines, or tracheal and cloacal swabs collected from dead or moribund animals were processed for attempted virus isolation as described ( 6 ). Hemagglutinating isolates were typed either by reverse transcription–PCR (RT-PCR) or by serologic methods ( 7 ). RNA was extracted with the High Pure Extraction Kit (Roche, Indianapolis, IN, USA), according to manufacturer’s instructions. Primer Design Sequences from recent human and avian influenza (H5N1) isolates were downloaded from GenBank and were aligned with MUSCLE ( 8 ). Degenerate primers were designed on the basis of consensus sequences generated with BioEdit ( 9 ). An M13 sequence tag was added to the 5′ end of each primer to be used for sequencing. Four of the reactions were analyzed by electrophoresis on an agarose gel for quality control purposes. Primer design was optimized by analysis of the sequence success rate of each primer pair. Primers that did not perform well were redesigned and replaced in the primer set. Primers were designed to produce ≈500-nt overlapping amplicons to provide 2× coverage of each genomic segment. Additionally, a second set of primers was designed to produce 500-nt amplicons offset ≈250 nt from the original primer pair, which gave at least 4× sequence coverage of each segment. cDNA Synthesis Amplicons tiling the genome of the influenza isolates were generated with a OneStep RT-PCR kit (QIAGEN, Valencia, CA, USA). They were treated with shrimp alkaline phosphatase-exonuclease I (U.S. Biologicals, Swampscott, MA, USA) before sequencing. Sequencing and Assembly Sequencing reactions were performed as described previously ( 5 ). After sequencing, each segment was downloaded, trimmed to remove amplicon primer-linker sequence as well as low-quality sequence, and assembled. A small genome assembler called Elvira, based on the open-source Minimus assembler (http://cbcb.umd.edu/software), has been developed to automate these tasks. The Elvira pipeline delivers exceptions, including failed reads, failed amplicons, insufficient coverage of a reference sequence (as obtained from GenBank), ambiguous consensus sequence calls, and low-coverage areas. Additional sequencing and targeted RT-PCR were conducted to close gaps and to increase coverage in low-coverage or ambiguous regions. All sequence data used in this study are available from GenBank and also from ftp.cbcb.umd.edu/pub/data/flu. GenBank accession numbers are available in the supplementary data (Technical Appendix 1). Phylogenetic Analysis Multiple sequence alignments of nucleotide data were performed by using MUSCLE ( 8 ) with default parameters. Most alignments of segments within a subtype lack internal gaps. Leading and trailing gaps were not considered in tree-length calculations, but all nucleotide positions were considered. The phylogenetic trees for Figures 1, 2A, and Appendix Figures 1–3 were constructed by using the neighbor-joining method as implemented in PAUP* version 4.0b10 ( 10 , 11 ) using the F84 distance between nucleotide sequences and the default parameters. The phylogeny of 71 complete genomes (avian isolates) and 3 hemagglutinin (HA) sequences (human isolates) in Figure 2B comprises isolates chosen because they formed the European-Middle Eastern-African (EMA) clades and the Russian and Chinese sister clades in a larger analysis of 759 influenza (H5N1) isolates from the locales and host range of all H5N1 sequences published since 1996. The figure includes every member of the EMA clade for which the complete genome sequence is currently available, except chicken/Nigeria/1047–62/2006 and chicken/Kurgan/05/2005, which appear to be reassortants. Figure 1 Phylogenetic tree of hemagglutinin (HA) segments from 36 avian influenza samples. A 2001 strain (A/duck/Anyang/AVL-1/2001) is used as an outgroup at top. Clade V1 comprises the 5 Vietnamese isolates at the bottom of the tree, and clade V2 comprises the 9 Vietnamese isolates near the top of the tree. The European-Middle Eastern-African (EMA) clade contains the remaining 22 isolates sequenced in this study; the 3 subclades are indicated by red, blue, and purple lines. The reassortant strain, A/chicken/Nigeria/1047–62/2006, is highlighted in red. Note that 4 segments including HA from this reassortant fall in EMA-1; the other 4 fall in EMA-2, as shown in Appendix Figure 1. Bootstrap values supporting the 3 distinct EMA clades are taken from a consensus tree based on concatenated whole-genome sequences, excluding the reassortant strain. The consensus tree is provided as Appendix Figure 2. Figure 2 A) Phylogenetic tree relating the influenza A (H5N1) hemagglutinin (HA) segments of 589 avian, feline, and human viruses. The tree includes all HA segments isolated since 2000 from humans (82 isolates, minimum sequence length 1,000 nt), birds (503 isolates, minimum length 1500 nt), and cats (4 isolates). The 36 newly sequenced genomes are highlighted in color. Human cases, which occur in all 4 of the major influenza (H5N1) clades, are highlighted in red. The scale bar indicates an F84 distance of 0.01. A full-scale version of this tree is provided as Figure 3. B) Phylogeny of 71 complete genomes (avian isolates, all 8 segments concatenated) and 3 HA sequences (human isolates, marked with red arrows) from Europe, the Middle East, Africa, Russia, and Asia. Bootstrap values represent the percentage of 1,000 bootstrap replicates for which the partition implied by the edge was observed; see Methods for further details. The 3 European-Middle Eastern-African (EMA) subclades from Figure 1 are indicated with the same color scheme. Isolates from human hosts are found only in EMA-1. Colors indicate locales. The names of the isolates newly sequenced in this study are shown in boldface text. To find optimal phylogenetic trees for Figure 2B, we used a combination of tree search algorithms available in the “new technology” heuristic strategies in the TNT ( 12 ) software package (available from www.zmuc.dk/public/phylogeny/TNT). These strategies include a successive combination of hill-climbing techniques (branch swapping) followed by simulated annealing (ratcheting), divide-and-conquer (sectorial searches), and genetic algorithms (tree fusion). Figure 2B depicts a strict consensus based on 286 minimal-length trees resulting from a parsimony search of 1,000 replicates in TNT under the command “xmult = lev5.” Each component tree had a tree length of 1,613 steps. Gaps were treated as a fifth state, and all edit costs were given equal weights under the parsimony criterion. The heuristic tree strategy was run until a stable strict consensus was achieved. This strict consensus is a conservative estimate of the phylogenetic relationship between the isolates, where an edge is included only if it was observed in all 286 optimal trees. Separately, RAxML ( 13 ) was run over the same data for maximum likelihood analyses under the general time-reversible (GTR) mixed model of nucleotide substitution. This likelihood analysis produced a tree with the same clade contents as the parsimony tree, preserving the 3 EMA clades. Branches were traced with colors to represent the locale of isolation of the virus. Results and Discussion The 36 new isolates reported here greatly expand the amount of whole-genome sequence data available from recent avian influenza (H5N1) isolates. Before our project, GenBank contained only 5 other complete genomes from Europe for the 2004–2006 period, and it contained no whole genomes from the Middle East or northern Africa. Our analysis showed several new findings. First, all European, Middle Eastern, and African samples fall into a clade that is distinct from other contemporary Asian clades, all of which share common ancestry with the original 1997 Hong Kong strain. Phylogenetic trees built on each of the 8 segments show a consistent picture of 3 lineages, as illustrated by the HA tree shown in Figure 1. Two of the clades contain exclusively Vietnamese isolates; the smaller of these, with 5 isolates, we label V1; the larger clade, with 9 isolates, is V2. The remaining 22 isolates all fall into a third, clearly distinct clade, labeled EMA, which comprises samples from Europe, the Middle East, and Africa. Trees for the other 7 segments display a similar topology, with clades V1, V2, and EMA clearly separated in each case. Analyses of all available complete influenza (H5N1) genomes and of 589 HA sequences placed the EMA clade as distinct from the major clades circulating in People’s Republic of China, Indonesia, and Southeast Asia. The influenza (H5N1) viruses isolated in Europe, the Middle East, and Africa show a close relationship, despite the fact that they were collected from a widely dispersed geographic region, including Côte d’Ivoire, Nigeria, Niger, Sudan, Egypt, Afghanistan, Iran, Slovenia, Croatia, and Italy. The shared lineage of the viruses suggests a single genetic source for introduction of influenza (H5N1) into western Europe and northern and western Africa; our analysis places this source most recently in either Russia or Qinghai Province in China (Figure 2B; Appendix Table. The broad dispersal of these isolates throughout these countries during a relatively short period, coupled with weak biosecurity standards in place in most rural areas, implicates human-related movement of live poultry and poultry commodities as the source of introduction of influenza (H5N1) into some of these countries. The virus’ presence in wild birds leaves open the alternative possibility that migratory birds may have been the primary source, with secondary spread possibly caused by human-related activities. A phylogenetic tree containing 589 isolates from 2001 through 2006 (Figure 2A and Appendix Figure 3) shows the relationship of the 36 recent isolates from this study to previous isolates and shows the 3 major lineages of influenza (H5N1) that are now circulating in Asia plus the fourth lineage, EMA, that has spread west into Europe and Africa. Figure 2B depicts a consensus view of the parsimony-based analysis of 74 isolates of complete genomes from the EMA lineage. The EMA clade contains all known European, Middle Eastern, and North African cases (which began appearing in late 2005), as well as cases from China, Russia, and Mongolia in 2005 and 2006. Some of the EMA clade isolates appear in clusters of influenza (H5N1) infection that were reported in geese in Qinghai Province, China ( 14 ), and in mute swans in Astrakhan ( 15 ), both of which are possible sources of spread through migration. The evolutionary relationships shown in Figure 2B provide clear evidence that 3 distinct clades, labeled EMA 1–3, are circulating in the European and African region. These clades clearly share a common ancestor in Asia. The 3 clades may represent separate introductions or, alternatively, a single introduction from Asia into Russia, Europe, or another western site that has subsequently evolved into 3 lineages. More data will be required to pinpoint when and where the 3 clades split apart. All previously reported European and Middle Eastern isolates belong to EMA-1. Our results show that EMA-2 has spread to Europe and that EMA-3 has spread to both Europe and the Middle East. These results agree in part with a recent study ( 16 ) that reported 3 distinct introductions of influenza (H5N1) into Nigeria. Our analysis, based on all available HA sequences (Appendix Figure 3), indicates that the Nigerian isolates fall into just 2 clades, EMA 1–2, that likely resulted from at least 2 introductions of influenza (H5N1). European countries have been affected by each of the 3 introductions of the EMA strains. For example, the Italian sequences can be segregated into 2 subgroups (Figure 2B). Two isolates in EMA-1 (Co/Italy/808/06 and Md/Italy/835/2006) are closely related in all segments and likely share a common ancestor with isolates found in Slovenia (Sw/Slovenia/760/2006), Bavaria, and the Czech Republic (Co/Czech Republic/5170/2006). The third Italian strain from our study (Co/Italy/742/2006) falls into EMA-3, along with our newly sequenced isolates from Iran (Co/Iran/754/2006) and Afghanistan (Ck/Afghanistan/1207/2006). EMA-2 contains 1 European isolate, from a swan in Croatia, and multiple isolates from domesticated birds in Nigeria and Niger. This group shares a common ancestor with a group of isolates from Astrakhan and Kurgan (Russia). Of the 22 EMA isolates newly sequenced in this study, 20 have the amino acid lysine (K) at position 627 of the polymerase basic protein 2 (PB2), while only 2 have glutamic acid (E). (These last 2 are both from Italy and both in EMA-1.) The 627K mutation is associated with virulence in mice and adaptation to mammalian hosts ( 17 ) and with increased host range ( 18 ). Lysine at this position is common in human viruses: all 65 human influenza (H5N1) isolates from 2001 through 2006 for which the PB2 sequence is available have lysine at position 627. Before the analysis of our collection, the PB2 627K was a relatively rare finding in avian influenza (H5N1) viruses: it was present in only 42 of 385 isolates previously collected from 2001 through 2006. Our analysis shows that all 42 of these fall in the EMA clade (Figure 2 and supplementary data available in Technical Appendix 2. Excluding our current European, Middle Eastern, and African isolates, this mutation appears primarily in isolates obtained from wild birds in Astrakhan ( 15 ) and at Qinghai Lake ( 14 , 17 ). This mutation also occurs in the recent isolate A/Guinea fowl/Shantou/1341/2006 and in a mouse-adapted 2001 Asian isolate, A/pheasant/Hong Kong/Fy155/01-MB. This finding is in keeping with current knowledge of the acquisition of such mutations. Our study increases current knowledge on strains circulating in Asia before the westward spread of influenza A (H5N1). The Vietnamese samples fall into 2 clusters, the larger of which (V2 in Figure 1) is the same strain responsible for multiple cases in Southeast Asia since 2004, particularly in Vietnam and Thailand. These isolates all seem to derive from earlier Hong Kong samples (including 2 cases of human infection) in 2002 and 2003. The second cluster, V1, which contains 5 samples, significantly expands our understanding of this distinct Vietnamese influenza (H5N1) lineage. The only other isolate from this cluster was recently reported in a Vietnamese duck (A/duck/Vietnam/568/2005) and labeled a “recent Vietnam introduction” ( 4 ). This sample groups with the V1 clade when shown in the context of a larger tree of HA sequences (Appendix Figure 3). The 5 newly sequenced isolates in clade V1 show the same phylogenetic relationship for all segments except PB2 (Appendix Figure 1). The isolates in clade V1 appear to have undergone the same reassortment as was suggested ( 4 ) for the 1 previous example of this Vietnamese clade, A/duck/Vietnam/568/2005; i.e., they have acquired a new PB2 segment. This PB2 is similar to older (1996–2002), A/duck/Guangdong/1/96-like viruses from China. V1 clade isolates are associated with a distinct set of human cases, from China’s Anhui and Guangxi Provinces in 2005, a finding that provides additional support to the hypothesis that this group of influenza (H5N1) viruses was introduced into Vietnam from China ( 4 ). Although EMA has split into 3 independently evolving clades, 1 isolate, A/chicken/Nigeria/1047–62/2006, shows clear evidence of reassortment. In this genome, 4 segments—HA, (nucleocapsid protein, nonstructural protein, and PB1—belong to EMA-1, as seen in Figure 1 and Appendix Figure 1. The other 4 segments—neuraminidase, matrix protein, PA, and PB2—belong to EMA-2 (Appendix Figure 1). Individual segment trees based on all available sequences in GenBank corroborate this pattern and consistently split the 8 segments of this Nigerian isolate into 2 distinct clades. Reassortment events such as this can only be discovered by sequencing multiple virus segments. The presence of all 3 EMA sublineages in the same geographic region creates ample opportunities for reassortment. Isolate A/chicken/Nigeria/1047–62/2006 is the most recent of the Nigerian isolates, consistent with the hypothesis that this reassortant was generated in Africa. Additional surveillance will be necessary to determine if this reassortant strain spreads further in the avian population and to assess its ability to infect mammals. As shown in Figure 2A, the EMA clade is a distinct lineage evolving independently of the 3 exclusively Asian lineages. All 3 human influenza (H5N1) cases that have been sequenced outside east Asia—from Iraq ( 19 ), Djibouti, and Egypt—belong to the EMA lineage. The human sequences A/Djibouti/5691/NAMRU3/06 and A/Egypt/2782/NAMRU3/06 group closely together and consistently fall in EMA-1. The placement of A/Iraq/207/NAMRU3/06 is slightly less certain; it also groups with EMA-1 (Figure 2B) but with lower bootstrap support. EMA viruses isolated from humans are thus quite distinct from the recent large clusters of human cases in Indonesia and China, which fall into separate clades containing none of our samples. The EMA isolates are also distinct from other human cases in Southeast Asia, which fall into the clades (V1 and V2) containing our Vietnamese samples. The emergence of 3 (or more) substrains from the EMA clade represents multiple new opportunities for avian influenza (H5N1) to evolve into a human pandemic strain. In contrast to strains circulating in Southeast Asia, EMA viruses are derived from a progenitor that has the PB2 627K mutation. These viruses are expected to have enhanced replication characteristics in mammals, and indeed the spread of EMA has coincided with the rapid appearance of cases in mammals—including humans in Turkey, Egypt, Iraq, and Djibouti, and cats in Germany, Austria, and Iraq. Unfortunately, the EMA-type viruses appear to be as virulent as the exclusively Asian strains: of 34 human infections outside of Asia through mid-2006, 15 have been fatal ( 2 ). Analyses of the complete HA tree (Figure 2A and Appendix Figure 3) suggest that the earliest sequenced relatives of the EMA clade are from the Yunnan region of China (A/duck/Yunnan/6255,6445/2003), Hong Kong, (A/chicken/Hong Kong/WF157/2003), and South Korea (A/chicken/Korea/ES/2003, A/duck/Korea/ESD1/2003), which were part of a regional outbreak in 2003 ( 20 ). Experiments on the 2 Korean isolates showed them to be infectious but not fatal in mice ( 21 ). These findings show how whole-genome analysis of influenza (H5N1) viruses is instrumental to the better understanding of the evolution and epidemiology of this infection, which is now present in the 3 continents that contain most of the world’s population. This and related analyses, facilitated by global initiatives on sharing influenza data ( 22 , 23 ), will help us understand the dynamics of infection between wild and domesticated bird populations, which in turn should promote the development of control and prevention strategies. Supplementary Material Appendix Figure 1 Phylogenetic trees of neuraminidase (NA), matrix protein (MP), nucleocapsid protein (NP), nonstructural protein (NS), polymerase acidic protein (PA), polymerase basic protein 1 (PB1), and polymerase basic protein 2 (PB2) segments from the 36 influenza strains sequenced in this study. A 2001 strain is used as an outgroup. Tree constructed with PAUP (Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony [and Other Methods]. 4.0 Beta. Sunderland [MA]: Sinauer Associates; 2002) as explained in the Methods. Appendix Figure 2 Consensus of 1,000 neighbor-joining bootstrap replicates as calculated by PAUP 4.0b10 (Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony [and Other Methods]. Sunderland [MA]: Sinauer Associates; 2002) on 35 of our new 36 isolates, leaving aside the reassortant strain A/Ck/Nigeria/1047 62/2006, which-because of its multilineage ancestry-cannot be placed exclusively in either EMA clade 1 or 2. Each isolate was represented by the concatenation of the alignments of its 8 RNA segments. These bootstrap values are used in the labeling of Figure 1 in the main text. Appendix Figure 3 Phylogenetic tree relating hemagglutinin (HA) segments of 589 avian, feline, and human influenza A (H5N1) viruses. This figure is an enlarged view of Figure 2A in the main text. The tree includes all human-derived HA segments deposited in GenBank since the year 2000 that are at least 1000 nt in length (82 sequences) as well as all avian and feline sequences since the year 2000 that are at least 1500 nt in length (4 feline and 503 avian sequences). The sequences were aligned with MUSCLE (Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113), and the tree was created with the neighbor joining algorithm of PAUP* version 4.0b10 (Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony [and Other Methods]. Sunderland [MA]: Sinauer Associates; 2002) using the F84 distance between the nucleotide sequences and the default parameters. The scale bar in the upper left indicates an F84 distance of 0.01. Human isolates in the figure are red. The V3 clade is pink. The 36 newly sequenced avian isolates are colored according to the region from which they were obtained (blue, Africa; orange, Europe; purple, Middle East; and greenish blue, Vietnam). The isolate A/chicken/Nigeria/1047_62/2006 that has undergone reassortment is marked with an arrow. Appendix Table Isolate name… Technical Appendix 1 POSITION 627 IN PB2 PROTEIN FOR ALL 420 SEQUENCES AVAILABLE FROM 2001-2006 AS OF November 2006 Technical Appendix 2 1: CY017194 Influenza A virus (A/duck/Viet Nam/19/2005(H5N1)
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                Author and article information

                Journal
                Dis Mon
                Dis Mon
                Disease-a-Month
                Mosby
                0011-5029
                1557-8194
                6 August 2007
                July 2007
                6 August 2007
                : 53
                : 7
                : 343-347
                Article
                S0011-5029(07)00046-6
                10.1016/j.disamonth.2007.05.005
                7094238
                17689669
                2a0ccf03-63d8-491e-bbb9-04ebf4058fbd
                Copyright © 2007 Mosby, Inc. All rights reserved.

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