Emergence Of Pandemic Strains Research Articles

Highly pathogenic influenza H5: risks of a new pandemic strain developing

The review provides brief historical information on the highly pathogenic influenza A (H5) and presents data on massive outbreaks caused by this subtype. It includes historical background, data on outbreaks, and the formation of potentially pandemic viruses. The abstract also highlights the current state of the problem, such as the spread of H5 influenza in new territories and its ability to infect mammals and humans. The issues of vaccination for poultry and the challenges of implementing it globally are addressed. Furthermore, the risks of further spread of the virus and the emergence of pandemic strains are being discussed.

Identification of a Type-Specific Promoter Element That Differentiates between Influenza A and B Viruses.

Type A and type B influenza viruses (FluA and FluB viruses) are two major human pathogens that share common structural and functional features. FluA and FluB viruses can reassort within each type but never between the types. Here, we bioinformatically analyzed all promoter sequences of FluA and FluB viruses and confirmed the presence of the type-specific promoter elements. We then studied the promoter elements with cell-based in vivo assays and an in vitro replication initiation assay. Our results identified, for the first time, a type-specific promoter element-the nucleotide at position 5 in the 3' end of the viral RNA (vRNA)-that plays a key role(s) in modulating polymerase activity in a type-specific manner. Interestingly, swapping the promoter element between FluA and FluB recombinant viruses showed different tolerances: the replacement of FluA virus-specific U5 with FluB virus-specific C5 in influenza virus A/WSN/33 (H1N1) could be reverted to U5 after 2 to 3 passages, while the replacement of FluB virus-specific C5 with FluA virus-specific U5 in influenza virus B/Yamagata/88 could be maintained, but with significantly reduced replication efficiency. Therefore, our findings indicate that the nucleotide variation at position 5 in the 3' end of the vRNA promoter between FluA and FluB viruses contributes to their RNP incompatibility, which may shed new light on the mechanisms of intertypic exclusion of reassortment between FluA and FluB viruses.IMPORTANCE Genetic reassortment of influenza virus plays a key role in virus evolution and the emergence of pandemic strains. The reassortment occurs extensively within either FluA or FluB viruses but never between them. Here, we bioinformatically compared available promoter sequences of FluA and FluB viruses and confirmed the presence of the type-specific promoter elements. Our in vivo and in vitro mutagenesis studies showed that a type-specific promoter element-the nucleotide at position 5 in the 3' end of vRNA promoters-plays key roles in modulating polymerase activity. Interestingly, FluA and FluB viruses showed different tolerances upon key promoter element swapping in the context of virus infections. We concluded that the nucleotide at position 5 in the 3' end of the vRNA promoters of FluA and FluB viruses is a critical type-specific determinant. This work has implications for further elucidating the mechanisms of the intertypic exclusion of reassortment between FluA and FluB viruses.

Population Genomics of GII.4 Noroviruses Reveal Complex Diversification and New Antigenic Sites Involved in the Emergence of Pandemic Strains.

GII.4 noroviruses are a major cause of acute gastroenteritis. Their dominance has been partially explained by the continuous emergence of antigenically distinct variants. To gain insights into the mechanisms of viral emergence and population dynamics of GII.4 noroviruses, we performed large-scale genomics, structural, and mutational analyses of the viral capsid protein (VP1). GII.4 noroviruses exhibited a periodic replacement of predominant variants with accumulation of amino acid substitutions. Genomic analyses revealed (i) a large proportion (87%) of conserved residues; (ii) variable residues that map on the previously determined antigenic sites; and (iii) variable residues that map outside the antigenic sites. Residues in the third pattern category formed motifs on the surface of VP1, which suggested extensions of previously predicted and new uncharacterized antigenic sites. The role of two motifs (C and G) in the antigenic makeup of the GII.4 capsid protein was confirmed with monoclonal antibodies and carbohydrate blocking assays. Amino acid profiles from antigenic sites (A, C, D, E, and G) correlated with the circulation patterns of GII.4 variants, with three of them (A, C, and G) containing residues (352, 357, 368, and 378) linked with the diversifying selective pressure on the emergence of new GII.4 variants. Notably, the emergence of each variant was followed by stochastic diversification with minimal changes that did not progress toward the next variant. This report provides a methodological framework for antigenic characterization of viruses and expands our understanding of the dynamics of GII.4 noroviruses and could facilitate the design of cross-reactive vaccines.IMPORTANCE Noroviruses are an important cause of viral gastroenteritis around the world. An obstacle delaying the development of norovirus vaccines is inadequate understanding of the role of norovirus diversity in immunity. Using a population genomics approach, we identified new residues on the viral capsid protein (VP1) from GII.4 noroviruses, the predominant genotype, that appear to be involved in the emergence and antigenic topology of GII.4 variants. Careful monitoring of the substitutions in those residues involved in the diversification and emergence of new viruses could help in the early detection of future novel variants with pandemic potential. Therefore, this novel information on the antigenic diversification could facilitate GII.4 norovirus vaccine design.

1918 influenza virus: 100 years on, are we prepared against the next influenza pandemic?

As we commemorate 100 years since the 1918 pandemic, research has advanced our knowledge of influenza virulence and pathogenesis, and has highlighted the role of animal reservoirs in the emergence of pandemic strains. Future efforts in understanding viral ecology, zoonosis and in integrating human and animal epidemiology should aid pandemic preparedness.

Broadly neutralizing anti-influenza virus antibodies: enhancement of neutralizing potency in polyclonal mixtures and IgA backbones.

Current influenza virus vaccines rely upon the accurate prediction of circulating virus strains months in advance of the actual influenza season in order to allow time for vaccine manufacture. Unfortunately, mismatches occur frequently, and even when perfect matches are achieved, suboptimal vaccine efficacy leaves several high-risk populations vulnerable to infection. However, the recent discovery of broadly neutralizing antibodies that target the hemagglutinin (HA) stalk domain has renewed hope that the development of "universal" influenza virus vaccines may be within reach. Here, we examine the functions of influenza A virus hemagglutinin stalk-binding antibodies in an endogenous setting, i.e., as polyclonal preparations isolated from human sera. Relative to monoclonal antibodies that bind to the HA head domain, the neutralization potency of monoclonal stalk-binding antibodies was vastly inferior in vitro but was enhanced by several orders of magnitude in the polyclonal context. Furthermore, we demonstrated a surprising enhancement in IgA-mediated HA stalk neutralization relative to that achieved by antibodies of IgG isotypes. Mechanistically, this could be explained in two ways. Identical variable regions consistently neutralized virus more potently when in an IgA backbone compared to an IgG backbone. In addition, HA-specific memory B cells isolated from human peripheral blood were more likely to be stalk specific when secreting antibodies of IgA isotypes compared to those secreting IgG. Taken together, our data provide strong evidence that HA stalk-binding antibodies perform optimally when in a polyclonal context and that the targeted elicitation of HA stalk-specific IgA should be an important consideration during "universal" influenza virus vaccine design. Influenza viruses remain one of the most worrisome global public health threats due to their capacity to cause pandemics. While seasonal vaccines fail to protect against the emergence of pandemic strains, a new class of broadly neutralizing antibodies has been recently discovered and may be the key to developing a "universal" influenza virus vaccine. While much has been learned about the biology of these antibodies, most studies have focused only on monoclonal antibodies of IgG subtypes. However, the study of monoclonal antibodies often fails to capture the complexity of antibody functions that occur during natural polyclonal responses. Here, we provide the first detailed analyses of the biological activity of these antibodies in polyclonal contexts, comparing both IgG and IgA isotypes isolated from human donors. The striking differences observed in the functional properties of broadly neutralizing antibodies in polyclonal contexts will be essential for guiding design of "universal" influenza virus vaccines and therapeutics.

Influenza A virus transmission bottlenecks are defined by infection route and recipient host.

Despite its global relevance, our understanding of how influenza A virus transmission impacts the overall population dynamics of this RNA virus remains incomplete. To define this dynamic, we inserted neutral barcodes into the influenza A virus genome to generate a population of viruses that can be individually tracked during transmission events. We find that physiological bottlenecks differ dramatically based on the infection route and level of adaptation required for efficient replication. Strong genetic pressures are responsible for bottlenecks during adaptation across different host species, whereas transmission between susceptible hosts results in bottlenecks that are not genetically driven and occur at the level of the recipient. Additionally, the infection route significantly influences the bottleneck stringency, with aerosol transmission imposing greater selection than direct contact. These transmission constraints have implications in understanding the global migration of virus populations and provide a clearer perspective on the emergence of pandemic strains.

Developing a production process for influenza VLPs: a comparison between HEK 293SF and Sf9 production platforms

Background Influenza virus-like particle (VLP) vaccines are one of the most promising approaches to respond to the constant threat of the emergence of pandemic strains, as they possess the potential for higher production capabilities compared to traditional vaccines made in egg-based technology. VLPs are particles produced in cell culture utilizing recombinant protein technology composed of viral antigens that are able to elicit an immune response but lack viral genetic material. Thus far, influenza VLPs have been produced in mammalian, insect and plant based platforms [1], with production in insect cells being the most explored. Baculovirus with mammalian promoters (Bacmam) have been shown to efficiently transduce mammalian cells and further express genes but are unable to replicate, efficiently repressing baculovirus (BV) production that leads to contamination downstream [2]. Influenza VLP production was performed in HEK 293SF cells using the Bacmam gene delivery system. The proposed system was assessed for its ability to produce influenza VLPs composed of Hemagglutinin (HA), Neuraminidase (NA) and Matrix Protein (M1) and compared to VLPs produced in Sf9 cells through the lens of bioprocessing.

The Evolving Threat of Influenza Viruses of Animal Origin and the Challenges in Developing Appropriate Diagnostics

An H1N1 subtype of swine origin caused the first influenza pandemic in this century. This pandemic strain was a reassortant of avian, swine, and human influenza viruses. Many diagnostic laboratories were overwhelmed by the testing demands related to this pandemic. Nevertheless, there remains the threat of other animal influenza viruses, such as highly pathogenic H5N1. As a part of pandemic preparedness, it is essential to identify the diagnostic challenges that will accompany the next pandemic. We discuss the natural reservoir of influenza viruses and the possible role of livestock in the emergence of pandemic strains. The current commonly used molecular tests for influenza diagnosis or surveillance are also briefly reviewed. Some of these approaches are also used to detect animal viruses. Unfortunately, owing to a lack of systematic surveillance of animal influenza viruses, established tests may not be able to detect pandemic strains that have yet to emerge from the animal reservoir. Thus, multiple strategies need to be developed for better identification of influenza viruses. In addition, molecular assays for detection of mutations associated with antiviral resistance and for viral segment reassortments should also be encouraged. Influenza viruses are highly dynamic viruses. Regular and systematic influenza surveillance in both humans and animals is essential to provide a more comprehensive picture of the prevalent influenza viruses. To better prepare for the next pandemic, we should develop some simple and easy-to-use tests for characterizing newly emerging influenza viruses.

Foot-and-Mouth Disease Virus Serotype O Phylodynamics: Genetic Variability Associated with Epidemiological Factors in Pakistan

One of the most challenging aspects of foot-and-mouth disease (FMD) control is the high genetic variability of the FMD virus (FMDV). In endemic settings such as the Indian subcontinent, this variability has resulted in the emergence of pandemic strains that have spread widely and caused devastating outbreaks in disease-free areas. In countries trying to control and eradicate FMD using vaccination strategies, the constantly evolving and wide diversity of field FMDV strains is an obstacle for identifying vaccine strains that are successful in conferring protection against infection with field viruses. Consequently, quantitative knowledge on the factors that are associated with variability of the FMDV is prerequisite for preventing and controlling FMD in the Indian subcontinent. A hierarchical linear model was used to assess the association between time, space, host species and the genetic variability of serotype O FMDV using viruses collected in Pakistan from 2005 to 2011. Significant (P<0.05) amino acid and nucleotide variations were associated with spatial distance, but not with differences in host species, which is consistent with the frequent multi-species infection of this serotype O FMDV. Results from this study will contribute to the understanding of FMDV variability and to the design of FMD control strategies in Pakistan. Viruses sequenced here also provide the earliest reported isolate from the Pan Asia II(ANT-10) sublineage, which has caused several outbreaks in the Middle East and spread into Europe (Bulgaria) and Africa (Libya).

A comprehensive analysis of reassortment in influenza A virus

SummaryGenetic reassortment plays a vital role in the evolution of the influenza virus and has historically been linked with the emergence of pandemic strains. Reassortment is believed to occur when a single host - typically swine - is simultaneously infected with multiple influenza strains. The reassorted viral strains with novel gene combinations tend to easily evade the immune system in other host species, satisfying the basic requirements of a virus with pandemic potential. Therefore, it is vital to continuously monitor the genetic content of circulating influenza strains and keep an eye out for new reassortants. We present a new approach to identify reassortants from large data sets of influenza whole genome nucleotide sequences and report the results of the first ever comprehensive search for reassortants of all published influenza A genomic data. 35 of the 52 well supported candidate reassortants we found are reported here for the first time while our analysis method offers new insight that enables us to draw a more detailed picture of the origin of some of the previously reported reassortants. A disproportionately high number (13/52) of the candidate reassortants found were the result of the introduction of novel hemagglutinin and/or neuraminidase genes into a previously circulating virus. The method described in this paper may contribute towards automating the task of routinely searching for reassortants among newly sequenced strains.

Molecular Diversification in the Quorum-Sensing System of Vibrio cholerae : Role of Natural Selection in the Emergence of Pandemic Strains

Two haplotypes of the Vibrio cholerae quorum-sensing system regulator hapR are described: hapR1, common among nonpandemic, non-O1, non-O139 strains, and hapR2, associated with pandemic O1 and O139 and epidemic O37 V. cholerae strains. The hapR2 has evolved under strong natural selection, implying that its fixation was influenced by conditions that led to cholera pandemics.

Influenza: interspecies transmission and emergence of new pandemics.

Influenza is a well-known yearly threat, so why is it considered to be an emerging disease? It is because the virus evolves so rapidly that every year new viruses emerge, and every century three to four emergent strains are ‘new’ enough to cause pandemics. Historically, pandemics have been both unpredictable and devastating. As we learn more about how and where pandemic strains evolve, strategies for blocking their emergence and for recognition of potentially dangerous strains will become possible [1]. The single most significant characteristic of the influenza virus that makes it such an important threat is its enormous variability. Several features of the virus contribute to its variability. The first is that the polymerase complex makes mistakes when replicating the viral genes, and, since there is no built-in proofreading mechanism for RNA viruses, a lot of variation accumulates. Many of these variant viruses will not survive, because the acquired changes will make them unable to grow, but many genetic mistakes are well tolerated. Any preparation of influenza virus is a mixture of these variants, one of which might emerge and become a dominant new strain. The second, and probably more important, feature is the segmented nature of the genome. There are eight genetic segments, each specifying a unique viral function. When individual cells are infected by two different viruses, new strains can evolve that have some of their eight genetic segments derived from each of the infecting ‘parents’. ‘Genetic reassortment’, as this is called, is a pivotal factor in emergence of pandemic strains. Adding to the potential for variability, occasionally there also can be true genetic recombination between segments. The third feature is the large number of strains possible, because of the large number of potential permutations of the two viral surface glycoproteins, the principal determinants of humoral immunity. …

Influenza: Global surveillance for epidemic and pandemic variants

Influenza viruses, unlike other viruses for which vaccines have been developed, undergo rapid and unpredictable antigenic variation in the hemagglutinin (HA), the surface glycoprotein primarily responsible for eliciting neutralizing antibodies during infection. Because of this antigenic variability and its consequences, the World Health Organization (WHO) in 1947 established an international network of collaborating laboratories to monitor the emergence and spread of new epidemic and pandemic strains of influenza. This network now includes three international WHO collaborating centers and over 100 WHO national collaborating laboratories. The primary purpose of this network is to detect, through laboratory surveillance, the emergence and spread of antigenic variants of influenza that may signal a need to update the formulation of the influenza vaccine. This laboratory surveillance network has provided the strains needed to update the vaccine as well as a repository of influenza viruses useful for studying the antigenic and genetic evolution of this virus. Knowledge gained from molecular studies on the evolution of drift variants and on the emergence of pandemic strains has made influenza a useful model for understanding the potential threat of other emerging or reemerging microbial diseases.