A new concept of the epidemic process of influenza A virus

Modeling and Optimization of Continuous Viral Vaccine Production

A model that captures realistic viral growth dynamics has been developed based on a continuous and semi-continuous production model of an influenza A virus. This model considers viral growth parameters such as viral latency. It also captures the lag observed during the early production of viruses in a culture and explains later-phase growth dynamics. Furthermore, a sensitivity analysis was performed to investigate the effects of each input on each output. This revealed that production of defective interfering particles (DIPs) highly depends on the number of cells introduced to the viral reactor. The rationale for this is, as per the model, that a reduction in number of cells to be infected causes a reduction in DIPs formed as rate of viral infection decreases. Finally, a flowsheet model was created to optimize the continuous platform, including number of cells supplied to the viral reactor. From this, it was observed that the peak number of DIPs formed could be reduced by one-third. Finally, this model is tailorable to different viral particles using parameter estimation. Therefore, the proposed mathematical model provides a versatile, comprehensive platform that can be tailored to various viral cultures with or without a latent phase.

Community-level ambient fine particulate matter and seasonal influenza among children in Guangzhou, China: A Bayesian spatiotemporal analysis

BACKGROUND

Influenza is a major preventable infectious respiratory disease. However, there is little detailed long-term evidence of its associations with PM_2.5 among children. We examined the community-level associations between exposure to ambient PM_2.5 and incident influenza in Guangzhou, China.

METHODS

We used data from the city-wide influenza surveillance system collected by Guangzhou Centre for Disease Control and Prevention (GZCDC) over the period 2013 and 2019. Incident influenza was defined as daily new influenza (both clinically diagnosed and laboratory confirmed) cases as per standard diagnostic criteria. A 200-meter city-wide grid of daily ambient PM_2.5 exposure was generated using a random forest model. We developed spatiotemporal Bayesian hierarchical models to examine the community-level associations between PM_2.5 and the influenza adjusting for meteorological and socioeconomic variables and accounting for spatial autocorrelation. We also calculated community-wide influenza cases attributable to PM_2.5 levels exceeding the China Grade 1 and World Health Organization (WHO) regulatory thresholds.

RESULTS

Our study comprised N = 191,846 children from Guangzhou aged ≤19 years and diagnosed with influenza between January 1, 2013 and December 31, 2019. Each 10 μg/m³ increment in community-level PM_2.5 measured on the day of case confirmation (lag 0) and over a 6-day moving average (lag 0-5 days) was associated with higher risks of influenza (RR = 1.05, 95% CI: 1.05-1.06 for lag 0 and RR = 1.15, 95% CI: 1.14-1.16 for lag 05). We estimated that 8.10% (95%CI: 7.23%-8.57%) and 20.11% (95%CI: 17.64%-21.48%) influenza cases respectively were attributable to daily PM_2.5 exposure exceeding the China Grade I (35 μg/m³) and the WHO limits (25 μg/m³). The risks associated with PM_2.5 exposures were more pronounced among children of the age-group 10-14 compared to other age groups.

CONCLUSIONS

More targeted non-pharmaceutical interventions aimed at reducing PM_2.5 exposures at home, school and during commutes among children may constitute additional influenza prevention and control polices.

SARS-CoV-2 and Variant Diagnostic Testing Approaches in the United States

Purpose of Review Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2 and its associated variants including Omicron (B.1.1.529), many options are available to diagnose infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents. Recent Findings Additional testing platforms continue to be developed, including those to detect specific variants, but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain has improved, and more established companies are providing materials to support these testing efforts. In the United States (U.S.), the need for rapid assay development and subsequent approval through the attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. Through these efforts, the U.S. has been able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges still remain due to the diversity of the performance characteristics of tests being utilized and newly discovered viral variants. Summary This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology, variants and antibody responses that are available to diagnose infection in the U.S.

Diagnostic Testing for SARS-CoV-2 Infection

PURPOSE OF REVIEW

Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2, many options are available to assess infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents.

RECENT FINDINGS

Additional testing platforms continue to be developed but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain will improve and more companies will be providing materials to support these testing efforts. In the USA, the need for rapid assay development and subsequent approval through attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. It is anticipated that the USA will be able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges remain due to the diversity of the performance characteristics of tests being utilized.

SUMMARY

This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology and antibody responses, that is available to diagnose infection.

Temperature dependent viral tropism: understanding viral seasonality and pathogenicity as applied to the avoidance and treatment of endemic viral respiratory illnesses

This review seeks to explain three features of viral respiratory illnesses that have perplexed generations of virologists: (1) the seasonal timing of respiratory illness and the rapid response of outbreaks to weather, specifically temperature; (2) the common viruses causing respiratory illness worldwide, including year‐round disease in the Tropics; (3) the rapid arrival and termination of epidemics caused by influenza and other viruses. The inadequacy of the popular explanations of seasonality is discussed, and a simple hypothesis is proposed, called temperature dependent viral tropism (TDVT), that is compatible with the above features of respiratory illness. TDVT notes that viruses can spread more effectively if they moderate their pathogenicity (thereby maintaining host mobility) and suggests that endemic respiratory viruses accomplish this by developing thermal sensitivity within a range that supports organ‐specific viral tropism within the human body, whereby they replicate most rapidly at temperatures below body temperature. This can confine them to the upper respiratory tract and allow them to avoid infecting the lungs, heart, gut etc. Biochemical and tissue‐culture studies show that ‘wild’ respiratory viruses show such natural thermal sensitivity. The typical early autumn surge of colds and the occurrence of respiratory illness in the Tropics year‐round at intermediate levels are explained by the tendency for strains to adapt their thermal sensitivity to their local climate and season. TDVT has important practical implications for preventing and treating respiratory illness including Covid‐19. It is testable with many options for experiments to increase our understanding of viral seasonality and pathogenicity.

The Influence of Average Temperature and Relative Humidity on New Cases of COVID-19: Time-Series Analysis

BACKGROUND

The influence of meteorological factors on the transmission and spread of COVID-19 is of interest and has not been investigated.

OBJECTIVE

This study aimed to investigate the associations between meteorological factors and the daily number of new cases of COVID-19 in 9 Asian cities.

METHODS

Pearson correlation and generalized additive modeling (GAM) were performed to assess the relationships between daily new COVID-19 cases and meteorological factors (daily average temperature and relative humidity) with the most updated data currently available.

RESULTS

The Pearson correlation showed that daily new confirmed cases of COVID-19 were more correlated with the average temperature than with relative humidity. Daily new confirmed cases were negatively correlated with the average temperature in Beijing (r=-0.565, P<.001), Shanghai (r=-0.47, P<.001), and Guangzhou (r=-0.53, P<.001). In Japan, however, a positive correlation was observed (r=0.416, P<.001). In most of the cities (Shanghai, Guangzhou, Hong Kong, Seoul, Tokyo, and Kuala Lumpur), GAM analysis showed the number of daily new confirmed cases to be positively associated with both average temperature and relative humidity, especially using lagged 3D modeling where the positive influence of temperature on daily new confirmed cases was discerned in 5 cities (exceptions: Beijing, Wuhan, Korea, and Malaysia). Moreover, the sensitivity analysis showed, by incorporating the city grade and public health measures into the model, that higher temperatures can increase daily new case numbers (beta=0.073, Z=11.594, P<.001) in the lagged 3-day model.

CONCLUSIONS

The findings suggest that increased temperature yield increases in daily new cases of COVID-19. Hence, large-scale public health measures and expanded regional research are still required until a vaccine becomes widely available and herd immunity is established.

High Prevalence of Avian Influenza Virus Among Wild Waterbirds and Land Birds of Mexico

Aquatic wild birds, especially waterfowl, have been long considered the main reservoirs of the avian influenza A virus; however, recent surveys have found an important prevalence of these viruses among land birds as well. Migration has been suggested as an important factor in the avian influenza virus dissemination. We aimed to estimate the prevalence of influenza A viruses in wild birds (waterbirds and land birds; resident and migratory) in eastern Mexico, where the three main North American migration flyways converge and where there was no previous information on this subject. We detected influenza with reverse transcription coupled with a PCR approach. Of the 534 birds sampled between 2010 and 2012, we detected the influenza A virus in a high proportion of birds (39%). Prevalence was particularly high in land birds (49%) when compared to aquatic birds (26%); there was no difference in overall prevalence between resident (39%) and migratory birds (39%). The high prevalence of the avian influenza virus in land birds was noteworthy in the innermost sampling areas in northern Mexico (Coahuila [82%] and Nuevo Leon [43%]).

Drug resistance in influenza A virus: the epidemiology and management

Influenza A virus (IAV) is the sole cause of the unpredictable influenza pandemics and deadly zoonotic outbreaks and constitutes at least half of the cause of regular annual influenza epidemics in humans. Two classes of anti-IAV drugs, adamantanes and neuraminidase (NA) inhibitors (NAIs) targeting the viral components M2 ion channel and NA, respectively, have been approved to treat IAV infections. However, IAV rapidly acquired resistance against both classes of drugs by mutating these viral components. The adamantane-resistant IAV has established itself in nature, and a majority of the IAV subtypes, especially the most common H1N1 and H3N2, circulating globally are resistant to adamantanes. Consequently, adamantanes have become practically obsolete as anti-IAV drugs. Similarly, up to 100% of the globally circulating IAV H1N1 subtypes were resistant to oseltamivir, the most commonly used NAI, until 2009. However, the 2009 pandemic IAV H1N1 subtype, which was sensitive to NAIs and has now become one of the dominant seasonal influenza virus strains, has replaced the pre-2009 oseltamivir-resistant H1N1 variants. This review traces the epidemiology of both adamantane- and NAI-resistant IAV subtypes since the approval of these drugs and highlights the susceptibility status of currently circulating IAV subtypes to NAIs. Further, it provides an overview of currently and soon to be available control measures to manage current and emerging drug-resistant IAV. Finally, this review outlines the research directions that should be undertaken to manage the circulation of IAV in intermediate hosts and develop effective and alternative anti-IAV therapies.

Human Rhinovirus Diversity and Evolution: How Strange the Change from Major to Minor

Rhinoviruses are the most common causes of the common cold. Their many distinct lineages fall into "major" and "minor" groups that use different cell surface receptors to enter host cells. Minor-group rhinoviruses are more immunogenic in laboratory studies, although their patterns of transmission and their cold symptoms are broadly similar to those of the major group. Here we present evolutionary evidence that minor-group viruses are also more immunogenic in humans. A key finding is that rates of amino acid substitutions at exposed sites in the capsid proteins VP2, VP3, and VP1 tend to be elevated in minor-group relative to major-group viruses, while rates at buried sites show no consistent differences. A reanalysis of historical virus watch data also indicates a higher immunogenicity of minor-group viruses, consistent with our findings about evolutionary rates at amino acid positions most directly exposed to immune surveillance. The increased immunogenicity and speed of evolution in minor-group lineages may contribute to the very large numbers of rhinovirus serotypes that coexist while differing in virulence.IMPORTANCE Most colds are caused by rhinoviruses (RVs). Those caused by a subset known as the minor-group members of rhinovirus species A (RV-A) are correlated with the inception and aggravation of asthma in at-risk populations. Genetically, minor-group viruses are similar to major-group RV-A, from which they were derived, although they tend to elicit stronger immune responses. Differences in their rates and patterns of molecular evolution should be highly relevant to their epidemiology. All RV-A strains show high rates of amino acid substitutions in the capsid proteins at exposed sites not previously identified as being immunogenic, and this increase is significantly greater in minor-group viruses. These findings will inform future studies of the recently discovered RV-C, which also appears to exacerbate asthma in adults and children. In addition, these findings draw attention to the difficult problem of explaining the long-term coexistence of many serotypes of major- and minor-group RVs.

Seasonality and selective trends in viral acute respiratory tract infections

Influenza A and B, and many unrelated viruses including rhinovirus, RSV, adenovirus, metapneumovirus and coronavirus share the same seasonality, since these viral acute respiratory tract infections (vARIs) are much more common in winter than summer. Unfortunately, early investigations that used recycled “pedigree” virus strains seem to have led microbiologists to dismiss the common folk belief that vARIs often follow chilling. Today, incontrovertible evidence shows that ambient temperature dips and host chilling increase the incidence and severity of vARIs. This review considers four possible mechanisms, M1 - 4, that can explain this link: (M1) increased crowding in winter may enhance viral transmission; (M2) lower temperatures may increase the stability of virions outside the body; (M3) chilling may increase host susceptibility; (M4) lower temperatures or host chilling may activate dormant virions. There is little evidence for M1 or M2, which are incompatible with tropical observations. Epidemiological anomalies such as the repeated simultaneous arrival of vARIs over wide geographical areas, the rapid cessation of influenza epidemics, and the low attack rate of influenza within families are compatible with M4, but not M3 (in its simple form). M4 seems to be the main driver of seasonality, but M3 may also play an important role.

Role of Fat-Soluble Vitamins A and D in the Pathogenesis of Influenza: A New Perspective

Reduced exposure to solar radiation, leading to a deficiency of vitamin D and hence impaired innate immunity, has been suggested as a trigger for influenza viral replication and as an explanation of seasonal influenza. Although this hypothesis accounts for many unexplained facts about the epidemiology of influenza, gaps remain in understanding the pathogenesis and manifestations of the disease. Several observations suggest a role for vitamin A compounds (retinoids) in the disease. This paper presents a new model of the etiopathogenesis of influenza, suggesting that host resistance and susceptibility depend importantly on the ratio of vitamin D to vitamin A activity. Retinoid concentrations within normal physiological limits appear to inhibit influenza pathogenesis whereas higher background concentrations (i.e., very low vitamin D : A ratios) increase the risk of severe complications of the disease. There is also evidence that influenza-induced or preexisting liver disease, diabetes, and obesity worsen the severity of infection, possibly via liver dysfunction and alterations in retinoid metabolism. The model could be tested by determining the presence of retinoids in the secretions of patients with influenza and by studies of retinoid profiles in patients and controls. Potential strategies for prevention and treatment are discussed.

Subtype- and antigenic site-specific differences in biophysical influences on evolution of influenza virus hemagglutinin

Background

Influenza virus undergoes rapid evolution by both antigenic shift and antigenic drift. Antibodies, particularly those binding near the receptor-binding site of hemagglutinin (HA) or the neuraminidase (NA) active site, are thought to be the primary defense against influenza infection, and mutations in antibody binding sites can reduce or eliminate antibody binding. The binding of antibodies to their cognate antigens is governed by such biophysical properties of the interacting surfaces as shape, non-polar and polar surface area, and charge.

Methods

To understand forces shaping evolution of influenza virus, we have examined HA sequences of human influenza A and B viruses, assigning each amino acid values reflecting total accessible surface area, non-polar and polar surface area, and net charge due to the side chain. Changes in each of these values between neighboring sequences were calculated for each residue and mapped onto the crystal structures.

Results

Areas of HA showing the highest frequency of pairwise changes agreed well with previously identified antigenic sites in H3 and H1 HAs, and allowed us to propose more detailed antigenic maps and novel antigenic sites for H1 and influenza B HA. Changes in biophysical properties differed between HAs of different subtypes, and between different antigenic sites of the same HA. For H1, statistically significant differences in several biophysical quantities compared to residues lying outside antigenic sites were seen for some antigenic sites but not others. Influenza B antigenic sites all show statistically significant differences in biophysical quantities for all antigenic sites, whereas no statistically significant differences in biophysical quantities were seen for any antigenic site is seen for H3. In many cases, residues previously shown to be under positive selection at the genetic level also undergo rapid change in biophysical properties.

Conclusions

The biophysical consequences of amino acid changes introduced by antigenic drift vary from subtype to subtype, and between different antigenic sites. This suggests that the significance of antibody binding in selecting new variants may also be variable for different antigenic sites and influenza subtypes.

Effect of 25-hydroxyvitamin D status on serological response to influenza vaccine in prostate cancer patients

BACKGROUND

Epidemiologic data suggest that there is an association between vitamin D deficiency and influenza infection. We conducted a prospective influenza vaccination study to determine the influence of vitamin D status on serological response to influenza vaccine in prostate cancer (CaP) patients.

METHODS

During the 2006-2007 influenza season, CaP patients treated at Roswell Park Cancer Institute were offered vaccination with the trivalent influenza vaccine (Fluzone®, 2006-2007) and sera collected for hemagglutination inhibition (HI) assay titers before and 3 months after vaccination. Response to vaccination was defined as ≥1:40 titer ratio or a fourfold increase in titer at 3 months, against any of the three strains. Serum 25-hydroxyvitamin D (25-D₃) levels were measured using DiaSorin ¹²⁵I radioimmunoassay kits.

RESULTS

Thirty-five patients with CaP participated in the study. Median baseline 25-D₃ level was 44.88 ng/ml (range: 9.16-71.98 ng/ml) Serological response against any of the three strains was noted in 80%. There was a significant effect of baseline 25-D3 level when tested as a continuous variable in relation to serological response (P = 0.0446). All patients in the upper quartile of 25-D3 level responded by mounting a serological response (P = 0.0344). None of the other baseline variables (age, race, chemotherapy status, or white cell count) had an effect on serological response.

CONCLUSIONS

In this study in CaP patients, a replete vitamin D status was associated with more frequent serological response to influenza vaccine.

Influenza A viruses: an ecology review

In humans, influenza A viruses cause yearly outbreaks with high morbidity and excess fatality rates as a direct effect. Placed in its ecological niche, however - in dabbling ducks - avian influenza virus (AIV) induces quite a mild disease. It is when the virus crosses the species barrier that pathogenic traits are attributed to infection. When infecting phylogenetically more distant species (i.e. chicken and turkeys), the AIV can cause high morbidity and may in some cases change the virus into a highly pathogenic variant with nearly 100% fatality rate. Being a very adaptable virus, these spill-over events are frequent and numerous species are susceptible to influenza virus. When a subtype of AIV that has not previously infected humans crosses the species barrier, adapts to humans, and spreads easily, a pandemic event is imminent. There is no cure for influenza infection and vaccination is a cumbersome endeavor so, currently, the strategy when a pandemic strikes is damage control. The interest in AIV ecology has increased dramatically since the beginning of the millennium as a key factor for preventive work for future pandemics. This review gives a broad overview of influenza A virus ecology: in the natural host, accidental hosts, new endemic hosts, and humans.

Viral carrier status is instilled by viral regulatory particles

Human viral carriers are important agents in the periodic resurgence of many pathogens. Instillation of virus in human carriers explains several of the unusual epidemiological features of viral epidemics, such as where viruses linger between epidemics and how epidemics can arise without an apparent source. By inactivating itself, a virus can easily reside in a host for months or years without being noticed by the immune system, enabling the virus to be dispersed inconspicuously in the future and into new regions. When this silent activity of human carriers is appreciated, it is easier to understand the dynamics of viral epidemics, such as the explosive appearance of influenza epidemics. During viral illnesses, virus in infected cells is put into a latent state by regulatory sequences delivered by particles produced by other virus-infected cells. These regulatory particles are similar to the virus's virion but contain specific subsets of the viral genome and cannot replicate in cells that are not infected by the complete viral genome. Regulatory particles have previously been referred to as defective interfering particles, noninfective viruses, inactive viruses, incomplete viruses, satellite viruses, and defective viruses. There are still many unanswered questions regarding viral carrier creation and the role human carriers play in the pathology and epidemiology of viral diseases. Some of these questions are presented and discussed in relation to regulatory particles, possible investigations and how carrier status may affect the health of the carrier. Viral regulatory particles limit the extent of viral infections and shift the active infection to a latent infection. Just as multicellular creatures use hormones as chemical messengers to coordinate cellular functions, viruses utilize regulatory particles to coordinate viral modes among infected cells within a host. Many viruses depend on these particles for their continued existence. If we wish to comprehend and effectively treat viral infections, we must secure a thorough understanding of viral regulatory particles.

A randomized controlled trial of vitamin D3 supplementation for the prevention of symptomatic upper respiratory tract infections

Vitamin D has been shown to be an important immune system regulator. Vitamin D insufficiency during winter may cause increased susceptibility to upper respiratory tract infections (URIs). To determine whether vitamin D supplementation during the winter season prevents or decreases URI symptoms, 162 adults were randomized to receive 50 microg vitamin D3 (2000 IU) daily or matching placebo for 12 weeks. A bi-weekly questionnaire was used to record the incidence and severity of URI symptoms. There was no difference in the incidence of URIs between the vitamin D and placebo groups (48 URIs vs. 50 URIs, respectively, P=0.57). There was no difference in the duration or severity of URI symptoms between the vitamin D and placebo groups [5.4+/-4.8 days vs. 5.3+/-3.1 days, respectively, P=0.86 (95% CI for the difference in duration -1.8 to 2.1)]. The mean 25-hydroxyvitamin D level at baseline was similar in both groups (64.3+/-25.4 nmol/l in the vitamin D group; 63.0+/-25.8 nmol/l in the placebo group; n.s.). After 12 weeks, 25-hydroxyvitamin D levels increased significantly to 88.5+/-23.2 nmol/l in the vitamin D group, whereas there was no change in vitamin D levels in the placebo group. There was no benefit of vitamin D3 supplementation in decreasing the incidence or severity of symptomatic URIs during winter. Further studies are needed to determine the role of vitamin D in infection.

On the epidemiology of influenza

The epidemiology of influenza swarms with incongruities, incongruities exhaustively detailed by the late British epidemiologist, Edgar Hope-Simpson. He was the first to propose a parsimonious theory explaining why influenza is, as Gregg said, "seemingly unmindful of traditional infectious disease behavioral patterns." Recent discoveries indicate vitamin D upregulates the endogenous antibiotics of innate immunity and suggest that the incongruities explored by Hope-Simpson may be secondary to the epidemiology of vitamin D deficiency. We identify – and attempt to explain – nine influenza conundrums: (1) Why is influenza both seasonal and ubiquitous and where is the virus between epidemics? (2) Why are the epidemics so explosive? (3) Why do they end so abruptly? (4) What explains the frequent coincidental timing of epidemics in countries of similar latitude? (5) Why is the serial interval obscure? (6) Why is the secondary attack rate so low? (7) Why did epidemics in previous ages spread so rapidly, despite the lack of modern transport? (8) Why does experimental inoculation of seronegative humans fail to cause illness in all the volunteers? (9) Why has influenza mortality of the aged not declined as their vaccination rates increased? We review recent discoveries about vitamin D's effects on innate immunity, human studies attempting sick-to-well transmission, naturalistic reports of human transmission, studies of serial interval, secondary attack rates, and relevant animal studies. We hypothesize that two factors explain the nine conundrums: vitamin D's seasonal and population effects on innate immunity, and the presence of a subpopulation of "good infectors." If true, our revision of Edgar Hope-Simpson's theory has profound implications for the prevention of influenza.

Phylogenetic analysis reveals the global migration of seasonal influenza A viruses

The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized, yet least understood, epidemiological patterns in infectious disease. Central to understanding what drives the seasonal emergence of this important human pathogen is determining what becomes of the virus during the non-epidemic summer months. Herein, we take a step towards elucidating the seasonal emergence of influenza virus by determining the evolutionary relationship between populations of influenza A virus sampled from opposite hemispheres. We conducted a phylogenetic analysis of 487 complete genomes of human influenza A/H3N2 viruses collected between 1999 and 2005 from Australia and New Zealand in the southern hemisphere, and a representative sub-sample of viral genome sequences from 413 isolates collected in New York state, United States, representing the northern hemisphere. We show that even in areas as relatively geographically isolated as New Zealand's South Island and Western Australia, global viral migration contributes significantly to the seasonal emergence of influenza A epidemics, and that this migration has no clear directional pattern. These observations run counter to suggestions that local epidemics are triggered by the climate-driven reactivation of influenza viruses that remain latent within hosts between seasons or transmit at low efficiency between seasons. However, a complete understanding of the seasonal movements of influenza A virus will require greatly expanded global surveillance, particularly of tropical regions where the virus circulates year-round, and during non-epidemic periods in temperate climate areas.

The winter seasonality of influenza A virus in temperate climates is one of the most puzzling epidemiological patterns in infectious disease. To help resolve the issue of influenza seasonality, we studied, using viral genome sequence data, the patterns of global migration of influenza A virus, particularly between the northern and southern hemispheres. A phylogenetic analysis of approximately 900 complete genomes of the H3N2 subtype of human influenza A virus sampled from New Zealand and Australia (southern hemisphere), and New York state, United States (northern hemisphere), revealed that cross-hemisphere migration frequently occurs in both directions and involves multiple viral strains. Such global viral traffic therefore contributes significantly to the introduction of new influenza epidemics in both northern and southern hemispheres. These results also show that influenza A virus migrates afar during non-epidemic periods, rather than persisting locally at low levels during the influenza “off-season”. However, although this represents the largest and first bihemisphere study of its kind to our knowledge, the results highlight the need for sampling from tropical regions and during non-epidemic periods in temperate areas. Studies of this kind are critical to fully understand the geographical dispersal of influenza A virus and the role of climate in triggering seasonal epidemics.

Mutation trend of hemagglutinin of influenza A virus: a review from a computational mutation viewpoint

Since 1999 we have developed two computational mutation approaches to analyze the protein primary structure whose methodology and implications were reviewed in 2002. Our first approach is the calculation of predictable and unpredictable portions of amino-acid pairs in a protein, and the second is the calculation of amino-acid distribution rank in a protein. Both approaches provide quantitative measures to present a protein, which we have used to study a number of proteins with numerous mutations such as p53 proteins. More recently, we focussed our efforts on analyzing the proteins mutating frequently over time such as hemagglutinins of influenza A viruses. In this review we summarise our findings and their implications for hemagglutinin mutations in combination with some newly available data. Our approaches throw light on the true nature of genetic heterogeneity of influenza virus hemagglutinins; that is, the protein variability is highly relevant to its amino-acid construction. Using these approaches, we can monitor new mutations from influenza virus hemagglutinins and may predict their mutations in the future.

The SIRC model and influenza A

We develop a simple ordinary differential equation model to study the epidemiological consequences of the drift mechanism for influenza A viruses. Improving over the classical SIR approach, we introduce a fourth class (C) for the cross-immune individuals in the population, i.e., those that recovered after being infected by different strains of the same viral subtype in the past years. The SIRC model predicts that the prevalence of a virus is maximum for an intermediate value of R(0), the basic reproduction number. Via a bifurcation analysis of the model, we discuss the effect of seasonality on the epidemiological regimes. For realistic parameter values, the model exhibits a rich variety of behaviors, including chaos and multi-stable periodic outbreaks. Comparison with empirical evidence shows that the simulated regimes are qualitatively and quantitatively consistent with reality, both for tropical and temperate countries. We find that the basins of attraction of coexisting cycles can be fractal sets, thus predictability can in some cases become problematic even theoretically. In accordance with previous studies, we find that increasing cross-immunity tends to complicate the dynamics of the system.

Seasonality of infectious diseases and severe acute respiratory syndrome-what we don't know can hurt us

The novel severe acute respiratory syndrome (SARS) coronavirus caused severe disease and heavy economic losses before apparently coming under complete control. Our understanding of the forces driving seasonal disappearance and recurrence of infectious diseases remains fragmentary, thus limiting any predictions about whether, or when, SARS will recur. It is true that most established respiratory pathogens of human beings recur in wintertime, but a new appreciation for the high burden of disease in tropical areas reinforces questions about explanations resting solely on cold air or low humidity. Seasonal variation in host physiology may also contribute. Newly emergent zoonotic diseases such as ebola or pandemic strains of influenza have recurred in unpredictable patterns. Most established coronaviruses exhibit winter seasonality, with a unique ability to establish persistent infections in a minority of infected animals. Because SARS coronavirus RNA can be detected in the stool of some individuals for at least 9 weeks, recurrence of SARS from persistently shedding human or animal reservoirs is biologically plausible.

Seasonal variation in host susceptibility and cycles of certain infectious diseases

Seasonal cycles of infectious diseases have been variously attributed to changes in atmospheric conditions, the prevalence or virulence of the pathogen, or the behavior of the host. Some observations about seasonality are difficult to reconcile with these explanations. These include the simultaneous appearance of outbreaks across widespread geographic regions of the same latitude; the detection of pathogens in the off-season without epidemic spread; and the consistency of seasonal changes, despite wide variations in weather and human behavior. In contrast, an increase in susceptibility of the host population, perhaps linked to the annual light/dark cycle and mediated by the pattern of melatonin secretion, might account for many heretofore unexplained features of infectious disease seasonality. Ample evidence indicates that photoperiod-driven physiologic changes are typical in mammalian species, including some in humans. If such physiologic changes underlie human resistance to infectious diseases for large portions of the year and the changes can be identified and modified, the therapeutic and preventive implications may be considerable.

Evolution and ecology of influenza A viruses

In this review we examine the hypothesis that aquatic birds are the primordial source of all influenza viruses in other species and study the ecological features that permit the perpetuation of influenza viruses in aquatic avian species. Phylogenetic analysis of the nucleotide sequence of influenza A virus RNA segments coding for the spike proteins (HA, NA, and M2) and the internal proteins (PB2, PB1, PA, NP, M, and NS) from a wide range of hosts, geographical regions, and influenza A virus subtypes support the following conclusions. (i) Two partly overlapping reservoirs of influenza A viruses exist in migrating waterfowl and shorebirds throughout the world. These species harbor influenza viruses of all the known HA and NA subtypes. (ii) Influenza viruses have evolved into a number of host-specific lineages that are exemplified by the NP gene and include equine Prague/56, recent equine strains, classical swine and human strains, H13 gull strains, and all other avian strains. Other genes show similar patterns, but with extensive evidence of genetic reassortment. Geographical as well as host-specific lineages are evident. (iii) All of the influenza A viruses of mammalian sources originated from the avian gene pool, and it is possible that influenza B viruses also arose from the same source. (iv) The different virus lineages are predominantly host specific, but there are periodic exchanges of influenza virus genes or whole viruses between species, giving rise to pandemics of disease in humans, lower animals, and birds. (v) The influenza viruses currently circulating in humans and pigs in North America originated by transmission of all genes from the avian reservoir prior to the 1918 Spanish influenza pandemic; some of the genes have subsequently been replaced by others from the influenza gene pool in birds. (vi) The influenza virus gene pool in aquatic birds of the world is probably perpetuated by low-level transmission within that species throughout the year. (vii) There is evidence that most new human pandemic strains and variants have originated in southern China. (viii) There is speculation that pigs may serve as the intermediate host in genetic exchange between influenza viruses in avian and humans, but experimental evidence is lacking. (ix) Once the ecological properties of influenza viruses are understood, it may be possible to interdict the introduction of new influenza viruses into humans.

Genetic relationship between the HA genes of type A influenza viruses isolated in off-seasons and later epidemic seasons

From January 1985 to March 1989, off-season viruses of H1N1 and H3N2 subtypes of influenza A viruses were isolated on five occasions in Japan. The HA gene sequences of the influenza A(H1N1) and A(H3N2) viruses isolated in Japan from 1985-9 were analysed and the phylogenetic tree for each subtype virus was constructed to determine any genetic relationship between viruses isolated in off-seasons and the epidemic viruses of the following influenza seasons. In one instance with H1N1 viruses in 1986 and in two instances with H3N2 viruses in 1985 and 1987, the spring isolates were genetically close to some of the winter isolates and were considered to be the parental viruses of the following influenza seasons. However, even in these cases, influenza viruses of the same subtype with different lineages co-circulated in Japan.

Similarities of guamanian ALS/PD to post-encephalitic parkinsonism/ALS: possible viral cause

Guamanian amyotrophic lateral sclerosis with parkinsonism-dementia (ALS/PD) has been the subject of intensive study since its discovery in 1947 because of its extraordinarily high incidence in a small ethnic group (Chamorros) whose dietary lack and customs have suggested possible causes. As yet, these and other suspected causes have eluded proof. Because of marked similarities between Guamanian ALS/PD and late onset post-encephalitic (encephalitis lethargica) parkinsonism and ALS it is suggested that they have a common cause. The parkinsonism and ALS in the two disorders are clinically very similar and neuropathological studies have shown a very similar distribution of neurofibrillary tangles in neurons. Some clinical differences, such as ocular features in the post-encephalitic cases and dementia in Guamanian ALS/PD, can be explained by differences in the severity of infection and the interval between the encephalitis and onset of sequelae. Although unproven, influenza A (HswilN1 strain) has long been suspected as the cause of encephalitis lethargica because of simultaneous pandemics of the two diseases in the 1920s. Because influenza A can persistently infect cells and has a marked propensity to mutate it is an optimal candidate among other RNA viruses for delayed nervous system infection as a possible cause of ALS/PD.