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Register a new userPredicting influenza H3N2 vaccine efficacy from evolution of the dominant epitope
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We predict vaccine efficacy with a measure of antigenic distance between influenza A(H3N2) and candidate vaccine viruses based on amino acid substitutions in the dominant epitopes. In 2016-2017, our model predicts 19% efficacy compared to 20% observed. This tool assists candidate vaccine selection by predicting human protection against circulating strains.
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Objectives Influenza outbreaks have been widely studied. However, the patterns between influenza and religious festivals remained unexplored. This study examined the patterns of influenza and Hanukkah in Israel, and that of influenza and Hajj in Bahrain, Egypt, Iraq, Jordan, Oman and Qatar. Method Influenza surveillance data of these seven countries from 2009 to 2017 were downloaded from the FluNet of the World Health Organization. Secondary data were collected for the countries population, and the dates of Hajj and Hanukkah. We aggregated the weekly influenza A and B laboratory confirmations for each country over the study period. Weekly influenza A patterns and religious festival dates were further explored across the study period. Results We found that influenza A peaks closely followed Hanukkah in Israel in six out of seven years from 2010 to 2017. Aggregated influenza A peaks of the other six Middle East countries also occurred right after Hajj every year during the study period. Conclusions We predict that unless there is an emergence of new influenza strain, such influenza patterns are likely to persist in future years. Our results suggested that the optimal timing of mass influenza vaccination should take into considerations of the dates of these religious festivals.
We proposed a Monte-Carlo method to estimate temporal reproduction number without complete information about symptom onsets of all cases. Province-level analysis demonstrated the huge success of Chinese control measures on COVID-19, that is, provinces reproduction numbers quickly decrease to <1 by just one week after taking actions.
We study the spatio-temporal patterns of the proportion of influenza B out of laboratory confirmations of both influenza A and B, with data from 139 countries and regions downloaded from the FluNet compiled by the World Health Organization, from January 2006 to October 2015, excluding 2009. We restricted our analysis to 34 countries that reported more than 2000 confirmations for each of types A and B over the study period. We find that Pearsons correlation is 0.669 between effective distance from Mexico and influenza B proportion among the countries from January 2006 to October 2015. In the United States, influenza B proportion in the pre-pandemic period (2003-2008) negatively correlated with that in the post-pandemic era (2010-2015) at the regional level. Our study limitations are the country-level variations in both surveillance methods and testing policies. Influenza B proportion displayed wide variations over the study period. Our findings suggest that even after excluding 2009s data, the influenza pandemic still has an evident impact on the relative burden of the two influenza types. Future studies could examine whether there are other additional factors. This study has potential implications in prioritizing public health control measures.
The evolutionary dynamics of human Influenza A virus presents a challenging theoretical problem. An extremely high mutation rate allows the virus to escape, at each epidemic season, the host immune protection elicited by previous infections. At the same time, at each given epidemic season a single quasi-species, that is a set of closely related strains, is observed. A non-trivial relation between the genetic (i.e., at the sequence level) and the antigenic (i.e., related to the host immune response) distances can shed light into this puzzle. In this paper we introduce a model in which, in accordance with experimental observations, a simple interaction rule based on spatial correlations among point mutations dynamically defines an immunity space in the space of sequences. We investigate the static and dynamic structure of this space and we discuss how it affects the dynamics of the virus-host interaction. Interestingly we observe a staggered time structure in the virus evolution as in the real Influenza evolutionary dynamics.
The 1918 influenza pandemic was characterized by multiple epidemic waves. We investigated into reactive social distancing, a form of behavioral responses, and its effect on the multiple influenza waves in the United Kingdom. Two forms of reactive social distancing have been used in previous studies: Power function, which is a function of the proportion of recent influenza mortality in a population, and Hill function, which is a function of the actual number of recent influenza mortality. Using a simple epidemic model with a Power function and one common set of parameters, we provided a good model fit for the observed multiple epidemic waves in London boroughs, Birmingham and Liverpool. Our approach is different from previous studies where separate models are fitted to each city. We then applied these model parameters obtained from fitting three cities to all 334 administrative units in England and Wales and including the population sizes of individual administrative units. We computed the Pearsons correlation between the observed and simulated data for each administrative unit. We achieved a median correlation of 0.636, indicating our model predictions perform reasonably well. Our modelling approach which requires reduced number of parameters resulted in computational efficiency gain without over-fitting the model. Our works have both scientific and public health significance.
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