Molecular Evidence of Transmission of Influenza A/H1N1 2009 on a University Campus

Abstract

BackgroundIn the recent years, the data on the molecular epidemiology of influenza viruses have expanded enormously because of the availability of cutting-edge sequencing technologies. However, much of the information is from the temperate regions with few studies from tropical regions such as South-east Asia. Despite the fact that influenza has been known to transmit rapidly within semi-closed communities, such as military camps and educational institutions, data are limited from these communities.ObjectivesTo determine the phylogeography of influenza viruses on a university campus, we examined the spatial distribution of influenza virus on the National University of Singapore (NUS) campus.MethodsConsenting students from the NUS who sought medical attention at the UHC provided two nasopharyngeal swabs and demographic data. PCR was used for detection of influenza viruses. 34 full-genomes of pH1N1/09 viruses were successfully sequenced by Sanger method and concatenated using Geneious R7. Phylogenetic analysis was conducted using these 34 sequences and 1518 global sequences. Phylogeographic analysis was done using BaTS software and Association index and Fitch parsimony scores were determined.ResultsIntegrating whole genome sequencing data with epidemiological data, we found strong evidence of influenza transmission on campus as isolates from students residing on-campus were highly similar to each other (AI, P value = 0.009; PS, P value = 0.04). There was also evidence of multiple introductions from the community.ConclusionsSuch data are useful in formulating pandemic preparedness plans which can use these communities as sentinel sites for detection and monitoring of emerging respiratory viral infections.

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

“…The consensus sequences from these strains were deposited in GenBank (numbers will be available upon acceptance of the manuscript). We aligned the consensus sequences using muscle v3.8.31 47 and used the concatenated alignment of all segments to calculated a maximum likelihood tree 8,48 using RaxML ( 49 ; version 8.2.8, options: -x 1522 -f a -m GTRGAMMA -p 1522 - # 100) to depict the relationship between the isolates.…”

“…Whole viral genome sequencing has enabled reconstruction of phylogenetic relatedness at high resolution. Using these approaches, the interactions and dynamics of influenza transmission events have been described across a range of scales: globally 4-6 , across continents 1,7 , in university campuses 8 , or within households 9-12 . With two-thirds of the global population projected to be living in urban areas by 2050, understanding the transmission patterns of influenza within cities is crucial for effective prevention strategies and may help to prepare for pandemic threats.…”

Melatonin: A potential therapeutic agent against COVID-19

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“…This finding highlights the importance of local or regional vaccine strategy and warrants influenza virus surveillance. Indeed, surveillance studies in Singapore have been carried out regularly by the Singapore National Surveillance Program for Influenza that is part of the WHO international laboratory-based surveillance network (Ang et al, 2016a), in addition to other studies under various settings (Seah et al, 2010;Yap et al, 2012;Virk et al, 2017). However, only a few of these surveillance studies were linked to genomic information.…”