Fatima Aziz , Nida Farooqui , Tanveer Abbas , Mahnoor Javaid , Wardah Rafaqat , Alnara Zhamalbekova , Syed Asad Ali , Syed Ali , Syed Hani Abid
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引用次数: 0
Abstract
Background
Respiratory syncytial virus (RSV) is one of the leading causes of infant morbidity and mortality worldwide, especially in Pakistan. To date, few studies have explored RSV epidemiology in different areas of Pakistan. However, none have performed comprehensive phylogenetic and phylodynamic analyses of RSV strains. This study presents a comprehensive genetic and phylodynamic analysis of RSV strains in children less than five years old in Karachi, Pakistan.
Methods
This study used retrospectively collected nasopharyngeal (swab) samples from 155 children with qPCR-confirmed RSV infection. The samples were used to perform RSV genotyping using PCR employing RSV glycoprotein gene-specific primers. The RSVA and RSVB genotyping was performed using BLAST and Maximum-likelihood (ML) phylogenetic methods. Similarly, the relationship with other RSV strains was analyzed using ML phylogenetic cluster analysis. The RSVA and RSVB mean genetic diversity and coefficient of differentiation were calculated using MEGA7 software. Furthermore, the time to the most common recent ancestor (tMRCA) and effective population size of RSV genotypes A and B were estimated using a Bayesian MCMC analysis. Finally, site selection pressure and glycosylation analyses were performed using FUBAR and NetNGlyc/NetOGlyc tools.
Results
Out of 155, 98 and 57 sequences were RSVA and RSVB, respectively. The tMRCA was estimated to be around 2002 and 2005 for RSVA and RSVB, respectively. RSVA sequences formed two NA1 genotype clusters, comprising 95 and three sequences, respectively. RSVB formed three clusters, where 24 and two sequences clustered with BA9 and BA12 genotypes, respectively, while 31 sequences formed a unique cluster. The RSVA and RSVB glycoprotein gene sequences exhibited N- and O- glycosylation and selection pressure at several sites. RSV B exhibited slightly higher (0.042) nucleotide diversity per site (π) as compared to RSVA (0.019).
Conclusions
Our results suggest that RSVA and RSVB strains in Pakistan exhibit distinct genotypic clusters and differ in their estimated tMRCA. Additionally, both genotypes showed glycosylation and selection pressure at specific sites, with RSVB exhibiting higher nucleotide divergence per site (π), indicating its potential to undergo further evolutionary changes and adaptation. Overall, this study provides unique insights into RSV molecular epidemiology. The study may also help improve our understanding of RSV evolutionary changes and the emergence of new genotypes in different regions worldwide and within Pakistan.
期刊介绍：
(aka Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases -- MEEGID)
Infectious diseases constitute one of the main challenges to medical science in the coming century. The impressive development of molecular megatechnologies and of bioinformatics have greatly increased our knowledge of the evolution, transmission and pathogenicity of infectious diseases. Research has shown that host susceptibility to many infectious diseases has a genetic basis. Furthermore, much is now known on the molecular epidemiology, evolution and virulence of pathogenic agents, as well as their resistance to drugs, vaccines, and antibiotics. Equally, research on the genetics of disease vectors has greatly improved our understanding of their systematics, has increased our capacity to identify target populations for control or intervention, and has provided detailed information on the mechanisms of insecticide resistance.
However, the genetics and evolutionary biology of hosts, pathogens and vectors have tended to develop as three separate fields of research. This artificial compartmentalisation is of concern due to our growing appreciation of the strong co-evolutionary interactions among hosts, pathogens and vectors.
Infection, Genetics and Evolution and its companion congress [MEEGID](http://www.meegidconference.com/) (for Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases) are the main forum acting for the cross-fertilization between evolutionary science and biomedical research on infectious diseases.
Infection, Genetics and Evolution is the only journal that welcomes articles dealing with the genetics and evolutionary biology of hosts, pathogens and vectors, and coevolution processes among them in relation to infection and disease manifestation. All infectious models enter the scope of the journal, including pathogens of humans, animals and plants, either parasites, fungi, bacteria, viruses or prions. The journal welcomes articles dealing with genetics, population genetics, genomics, postgenomics, gene expression, evolutionary biology, population dynamics, mathematical modeling and bioinformatics. We also provide many author benefits, such as free PDFs, a liberal copyright policy, special discounts on Elsevier publications and much more. Please click here for more information on our author services .
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