Protein Sequence Analysis

Genome-wide Analysis of Protein-Coding Variants in Leprosy

Although genome-wide association studies (GWAS) have greatly advanced our understanding on the contribution of common non-coding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in 7,048 leprosy patients and 14,398 healthy controls of Han Chinese.

type: 
Journal Paper
journal: 
Journal of Investigative Dermatology, 2017, Aug 22, doi: 10.1016/j.jid.2017.08.004
pubmed: 
28842327
Url: 
http://www.jidonline.org/article/S0022-202X(17)32793-8/pdf
Impact Factor: 
6.287

Benchmarking selected computational gene network growing tools in context of virus-host interactions

Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens.

type: 
Journal Paper
journal: 
Scientific Reports, 2017 Jul 19;7(1):5805. doi: 10.1038/s41598-017-06020-6
pubmed: 
28724991
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28724991
Impact Factor: 
4.259
Date of acceptance: 
2017-06-07

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses

Objective To analyse the proportions of protein identity between Zika virus and dengue, Japanese encephalitis, yellow fever, West Nile and chikungunya viruses as well as polymorphism between different Zika virus strains.

type: 
Journal Paper
journal: 
Bulletin of the World Health Organization, 2017, Jul 1: 95(7): Pg 517-525i
Url: 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5487971/
Impact Factor: 
4.939
Date of acceptance: 
2017-01-19

Molecular features of influenza A (H1N1) pdm09 prevalent in Mexico during winter seasons 2012-2014

Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011-2012 winter season and finally, during the 2013-2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease.

type: 
Journal Paper
journal: 
PLOs One, July 10, 2017, doi: 10.1371/journal.pone.0180419
pubmed: 
28692701
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/28692701
Impact Factor: 
2.8
Date of acceptance: 
2017-07-20

Systems-based approach to examine the cytokine responses in primary mouse lung macrophages infected with low pathogenic avian Influenza virus circulating in South East Asia

BACKGROUND:
Influenza A virus (IAV) is a major public health concern, being responsible for the death of approximately half a million people each year. Zoonotic transmissions of the virus from swine and avian origin have occurred in the past, and can potentially lead to the emgergence of new IAV stains in future pandemics. Pulmonary macrophages have been implicated in disease severity in the lower airway, and understanding the host response of macrophages infected with avian influenza viruses should provide new therapeutic strategies.

RESULTS:

type: 
Journal Paper
journal: 
BMC Genomics. 2017 May 30;18(1):420. doi: 10.1186/s12864-017-3803-6
pubmed: 
28558796
Url: 
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3803-6
Impact Factor: 
3.867
Date of acceptance: 
2017-05-05

Cross-reactive dengue human monoclonal antibody prevents severe pathologies and death from Zika virus infections

Zika virus (ZIKV) infections have been linked with neurological complications and congenital Zika syndrome. Given the high level of homology between ZIKV and the related flavivirus dengue virus (DENV), we investigated the level of cross-reactivity with ZIKV using a panel of DENV human mAbs. A majority of the mAbs showed binding to ZIKV virions, with several exhibiting neutralizing capacities against ZIKV in vitro. Three of the best ZIKV-neutralizing mAbs were found to recognize diverse epitopes on the envelope (E) glycoprotein: the highly conserved fusion-loop peptide, a

type: 
Journal Paper
journal: 
JCI Insight. 2017 Apr 20;2(8). pii: 92428. doi: 10.1172/jci.insight.92428
Url: 
https://insight.jci.org/articles/view/92428
Date of acceptance: 
2017-04-21

Viral factors in influenza pandemic risk assessment

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus.

type: 
Journal Paper
journal: 
Elife, 2016 Nov 11;5. pii: e18491. doi: 10.7554/eLife.18491
pubmed: 
27834632
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27834632
Impact Factor: 
8.3

A large common-source outbreak of norovirus gastroenteritis in a hotel in Singapore, 2012

An outbreak of gastroenteritis affected 453 attendees (attack rate 28·5%) of six separate events held at a hotel in Singapore. Active case detection, case-control studies, hygiene inspections and microbial analysis of food, environmental and stool samples were conducted to determine the aetiology of the outbreak and the modes of transmission. The only commonality was the food, crockery and cutlery provided and/or handled by the hotel's Chinese banquet kitchen. Stool specimens from 34 cases and 15 food handlers were positive for norovirus genogroup II.

type: 
Journal Paper
journal: 
Epidemiology & Infection 2016, Pg 1-10, DOI: 10.1017/S095026881600248X
pubmed: 
27788694
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27788694
Impact Factor: 
2.4
Date of acceptance: 
2017-01-09

South-east Asian Zika virus strain linked to cluster of cases in Singapore, August 2016

Zika virus (ZIKV) is an ongoing global public health emergency with 70 countries and territories reporting evidence of ZIKV transmission since 2015. On 27 August 2016, Singapore reported its first case of local ZIKV transmission and identified an ongoing cluster. Here, we report the genome sequences of ZIKV strains from two cases and find through phylogenetic analysis that these strains form an earlier branch distinct from the recent large outbreak in the Americas.

type: 
Journal Paper
journal: 
Eurosurveillance, Volume 21, Issue 38, 22 September 2016, DOI: http://dx.doi.org/10.2807/1560-7917.ES.2016.21.38.30347
Url: 
http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22588
Impact Factor: 
5.8
Date of acceptance: 
2016-09-22

Identification of a Lineage D Betacoronavirus in Cave Nectar Bats (Eonycteris spelaea) in Singapore and an Overview of Lineage D Reservoir Ecology in SE Asian Bats

Coronaviruses are a diverse group of viruses that infect mammals and birds. Bats are reservoirs for several different coronaviruses in the Alphacoronavirus and Betacoronavirus genera. They also appear to be the natural reservoir for the ancestral viruses that generated the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus outbreaks. Here, we detected coronavirus sequences in next-generation sequence data created from Eonycteris spelaea faeces and urine.

type: 
Journal Paper
journal: 
Transboundary and Emerging Diseases, 2016 Sep 16. doi: 10.1111/tbed.12568
pubmed: 
27637887
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/?term=27637887
Impact Factor: 
2.714
Syndicate content