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Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Updated: May 31, 2025

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

Published on: November 23, 2012

Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023.

Claudia Torresi¹, Roberta Biccheri¹, Cesare Cammà²

¹National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell' Umbria e delle Marche "Togo Rosati", 06126 Perugia, Italy.

Pathogens (Basel, Switzerland)

|January 25, 2025

Summary

African swine fever virus (ASFV) genotype II strains in Italy show unique genomic deletions and translocations. These naturally occurring deleted ASFV strains cause severe disease, similar to wild-type virus in pigs.

Keywords:

African swine fever virus experimental infection genotype II large-fragment deletion natural deleted strains

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Last Updated: May 31, 2025

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Published on: November 23, 2012

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Comparative Lesions Analysis Through a Targeted Sequencing Approach

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Published on: November 5, 2019

Area of Science:

Veterinary Virology
Genomics
Molecular Biology

Background:

African swine fever (ASF) poses a significant global veterinary and economic threat due to the widespread ASF virus (ASFV) genotype II.
The virus causes high mortality rates in infected animals, impacting swine populations worldwide.

Purpose of the Study:

To characterize the genomic features of ASFV strains collected in Italy between 2022-2023.
To investigate the in vivo pathogenicity of naturally deleted ASFV strains.

Main Methods:

Full genome sequencing of 30 ASFV strains from Alessandria and Calabria, Italy.
Analysis of genomic deletions and translocations.
In vivo experiment in pigs to assess disease progression of a deleted strain.

Main Results:

Complete genomic sequencing revealed large-fragment deletions and translocations in Italian ASFV strains.
Specific deletions (~4340 bp, 2162 bp, 5137 bp) and 3' truncations were identified in different geographical clusters.
Two strains exhibited translocations, and an in vivo study confirmed that a deleted strain caused severe ASF symptoms, comparable to wild-type virus.

Conclusions:

This study reports the first natural occurrence of deleted ASFV strains in Italy.
The identified genomic alterations are unique and distinct from previously documented strains.
Deleted ASFV strains maintain pathogenicity, highlighting their continued threat to swine health.