Using Nanopore sequencing technology, scientists from the Chinese Academy of Sciences gain understanding of African Swine Fever Virus genome.
African Swine Fever Virus (ASFV) causes one of the most pathogenic viral disease known as African Swine Fever (ASF) in pigs. With a fatality rate of almost 100 percent ASFV results in much concern for the economic durability of the hog industry in countries with the epidemic.
In August 2018, China became one of the first Asian countries to be contracted with an ASF epidemic which quickly spread across the country. Mongolia, Vietnam, Cambodia and North Korea soon began reporting of an ASF epidemic.
ASFV is part of the Asfarviridae family which are double-stranded DNA viruses that can be transmitted by ticks. In pigs, ASFV is able to replicate in the cytoplasm of a variety of cells, especially reticuloendothelial cells and mononuclear macrophages.
The complex nature of the ASFV genome has resulted in inadequate whole genome information, which is essential to obtain for genomic and epidemiological studies of the viral disease.
“We first use the nanopore platform to directly sequence clinical samples from pigs infected with ASFV and explore the possibility of TGS (Third-generation sequencing) acquiring large viral genomes such as ASFV.” said Dr Jia Lijia, the first author for this study.
The results of this research indicated that the Nanopore technology can obtain ASFV genome faster than next-generation sequencing (NGS).
“As for working time, the NGS library preparation and on-machine sequencing took significantly longer than the TGS. The Hiseq X10 yields 100 Gb data for 76 hours, while the nanopore library preparation time and the time to generate 100 Gb data on the promethION sequencer add up to less than 24 hours”, added Dr Jia.
One advantage of nanopore sequencing is the rapid turnaround time of the genome sequence, but NGS has better sequencing accuracy. The method of combining TGS and NGS would be ideal for time saving and accuracy.
“Although the current data suggest that the outbreak of African swine fever in China seemed like a single source, our results show that there are still 6-93 variations in the genome of ASFV isolates in different provinces and cities. As a large double-stranded DNA virus, ASFV has a relatively conservative genome, and its natural variation is very slow, but it can be accelerated by interaction with the host and stimulation of environmental factors. In this context, it is necessary to promote whole genome sequencing of ASFVs in different regions, which can provide us with more meaningful variation information and may play an important role in re-establishing the ASFV transmission route”, said Professor Liu Di, the co-corresponding author.
These results confirm the utility of ONT (Oxford Nanopore Technology) sequencing as a non-cultured direct sequencing method for ASFV genomes from PCR-positive clinical tissue. Real time sequencing of the entire genome of the outbreak strain provides a baseline for subsequent epidemiological and evolutionary studies. [APBN]