Sequencing the monkeypox genome with Ion Torrent NGS

The monkeypox* virus is a member of the smallpox family and is currently endemic to western and central Africa. However, in 2022, a global monkeypox outbreak caused alarm with a rapid rise in cases in at least 50 counties¹. Researchers are now using genomic sequencing to investigate the spread and evolution of the monkeypox virus by tracking mutations across its ~197,000 nucleotide DNA sequence. To date, over 100 monkeypox genomes have been deposited GenBank², including a genome sequenced with Ion Torrent next-generation sequencing from the first Italian monkeypox case³.

The first monkeypox case in Italy was reported on May 18, 2022, from a 39-year-old Italian man returning from the Grand Canary Islands. Italy’s first available monkeypox genome was released on May 26, 2022, using DNA extracted from a scab sample from this case (GenBank ON614676.1).

Metagenomic sequencing was performed using an Ion Torrent GeneStudio S5 system. Major contigs were aligned to a German monkeypox sequence (GenBank ON568298.1) and then manually reviewed. All reads were mapped to the genome, and all variants were manually curated. The final genome assembly was deposited in GenBank with identifier MPXV-INMI-Pt1 and contains 190,280 nucleotides with a mean coverage of 159 reads. In total, 186 ORFs were annotated. Phylogenetic analysis was performed on representative Orthopoxvirus full-genome sequences in GenBank and included MPXV-INMI-Pt1 and monkeypox viral genomes from the USA, Germany, Belgium, and Portugal. MPXV-INMI-Pt1 was most closely related to other monkeypox genomes from the recent multi-country outbreak, which all belong to the West African clade. These results are consistent with the observation that genomes from the current monkeypox outbreak share around 40 mutations that distinguish them from 2018 monkeypox samples⁴.

Genomic sequencing provides valuable insights into pathogens like the monkeypox virus. As more samples are sequenced, researchers will continue to investigate how mutations in the monkeypox genome are potentially linked to viral properties. Ongoing surveillance will be necessary, and freely and widely available genomic data will help researchers monitor how the monkeypox genome is changing compared to previous isolates.

Fast Facts on Monkeypox

• Monkeypox is related to the virus that causes smallpox⁵
• Monkeypox was first identified in monkeys in 1958. The first human case was recorded in 1970⁵
• Prior to 2022, all monkeypox cases outside of Africa were linked to international travel or animal imports⁵. The virus has spread to more than 30 newly affected countries in the current monkeypox outbreak⁶

References:

1. Multi-country monkeypox outbreak: situation update. World Health Organization 27 June 2022
2. Benson, DA et al. (2013). GenBank. Nucleic acids research, 41(D1), D36-D42
3. Gruber, Cesare et al. First available Monkeypox genome sequence from the first case in Italy related to multi-country outbreak in May 2022. Genome reports. 31 May 2022
4. Joseph, Andrew. What the surprising mutations in the monkeypox virus could indicate about the new outbreak. STAT. 2 June 2022
5. About monkeypox. Centers for Disease Control and Prevention. 17 June 2022
6. WHO Director-General’s opening remarks at the COVID-19 media briefing. World Health Organization. 14 June 2022

 

*The World Health Organization has acknowledged that monkeypox is a discriminatory and stigmatizing name and is working with global experts to change the name of the virus, its clades, and the disease it causes. Future announcements on new naming conventions are expected.

For Research Use Only. Not for use in diagnostic procedures.