Novel network method Major Minor Variation Clustering (MMVC) enables identification of poliovirus clusters with high-resolution linkages

Details

• Alternative Title:
  J Comput Biol
• Personal Author:
  Tan, Jiahui ; Zhao, Yutong ; Burns, Cara C. ; Tian, Dechao ; Zhao, Kun
• Description:
  The Global Polio Eradication Initiative uses an outbreak response protocol that defines type 2 Sabin or Sabin-like virus as those with 0-5 nucleotides diverging from their parental strain in the complete VP1 genomic region. Sabin or Sabin-like viruses share highly similar genome sequences, regardless of their origin. Thus, it is challenging to distinguish viruses at a higher resolution to detect polio clusters or trace sources for local transmissions of viruses at an early stage. To identify type 2 Sabin or Sabin-like sources and improve our ability to map viral sources to campaigns during the polio endgame, we investigated the feasibility of a new method for genetic sequence analysis. We named the method Major Minor Variation Clustering (MMVC), which uses a network model to simultaneously incorporate sequence similarity in major and minor variants in addition to onset dates to detect fine-scale polio clusters. Each identified cluster represents a collection of sequences that are highly similar in both major and minor variants, enabling the discovery of new links between viruses. By applying the method to a published data set collected in Nigeria during 2009-2012, we found that clusters identified using this method have several improvements over clusters derived from a phylogenetic tree approach. Integrative data analysis reveals that sequences in the same cluster have greater genomic similarities and better agreement with onset dates. As a complement to current phylogenetic tree approaches, MMVC has the potential to improve epidemiological surveillance and investigation precision to guide polio eradication.
• Subjects:
  Cluster Analysis Genomics Humans Phylogeny Poliomyelitis Poliovirus
• Keywords:
  Genomic Epidemiology Network Modeling Polio Eradication Whole Genome Sequencing
• Source:
  J Comput Biol. 30(4):409-419
• Pubmed ID:
  36112351
• Pubmed Central ID:
  PMC11299649
• Document Type:
  Journal Article
• Funding:
  CC999999/ImCDC/Intramural CDC HHSUnited States/
• Volume:
  30
• Issue:
  4
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha-512:f9ea9f81b07a912de1369df515a12204f6a7fa56c15282444082f694ffdddb478fb1e374ea97f002f158ac982da564c960e65e9edc3d85e1a1d2d87b6f0e0a2e
• Download URL:
  https://stacks.cdc.gov/view/cdc/159583/cdc_159583_DS1.pdf
• File Type:
  [PDF - 769.06 KB ]