Genomic characteristics of the first five monkeypox virus clade Ib cases in Thailand: August 2024–March 2025
TL;DR
A 1,140-bp deletion in the C3L gene region that distinguishes clade Ib from clade Ia is identified, which directly affects the performance of some commercial real-time PCR assays designed for clade Ia, which rely on amplification of the missing genomic region.
Abstract
ABSTRACT Following the emergence of monkeypox virus clade Ib in the Democratic Republic of the Congo in August 2024, the World Health Organization declared a public health emergency of international concern because of sustained transmission and international spread. We characterized the first clade Ib cases detected in Thailand between August 2024 and March 2025 and assessed their phylogenetic relationships. Whole-genome sequencing was performed from lesion swabs of suspected cases. Phylogenetic analysis, incorporating clade Ia (DQ011155.1) and global clade Ib sequences from GISAID, confirmed all Thai isolates as clade Ib. The genomes showed close relatedness to clade Ib viruses reported internationally, consistent with patients’ travel histories. All isolates exhibited a 1,140-bp deletion in the C3L gene region and 52–61 amino acid substitutions compared with the clade Ia reference. Genome sequences were submitted to GISAID and NCBI to support outbreak response and improve understanding of epidemiologic patterns, enabling more effective public health interventions. IMPORTANCE On 14 August 2024, the World Health Organization declared the monkeypox virus outbreak in Africa a public health emergency of international concern following the emergence of clade Ib. One week later, Thailand confirmed the first monkeypox clade Ib case in Asia. Through whole-genome sequencing and phylogenomic analysis of five cases detected between August 2024 and March 2025, we identified a 1,140-bp deletion in the C3L gene region that distinguishes clade Ib from clade Ia. This deletion directly affects the performance of some commercial real-time PCR assays designed for clade Ia, which rely on amplification of the missing genomic region. Our findings highlight important diagnostic limitations that could lead to misinterpretation or reduced sensitivity in routine testing. Beyond confirming regional introduction linked to global spread, this study underscores the critical role of genomic surveillance in ensuring accurate diagnosis, monitoring viral evolution, and strengthening outbreak response as monkeypox continues to expand internationally. On 14 August 2024, the World Health Organization declared the monkeypox virus outbreak in Africa a public health emergency of international concern following the emergence of clade Ib. One week later, Thailand confirmed the first monkeypox clade Ib case in Asia. Through whole-genome sequencing and phylogenomic analysis of five cases detected between August 2024 and March 2025, we identified a 1,140-bp deletion in the C3L gene region that distinguishes clade Ib from clade Ia. This deletion directly affects the performance of some commercial real-time PCR assays designed for clade Ia, which rely on amplification of the missing genomic region. Our findings highlight important diagnostic limitations that could lead to misinterpretation or reduced sensitivity in routine testing. Beyond confirming regional introduction linked to global spread, this study underscores the critical role of genomic surveillance in ensuring accurate diagnosis, monitoring viral evolution, and strengthening outbreak response as monkeypox continues to expand internationally.