Study: Intrahost Monkeypox Virus Genome Variation in Patient with Early Infection, Finland, 2022. Image Credit: ART-ur/Shutterstock

Study shows within-host MPXV variation within a single lesion

In a recent study published in Emerging infectious diseaseresearchers reported the clinical and molecular characteristics of monkeypox virus (MPX) (MPXV) infections in Finland.

Study: Intra-host genome variation of Monkeypox virus in a patient with early infection, Finland, 2022. Image credit: ART-ur/Shutterstock


As of 2022, an unprecedented outbreak of MPXV has been observed worldwide, with MPXV detected in individuals without travel to MPXV-endemic nations, particularly among men who have sex with men (MSM). MPXV was introduced in Finland between May and June 2022. A better understanding of the evolutionary characteristics of MPXV and the clinical profiles of MPX is essential for the development of more effective vaccines and therapeutics against MPXV.

About studying

In this study, researchers described the clinical and genetic profiles of MPX patients in Finland.

Four MPX patients aged 20 to 40 years were examined, all of whom had recently traveled to southern Europe, were MSM individuals, and reported recent unprotected sex with unknown individuals. Two of the four patients were seropositive for the human immunodeficiency virus (HIV). Patient 1 had fever, inguinal lymphadenopathy, and synchronous penile MPX lesions. Samples were obtained from the corresponding area five days after symptom onset.

Patient 2 presented with fever, headache, exhaustion, and inguinal lymphadenopathy with asynchronous lesions on the face, neck, trunk, and penis. Samples were taken from the face and trunk on May 31, ten days after the onset of MPX symptoms. Patient 3 had fever, myalgia, lymphadenopathy, nausea, and asynchronous lesions on the trunk, arms, rectum, and legs. Samples were obtained from the hand four days after symptom onset.

Complete MPXV genomes were obtained from three patients: the first patient [penile lesion, Cq (quantitative cycle) 20], the second patient (facial lesion, Cq 26) and the fourth patient (perianal lesion, Cq 23). Only a fragment of the MPXV genome (Cq 33) was recovered from the hand lesions of the third patient. The genomes in all samples were subjected to sequencing analysis.

Real-time polymerase chain reaction (PCR) analysis was performed to detect the presence of orthopoxvirus to be confirmed as MPXV using hemagglutinin gene sequencing. Furthermore, a phylogenetic analysis of MPXV sequences was performed using a phylogenetic tree derived from the maximum likelihood technique.

The dataset was restricted to MPXV genomes with fewer than 5,000.0 ambiguous genomic sites. In addition, regions with bootstrapping values ​​below 70 and grouped without any designated lineage or Finnish representative were excluded from the analysis. Real-time PCR detected the presence of orthopoxvirus in all samples, subsequently confirmed as MPXV by hemagglutinin gene sequencing.


In the sample of the first patient, MPXV intrahost genomic variations were observed, which included one major strain with three nucleotide (nt) substitutions (nonsynonymous mutations G55133A and C64426T and nonsynonymous mutation G190660A) specific to B.1.3 and a minor strain containing B. .1 nucleotides. These three mutations were based on NCBI (National Center for Biotechnology Information) data. Phylogenetic analyzes showed clustering of MPXV sequences (from the first patient) with the genomes of strain B.1.3.

The three mutations in the sequence of the first patient included minor variations of 10.0% frequency (G55133A, depth 2231, 233 guanosine nucleotides and 1997 adenine nucleotides), 12.0% frequency (C64426T, depth 2685, 308 cytosine nucleotides, and 2 nucleotides, 308 cytosine nucleotides). nucleotides and nucleotides of 13.0% frequency (G190660A, depth 2685, 280 guanine nucleotides and 1,872 adenine nucleotides).

The MPXV sequence from the second patient was similar to those initially identified in Portugal, followed by several nations. The MPXV sequence from the fourth patient had four nucleotide substitutions, i.e., G94798A, C89906T, C188491T, and C150831T, of which the G94798A and C89906T sequences were observed in MPXV genomes detected in Portugal, United Kingdom, Germany, and Spain.

A characteristic SNV (single nucleotide variation) in the genome of the first patient was consistent with the impact of the enzyme APOBEC3 (apolipoprotein B mediator ribonucleic acid modifying catalytic polypeptide-like 3) present in humans, which is indicated as a driver of cytosine-thymine >thymine-thymine and guanosine- adenine > adenine-adenine transformation in MPXV.

Fixed minor SNVs in lesions were also observed in five Portuguese samples sequenced in May 2022 and reported in a publicly available dataset, suggesting that the SNV pattern could be a common evolutionary component of MPXV. However, in contrast to previous observations, the major SNV genotypes and minor single nucleotide variation genotypes in the first patient were reportedly fixed in previous MPXV genome sequence records.


In conclusion, based on the findings of the study, monkeypox epidemiology may indicate ongoing coinfection or APOBEC3-mediated evolution.

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