Study demonstrates intrahost MPXV variation within a single lesion

In a recent study published in Emerging Infectious Diseases, researchers reported on the clinical and molecular characteristics of monkeypox (MPX) virus (MPXV) infections in Finland.

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


Ever since 2022, an unprecedented MPXV outbreak has been observed across the globe, with MPXV being detected among individuals with no travel history to nations endemic to MPXV, particularly among males who have sex with males (MSM). MPXV was introduced in Finland between May and June of 2022. An improved understanding of the evolutionary characteristics of MPXV and clinical profiles of MPX is critical to developing more effective vaccines and therapeutics against MPXV.

About the study

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

Four MPX patients, aged between 20 and 40 years, were investigated, all of whom had a history of recent travel to South Europe, were self-declared MSM individuals, and reported having unprotected sex in recent times with unknown individuals. Two of the four patients were seropositive for human immunodeficiency virus (HIV). Patient 1 presented with fever, inguinal lymphadenopathy, and synchronous MPX lesions on the penis. Specimens were obtained from the corresponding region five days post-symptom onset.

Patient 2 presented with fever, headache, exhaustion, and inguinal lymphadenopathy, with asynchronous lesions on the face, neck, trunk, and penis. Specimens were collected from the face and trunk on 31 May, ten days after the onset of MPX symptoms. Patient 3 presented with fever, myalgia, lymphadenopathy, nausea, and asynchronous lesions on the trunk, hands, anus, and feet. Specimens were obtained from the hand four days post-symptom onset.

Full 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 was obtained from the third patient’s hand lesions (Cq 33). The genomes in all specimens were subjected to sequencing analysis.

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

The dataset was limited to MPXV genomes with less than 5,000.0 ambiguous genomic sites. In addition, regions with bootstrapping values below 70 and clustered without any designated lineage or Finnish representative were excluded from the analysis. Real-time PCR detected orthopoxvirus presence in all the specimens, subsequently confirmed to be MPXV using hemagglutinin gene sequencing.


Intrahost MPXV genomic variations were observed in the first patient’s sample, comprising one major strain with three nucleotide (nt) substitutions (non-synonymous G55133A and C64426T mutations and non-synonymous G190660A mutation) specific to B.1.3, and a minor strain comprising B.1 nucleotides. The three mutations were based on NCBI (national center for biotechnology information) data). Phylogenetic analyses showed clustering of MPXV sequences (from the first patient) with B.1.3 strain genomes.

The three mutations in the first patient’s sequence comprised minority variations with 10.0% frequency (G55133A, depth 2231, 233 guanosine nucleotides and 1,997 adenine nucleotides), 12.0% frequency (C64426T, depth 2685, 308 cytosine nucleotides and, 2,364 thymine nucleotides), and 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.

The characteristic SNV (single nucleotide variation) in the first patient’s genome was in line with the impact of the APOBEC3 (apolipoprotein B messenger ribonucleic acid-editing catalytic polypeptide-like 3) enzyme present in humans, indicated to be the driver of cytosine-thymine>thymine-thymine and guanosine-adenine> adenine-adenine transformations in MPXV.

Fixed minor SNVs within lesions were also observed in five Portuguese specimens which underwent sequencing in May of 2022 and were reported in a public-access dataset, indicating that the SNV pattern could be a usual evolutionary component of MPXV. However, contrasting to previous observations, the major SNV genotypes and minor single nucleotide variation genotypes in the first patient were reportedly fixed in previous records of MPXV genome sequences.


To conclude, based on the study findings, monkeypox epidemiology might be indicative of ongoing APOBEC3–mediated co-infection or evolution.

Journal reference:
Pooja Toshniwal Paharia

Written by

Pooja Toshniwal Paharia

Pooja Toshniwal Paharia is an oral and maxillofacial physician and radiologist based in Pune, India. Her academic background is in Oral Medicine and Radiology. She has extensive experience in research and evidence-based clinical-radiological diagnosis and management of oral lesions and conditions and associated maxillofacial disorders.


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