🧬 biology

Transmission Dynamics and Genomic Evolution of Monkeypox Virus in Nigeria Across Pre- and Post-COVID-19 Periods

This study analyzes 172 Monkeypox virus sequences from Nigeria to reveal that while the virus's transmission dynamics are primarily driven by the year of isolation rather than seasonal factors, Clade IIb has persisted across pre-, during, and post-COVID-19 periods, underscoring the urgent need for standardized surveillance and targeted interventions.

Original authors: Uwem Okon Edet, Kayode Abraham Olawuyi, Akaninyene Joseph, Md Zulfekar Ali, Okoroiwu Henshaw, Francisca Nwaokorie, Meseko Clement, Adedeji Adeyinka

Published 2026-07-09

📖 5 min read🧠 Deep dive

CC BY 4.0

Original authors: Uwem Okon Edet, Kayode Abraham Olawuyi, Akaninyene Joseph, Md Zulfekar Ali, Okoroiwu Henshaw, Francisca Nwaokorie, Meseko Clement, Adedeji Adeyinka

Original paper licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). ⚕️ This is an AI-generated explanation of a preprint that has not been peer-reviewed. It is not medical advice. Do not make health decisions based on this content. Read full disclaimer

Imagine the Monkeypox virus (MPXV) as a sneaky, shape-shifting traveler that has been hiding in the forests of Nigeria for decades. This research paper is like a detective's report card, looking at the virus's "passport" (genetic data) and "travel logs" (metadata) to see how it moved around before, during, and after the massive global disruption caused by the COVID-19 pandemic.

Here is the story of what the researchers found, broken down into simple concepts:

1. The Great Disappearance and Reappearance

Think of the virus as a ghost that went silent for a long time.

The Silence: Between 1978 and 2017, the virus seemed to vanish from the records. The researchers suggest this might mean the virus was truly gone, or more likely, it was just hiding in the shadows because nobody was looking for it.
The Return: In 2017, the ghost woke up. It started popping up again, with big spikes in cases in 2017, 2018, 2019, and a massive explosion in 2022.
The COVID Interruption: When the world got busy fighting COVID-19 (starting in 2020), the "searchlights" for Monkeypox were turned down. The paper notes that during the peak of the pandemic, fewer Monkeypox cases were reported. This wasn't necessarily because the virus stopped; it's like a library closing its doors—you stop seeing books being checked out, but the books are still on the shelves. The virus was likely still there, just under-reported because everyone was focused on the new pandemic.

2. Where and When Did It Show Up?

The researchers mapped out the virus's journey across Nigeria like a weather forecast.

The Hotspots: The virus loves the southern part of the country, specifically the lush, rainy forest zones (like Bayelsa and Rivers states). It's as if the virus prefers the "jungle" environment. While it did spread to the north, the southern states had the most "footprints."
The Seasonal Pattern: The virus seems to throw its biggest parties in September and October (the dry season) and again in January through March.
The Weak Link: However, when the researchers tried to draw a straight line between the weather (rainy vs. dry seasons) and the number of cases, the connection was weak. It's like trying to predict a storm just by looking at a calendar; the weather matters, but other invisible factors (like human behavior or how people interact with animals) are pulling the strings just as hard.

3. The "Passport" Problem (Data Messiness)

One of the most interesting findings is about how the data was written down.

Imagine trying to track a traveler, but their passport just says "Traveler" or "Bag" instead of "Passport" or "Suitcase."
The researchers found that many records in the global database were vague. Instead of saying "pustule swab" (a sample from a skin sore) or "blood," many entries just said "clinical sample" or "swab."
This lack of detail makes it hard to know exactly how the virus is jumping from person to person or from animals to people. It's like trying to solve a mystery with half the clues missing.

4. The Family Tree (Genetics)

The researchers built a family tree of the virus to see who is related to whom.

One Family: They found that the virus in Nigeria belongs to one specific family branch, called Clade IIb (the West African type). This is the "less severe" cousin compared to the "more severe" Central African type.
The Traveler: This specific family branch didn't change much over time. It stayed the same before, during, and after COVID-19.
The Export: This Nigerian family tree is the same one that showed up in Singapore, the UK, and the USA. It's like a seed that was carried by the wind from Nigeria to the rest of the world. The paper highlights that Nigeria was the starting point for these international trips.

5. What Drives the Outbreaks?

The researchers used a special math tool (called PCA) to figure out what makes the virus spread.

The Main Driver: The most important factor wasn't the weather or the location; it was Time. The year the virus was found mattered the most. This suggests that outbreaks happen in waves or "episodes" rather than being a constant, steady rain.
The Conclusion: The virus is a master of timing. It waits, it wakes up, and it spreads in bursts.

The Bottom Line

The paper concludes that Monkeypox in Nigeria is a persistent traveler that has been quietly circulating for years. The COVID-19 pandemic didn't stop it; it just made us stop counting it for a while. Now that the virus is back in the spotlight, the researchers are asking for better "passports" (standardized data) so we can track it more accurately. They warn that while this specific version of the virus is less deadly than its cousin, it is good at adapting and spreading, so we need to keep our eyes on it, especially in the southern forests where it seems to call home.

Technical Summary: Transmission Dynamics and Genomic Evolution of Monkeypox Virus in Nigeria Across Pre- and Post-COVID-19 Periods

Problem Statement
The COVID-19 pandemic significantly disrupted global healthcare systems and disease surveillance mechanisms, potentially altering the transmission dynamics and genomic evolution of zoonotic pathogens like the Monkeypox virus (MPXV). While the re-emergence of MPXV in Nigeria following decades of dormancy is documented, the specific changes in its transmission patterns, circulating clades, and seasonal drivers across pre-, during-, and post-COVID-19 periods remain poorly understood. Previous studies have identified contributing factors such as poverty and unsafe sexual practices, but gaps persist regarding the specific temporal and geographical clustering of cases and the viral lineages involved during the pandemic era. This study addresses the need to infer how the pandemic influenced MPXV transmission and evolution in Nigeria by analyzing available genomic sequences and metadata.

Methodology
The researchers conducted a retrospective bioinformatics and statistical analysis of MPXV data retrieved from the National Center for Biotechnology Information (NCBI) database.

Data Retrieval: A search for "monkeypox, complete genome, Nigeria" was performed on April 11, 2025. From an initial pool of 238 sequences, 172 whole-genome sequences with complete metadata were retained after filtering out partial and unverified sequences.
Temporal Categorization: Data were categorized into pre-COVID-19 (1971–2019), during-COVID-19 (2020–2021), and post-COVID-19 (2022–2023) periods.
Statistical Analysis: Descriptive statistics (bar charts, scatter plots, pie charts) were used to visualize monthly and yearly distributions. Seasonal analysis categorized months into dry (October–March) and wet (April–September) seasons to assess correlations with outbreak frequency using scatter plots with trend lines ( $R^2$ values).
Multivariate Analysis: Principal Component Analysis (PCA) was employed using OriginPro 2024 to evaluate the influence of isolation year, month, sample type, state of origin, and genome size on transmission dynamics.
Phylogenetic Analysis: Whole-genome sequences were aligned using MAFFT (version 7) and phylogenetic trees were constructed using the Maximum Likelihood (ML) method in RAxML with 1,000 bootstrap pseudo-replicates. Trees were visualized using PHYLOViZ to identify circulating clades and their relationship to exported cases.

Key Results

Temporal Trends: The analysis of 172 sequences (spanning 1971–2023) revealed distinct outbreak peaks in 2017, 2018, 2019, and a significant surge in 2022 (95 sequences). Notably, 2020 and 2021 recorded very few (5) or no sequences, suggesting under-reporting or surveillance gaps during the height of the pandemic.
Seasonality: Outbreaks showed a temporal preference for September and October, followed by January through March. While these months fall largely within the dry season, the statistical correlation between seasonality and outbreak frequency was weak ( $R^2$ values of 0.286 and 0.203), indicating that seasonal variation alone does not fully explain transmission dynamics.
Geographical Distribution: Cases were reported across 22 states and the Federal Capital Territory. Southern states, particularly Bayelsa, Rivers, Imo, Akwa Ibom, and Lagos, reported the highest number of sequences. The distribution suggests a spread from the southern equatorial rainforest zones toward the north.
Sample Standardization: Metadata analysis highlighted a lack of standardization in sample reporting. "Clinical sample" and "swabs" were the most common descriptors (112 and 22 cases, respectively), while specific types like pustule swabs, crusts, and serum were less frequently detailed.
Genomic Evolution: Phylogenetic analysis confirmed the persistent dominance of the West African clade (Clade IIb) across all periods (pre-, during, and post-COVID-19). The Nigerian sequences clustered closely with exported cases from Singapore (2019), the UK (2021), and the USA (2022).
PCA Findings: The Principal Component Analysis indicated that the "year of isolation" was the most influential variable driving transmission patterns, accounting for the majority of variance. Genome size showed no significant influence on outbreak dynamics.

Significance and Claims
The paper posits that the COVID-19 pandemic likely altered MPXV transmission dynamics in Nigeria, primarily through the diversion of resources and the under-reporting of cases during 2020–2021. The study claims that Nigeria serves as a persistent epicenter for the global transmission of Clade IIb, evidenced by the phylogenetic links between Nigerian strains and international exportations.

The authors emphasize that while the viral clade has remained stable (Clade IIb), the episodic nature of outbreaks and the potential for subtle mutations (such as APOBEC3-mediated changes observed in US strains) suggest ongoing viral adaptation. The study concludes that the lack of standardized metadata hinders effective epidemiological interpretation. Consequently, the authors argue for the urgent need to strengthen routine surveillance, standardize reporting protocols (specifically sample type documentation), and implement targeted One Health interventions to monitor the virus's evolution and transmission in Nigeria and the broader West African region.