The research team collected RSV-positive upper respiratory tract samples from patients who tested positive between October 2023 and March 2025, spanning two consecutive seasons that straddled the deployment of nirsevimab. Whole viral genomes were recovered using an amplicon-based sequencing protocol carried out on Illumina platforms, with assemblies generated through a consensus-building pipeline known as vcf-consensus-builder. This approach allowed the investigators to capture near-complete genomes from a substantial fraction of positive samples, providing the resolution needed to place each virus within a fine-grained phylogenetic framework and to examine amino acid variation in the proteins most relevant to prevention and treatment.

In total, the study retrieved 302 RSV genome sequences, with 129 derived from the 2023–2024 season and 173 from the 2024–2025 season. The clinical composition of the cohort reflects the burden of RSV disease in the region: most infections occurred in infants aged one year or younger, who accounted for 56.0 percent of cases, and males made up 57.3 percent of the sampled population. Lower respiratory tract infections were documented in 72.7 percent of cases, 67.2 percent of patients required hospitalization, and 15.0 percent were admitted to an intensive care unit. Notably, the dataset included 17 nirsevimab breakthrough infections, cases in which infants who had received the monoclonal antibody nonetheless developed symptomatic RSV disease.

Phylogenetic analysis using maximum-likelihood methods implemented in IQ-TREE, with a GTR plus F, invariant sites, and gamma model of substitution, assigned the circulating viruses to established clades within the two major RSV subgroups. The most frequently detected clades were A.D.3, representing 26.8 percent of sequences, and B.D.E.1, representing 20.2 percent, followed by A.D.1.2 at 17.5 percent and A.D.5.2 at 14.2 percent. This distribution confirms that multiple lineages of both RSV-A and RSV-B co-circulated in Lombardy throughout the study period, with no single clade achieving complete dominance across the two seasons.

Beyond clade assignment, the researchers applied Bayesian coalescent methods under a constant population size prior and a strict molecular clock to define what they termed large phylogenetic clusters, or LPCs. These were groups of more than ten sequences supported by a posterior probability of one, indicating tightly linked transmission chains or rapidly expanding lineages. Four such clusters were identified, and two of them proved particularly striking: a cluster of 56 A.D.3 strains and another of 17 A.D.1.2 strains were detected exclusively in the 2024–2025 season, the first season of routine nirsevimab use. The emergence of season-specific clusters suggests that new viral lineages established themselves in the population after the prophylaxis program began.

A central concern of the study was the monitoring of mutations associated with resistance to the preventive and therapeutic agents now deployed against RSV. The fusion protein, or F, is the target of the monoclonal antibodies palivizumab, nirsevimab, and clesrovimab, while the nucleoprotein, or N, is the target of the small-molecule inhibitor zelicapavir. Resistance-associated mutations were identified in two samples from the 2023–2024 season and two from the 2024–2025 season. These included K272E in an A.D.5.3 strain and N262Y in an A.D.3 strain, both associated with reduced susceptibility to palivizumab, and N208D in a B.D.E.1 strain as well as the combination of K68I and L204S in a B.D.E.1 nirsevimab breakthrough infection, mutations linked to nirsevimab resistance.

Among the 17 nirsevimab breakthrough infections, the investigators also detected the S213R substitution at antigenic site Ø of the F protein in an A.D.1.2 sample. Site Ø is the principal binding site for nirsevimab, and changes at this region can diminish antibody binding. By contrast, no mutations conferring resistance to clesrovimab, a newer monoclonal antibody that binds a different region of F, were detected during the study. However, four substitutions were observed at the clesrovimab binding site: K433R in a B.D.4.1.1 strain, C439R in an A.D.1.2 strain, N437S in an A.D.5.2 strain, and N444S in an A.D.3 strain, with three of the four appearing during the 2024–2025 season. These variants were not classified as resistance mutations, but their presence at a pharmacologically critical epitope warrants continued attention.

The nucleoprotein analysis likewise revealed signals relevant to antiviral therapy. The I129M substitution in the N protein, which is associated with resistance to zelicapavir, was detected in a B.D.E.1 sample from the 2024–2025 season at an intrapatient relative abundance of 0.05, indicating that the variant existed as a minor species within the quasispecies of that infection rather than as the dominant viral population. Such low-frequency variants are typically invisible to conventional diagnostic assays but can be resolved by deep sequencing, and their detection underscores the value of high-resolution genomic surveillance in identifying resistance determinants before they become established at the population level.

Multivariable analysis comparing the two seasons revealed several statistically significant differences associated with the 2024–2025 period. That season was characterized by an increased number of sequences belonging to large phylogenetic clusters, greater amino acid variability at antigenic site Ø of the F protein, and higher Ct values on diagnostic testing, which correspond to lower viral loads in respiratory samples. Hospital intensive care unit admissions were also fewer in the second season. While the observational design of the study precludes drawing direct causal links between nirsevimab deployment and these shifts, the concurrence of prophylaxis introduction with reduced disease severity, altered viral population structure, and expanded F protein variability provides a compelling rationale for sustained monitoring.

The overall message from the Lombardy surveillance program is one of cautious reassurance combined with vigilance. Nirsevimab breakthrough infections remained rare relative to the scale of the prophylaxis campaign, and bona fide resistance mutations were detected in only a handful of samples across two seasons. At the same time, the virus is demonstrably diversifying, with season-specific phylogenetic clusters and accumulating variation at antibody binding sites on the F protein. As monoclonal antibodies and vaccines become mainstays of RSV prevention worldwide, the Lombardy experience illustrates how whole-genome sequencing, phylogenetic clustering, and mutation-level analysis can be woven into routine public health practice, ensuring that shifts in viral evolution are detected early enough to inform and adjust prophylaxis strategies before they compromise protection of the most vulnerable patients.

Subject of Research: Genomic evolution and monoclonal antibody resistance of respiratory syncytial virus in Lombardy before and after nirsevimab introduction

Article Title: Genomic characterization of circulating respiratory syncytial virus strains in Lombardy before and after the introduction of nirsevimab prophylaxis

Article References: Uceda Renteria, S., Galli, C., Ferrari, G., Cossu, M. V., Lombardi, A., Tagliabue, C., Galli, G., Parisi, A., Pellegrinelli, L., Romano, G., Bono, P., Pitrolo, A. M. G., Salpini, R., Salvini, F., Svicher, V., Bosis, S., Callegaro, A., Gori, A., Baldanti, F., … Alteri, C. (2026). Genomic characterization of circulating respiratory syncytial virus strains in Lombardy before and after the introduction of nirsevimab prophylaxis. Genome Medicine. https://doi.org/10.1186/s13073-026-01768-x

Image Credits: AI Generated

DOI: 10.1186/s13073-026-01768-x

Keywords: respiratory syncytial virus, nirsevimab, genomic surveillance, viral evolution, monoclonal antibodies, fusion protein, phylogenetics, whole-genome sequencing, antiviral resistance, breakthrough infections, Lombardy, public health

The Democratic Republic of Congo carries a high burden of chronic hepatitis B, a condition that can progress silently over decades toward cirrhosis and hepatocellular carcinoma. Yet despite this substantial disease burden, the molecular characteristics of the virus circulating in the country had remained poorly defined. That gap matters for reasons that extend far beyond academic curiosity. The genotype of hepatitis B virus infecting a patient can influence the natural history of infection, the performance of diagnostic assays, the likelihood of antiviral resistance, and the effectiveness of vaccination strategies. Without a clear picture of viral diversity, surveillance systems, clinicians, and elimination programs are working with an incomplete map.

To address that gap, the researchers followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines, systematically searching publicly available databases for studies reporting molecular characteristics of hepatitis B virus isolated in the Democratic Republic of Congo. The quality of each eligible study was assessed using the Newcastle-Ottawa Scale, a standard instrument for appraising observational research. From the screened literature, eight studies published up to April 2026 met the inclusion criteria, together contributing 273 hepatitis B virus sequences collected between 2000 and 2023. The team extracted data on genotypes, subgenotypes, recombinant strains, antiviral resistance-associated mutations, and immune or vaccine escape mutations, then synthesized the findings quantitatively.

The headline result concerns genotype distribution. Genotype E accounted for the largest share of reported sequences at 53.8 percent, followed closely by genotype A at 43.6 percent, with genotype D making up the remaining 2.2 percent. That near-even split between two major genotypes is itself noteworthy, because many countries in the region are dominated by a single genotype, most commonly genotype E in West and Central Africa. More striking still, the researchers found that the distribution of genotypes varied significantly across geographic regions of the country, a statistically robust pattern with a p value below 0.001. Such regional heterogeneity hints at distinct historical transmission chains and migration dynamics shaping the epidemic in different parts of this vast nation.

Perhaps the most biologically intriguing finding lies within genotype A. Far from representing a homogeneous viral population, genotype A in the Democratic Republic of Congo exhibited considerable genetic diversity, encompassing subgenotypes A1 through A4, the more recently described subgenotype A8, quasi-A3 variants, unclassified subgenotype A* variants, and A/E recombinant strains. This depth of diversity suggests that multiple evolutionary lineages of the virus have circulated within the country, likely reflecting a long and complex history of introduction and local evolution. Recombinant strains, in which genetic material from different genotypes has been exchanged during mixed infections, are of particular interest to virologists because recombination can alter antigenic properties and complicate genotype-based diagnostic algorithms.

The review also identified mutations with direct clinical relevance. Antiviral resistance-associated substitutions, typically arising in the reverse transcriptase domain of the viral polymerase under selective pressure from drugs such as lamivudine or adefovir, were present in 6.7 percent of the reported sequences. Meanwhile, immune- and vaccine-escape substitutions, which alter surface antigen epitopes targeted by antibodies generated through natural infection or vaccination, were detected in 9.5 percent of isolates. Neither figure is alarmingly high in absolute terms, but both indicate that variants with potential implications for treatment response and vaccine effectiveness are already circulating within the population. In a country where diagnostic capacity varies widely, the presence of surface gene mutations raises practical questions about whether routine rapid diagnostic tests and enzyme-linked or chemiluminescent immunoassays reliably detect all circulating viral variants.

These findings arrive at a consequential moment. The World Health Organization has set ambitious targets for eliminating viral hepatitis as a public health threat, and national elimination strategies depend on accurate knowledge of which viral variants are circulating where. For the Democratic Republic of Congo, the review exposes critical gaps in molecular surveillance. With only eight studies and 273 sequences available for a country of its size and population, the available data represent a sparse sampling of the epidemic. The authors emphasize that the substantial genetic diversity and marked geographic variation they document limit the reliability of national-level summary estimates and argue that strengthening nationwide genomic monitoring will be essential to inform targeted prevention, optimize treatment strategies, and support progress toward elimination.

The technical underpinnings of the review are worth appreciating. Genotyping of hepatitis B virus conventionally relies on sequencing regions of the viral genome, most often the surface and polymerase genes, and comparing them against reference sequences. Subgenotype assignment demands higher-resolution analysis, and the identification of recombinant forms requires bootscanning or similar phylogenetic methods capable of detecting mosaic genomes. That such varied lineages were recoverable even from a limited dataset suggests that expanded sequencing efforts in the country would likely uncover additional diversity. It also underscores the value of depositing sequence data in publicly accessible databases, since the entire synthesis was built from studies whose molecular data were openly available.

For clinicians and public health authorities in the Democratic Republic of Congo and neighboring countries, the practical implications are tangible. High genotype diversity means that treatments and diagnostic tools validated primarily against other viral populations may behave differently in Congolese patients. The detection of vaccine-escape mutations, while preliminary, argues for sustained post-vaccination serological monitoring, particularly among infants vaccinated under the national program. The presence of polymerase resistance mutations supports the judicious use of antiviral therapy with appropriate monitoring, and it reinforces the case for tenofovir-based first-line regimens, which carry a higher genetic barrier to resistance than older nucleoside analogues. Regional variation in genotype distribution further suggests that surveillance and response efforts may need to be tailored at the provincial level rather than designed around a single national profile.

The study, conducted without external funding by a small team in Mbujimayi, also demonstrates the growing capacity of African researchers to synthesize continental evidence and direct attention to understudied epidemics. As genomic sequencing becomes cheaper and more accessible, the hope is that the picture sketched by this review will be repeatedly refined, with denser sampling across all provinces and over time. Until then, the message to policymakers is clear: hepatitis B in the Democratic Republic of Congo is not a single epidemic but a mosaic of genetically distinct viral populations, and eliminating it will require surveillance infrastructure capable of seeing that mosaic in full.

Subject of Research: Molecular epidemiology and genetic diversity of hepatitis B virus in the Democratic Republic of Congo

Article Title: Molecular characterization of hepatitis B virus in the Democratic Republic of Congo: a systematic review

Article References: Cindibu Kalonji, F., & Tshibangu-Kabamba, E. (2026). Molecular characterization of hepatitis B virus in the Democratic Republic of Congo: a systematic review. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14433-w

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14433-w

Keywords: hepatitis B virus, Democratic Republic of Congo, molecular epidemiology, genotype E, genotype A, systematic review, vaccine escape mutations, antiviral resistance, viral recombination, genomic surveillance, BMC Infectious Diseases, viral hepatitis