Influenza viruses continue to be an important public health threat. Vaccination is the most effective measure to control the influenza virus circulation. However, these viruses are continuously evolving through antigenic drift/shift, and thus the vaccine efficiency is affected. The aim of this study was to characterize the viral strains circulating in Romania, in a population with declining vaccination coverage, during the last three cold seasons by evaluating the hemagglutinin antigenic relatedness to the vaccine strains. All the available sequences collected between August 2021 and June 2024 were analyzed by using phylogenetic analysis and the P_epitope model to predict vaccine efficacy. The results showed that the 2021/2022 influenza season was dominated by the circulation of highly diverse clades of A(H3N2) viruses with high mutational divergence as compared to the vaccine strain, which might contribute to the reduction in vaccine efficacy. During the 2022/2023 influenza season, both influenza A and B viruses were reported, with few antigenic site mutations. The 2023/2024 influenza season was dominated by the circulation of influenza A viruses: A/H1N1pdm09 clade 6B.1A.5a.2a and A/H3N2 clade 2a.3a.1. The clade 2a.3a.1 also showed high variability when compared to the vaccine strain, presumably leading to reduced vaccine efficacy. This study illustrates the high diversity of influenza viruses circulating in a population with low vaccination coverage during the previous cold seasons. The viral diversity impacted vaccine efficacy, hence the need for public health programs to increase vaccine uptake and improve vaccine formulation in order to limit viral transmission.

Monitoring the HIV epidemic in Romania has proven challenging due to many factors, including the reluctance of newly diagnosed patients to disclose relevant epidemiological aspects during the clinical interview, such as sexual orientation or the existence of previous issues with injectable drug usage. We propose in this study a molecular approach to mitigate this problem with the help of bioinformatic tools, such as cluster analysis of phylogenetic trees. Both a maximum likelihood estimation, as implemented with FastTree, and a Bayesian approach, as used in BEAST, have been applied to our data set of 312 HIV subtype F1 pol gene sequences. ClusterPicker was used in order to identify groups of sequences and indicate similarities possibly related to the route of transmission. An important observation from this analysis is that transmission between men who have sex with men (MSM) is likely occurring in networks significantly larger than previously assessed by self-reported data (65% from the phylogenetic tree versus 37% from self-declared affiliation). Cluster analysis can help identify risk factors, reveal transmission trends, and, consequently, advise prevention programs.

Emerging SARS-CoV-2 strains continue to generate difficulties for authorities and health care professionals worldwide due to enhanced transmissibility and/or immune response evasion. The appearance of the Alpha and Delta strains has been associated with substantial increases in the number of COVID-19 cases and associated deaths. Whole Genome Sequencing (WGS) continues to be the gold standard for molecular surveillance of the pandemics but other assays such as mutation genotyping can be used to reduce costs and allocated time. This study investigates the efficiency of mutation screening tests compared to WGS and their predictive value to anticipate future waves. A very high degree of fidelity for this type of assay was found, regardless of the method used. The positive predictive value (PPV) of 4/5 markers was over 95% for the detection of Alpha and Delta variants. By estimating the prevalence of the Alpha and Delta strains using genotyping assays and fitting the data to a mathematical model, a five week period between the point of exponential growth of variant prevalence and a drastic increase in case numbers was found. For that reason, raising awareness about the efficacy of mutation screening could help authorities adopt better measures in the future.

The HIV epidemic in Romania started in the late eighties with a large cohort of children nosocomially infected with subtype F1 strains, in parallel with sexual transmission. The purpose of the present study was to investigate the transmitted drug resistance (TDR), subtype distribution, and transmission clusters among persons diagnosed with HIV between 2019 and 2022 in Romania. The prototype of a person recently diagnosed with HIV in Romania is male, 20–50 years old, a late presenter, infected with F1, B, or A subtype. The rate of TDR varied over time, from 5% in 2019 to 15% in 2022. TDR affected mainly the first generation of NNRTIs and the PI class. The rate of late presentation was almost 60%, with 35% of persons qualifying as very late presenters. Subtype F1 is still preponderant in Romania, whereas other subtypes (B, A) and recombinants account for a quarter of HIV-1 new cases. Several transmission networks were identified in the study population, two of them associated with TDR in subtypes F1 and A1. The largest cluster consisted of 26 sequences, originating from Western Romania and introduced around 2007. Molecular clock analysis indicated different origin time points for different clusters, with the most recent in subtypes A1 and B, and the oldest in subtype F1. In conclusion, the HIV-1 epidemic in Romania is currently driven by sexual transmission, with MSM contribution continuously rising in recent years; there are also increases in TDR and the circulation of HIV-1 strains other than F1 (subtype B, A, recombinants).