Kamil F. Khafizov

Relevance . In April 2026, an outbreak of hantavirus infection caused by Andes virus (Orthohantavirus andesense) was reported on the expedition vessel MV Hondius, which had departed from the port of Ushuaia, Argentina, on 1 April 2026. Clinical symptoms in the first affected passenger appeared on 6 April, and the patient died on board the vessel on 11 April. In the following weeks, severe cases were identified among passengers and crew members after some individuals had disembarked and subsequently travelled through several countries. Aim . To assess the epidemiological and genomic characteristics of the outbreak and identify lessons for biosafety systems. Materials and Methods . We analyzed data from the epidemiological investigation provided by WHO and national health authorities. Genomic sequencing was performed using metagenomic approaches, SISPA, and hybridization enrichment. Phylogenetic analysis was conducted using the maximum likelihood method in IQ-TREE 3. Results and Discussion. Following outbreak investigation and diagnostic testing of patients in different countries, a total of 13 cases of infection were identified including 11 laboratory-confirmed cases, 2 probable cases, and 3 deaths. The epidemiological investigation suggests primary zoonotic infection of the index patient before boarding the vessel in an endemic area of southern Argentina, followed by limited person-to-person transmission on board. Genomic analysis demonstrated a high degree of identity among viral sequences obtained from affected individuals, which is consistent with a single introduction followed by subsequent human-to-human transmission. Conclusions . The hantavirus outbreak on board MV Hondius represents an important example of an epidemiologically significant event in which a zoonotic pathogen with limited capacity for person-to-person transmission occurred within a closed international community. This event highlights the importance of early clinical diagnosis, sanitary and quarantine measures for contact persons, and rapid international exchange of genomic data to ensure biosafety during epidemic events caused by emerging, rare, or genetically altered pathogens.

Background: The diagnosis of infectious diseases currently relies predominantly on polymerase chain reaction (PCR) assays. However, the range of pathogens that can be detected simultaneously using these methods is limited, and their effective use depends on an a priori etiological hypothesis. Multiplex PCR-based targeted next-generation sequencing (mp-tNGS) is considered a promising complementary approach for expanded viral testing. This study aimed to develop an in-house mp-tNGS method, perform an initial evaluation of its analytical sensitivity, and explore its performance using clinical respiratory specimens. Methods: The method comprised a panel targeting 28 viruses and bioinformatics pipelines for mp-tNGS data processing. Analytical sensitivity was evaluated using positive control samples (PCSs) containing encapsulated RNA or DNA. Performance with clinical specimens was explored using 910 nasopharyngeal and oropharyngeal swab specimens, which were divided into three groups based on the results of prior PCR testing. Results: Of the 28 viral targets, 23 underwent experimental analytical evaluation, whereas five were assessed in silico only. For 19 of the 23 PCSs tested, the estimated limit of detection (LoD) ranged from 6.3 × 10² to 9.4 × 10³ copies/mL. In the group of 216 PCR-positive specimens, PCR and mp-tNGS results were fully concordant in 139 cases; in 28 specimens, mp-tNGS additionally detected other viruses. Among 394 PCR-negative specimens, mp-tNGS detected viruses in 81. In the group of 300 hospital-derived specimens, mp-tNGS detected at least one viral target in 131 specimens, including additional viral detections and coinfections not identified during the initial testing. A substantial proportion of the additional findings involved Epstein–Barr virus (EBV) and cytomegalovirus (CMV), warranting cautious clinical interpretation. Conclusions: The developed mp-tNGS approach demonstrated the potential to simultaneously detect a broad range of known viruses, provide viral typing, and identify coinfections. The method may be used as an adjunctive tool to broaden the laboratory diagnosis of respiratory infections; however, further optimization, validation, and standardization of criteria for result interpretation are required.

Lower respiratory tract infections caused by the respiratory syncytial virus (RSV) pose a major global public health challenge. The use of next-generation sequencing technologies enables detailed monitoring of viral genetic variability, which is crucial for evaluating the efficacy of immunoprophylactic measures. In this study, whole-genome sequencing of RSV was performed on 106 samples collected in the Russian Federation between September 2021 and April 2025. Three NGS platforms were employed: Illumina MiSeq, Oxford Nanopore Technologies MinION, and Qitan Tech QNome-3841. Using discrete phylogeographic methods, we estimated a minimum of 45 introduction events into Russia for RSV-A and 39 for RSV-B among the genomes included in the analysis. Most events were represented by a single Russian genome. These results indicate recurrent introductions of RSV into Russia from abroad. Given the limited genomic sampling available, most of these introductions were not associated with detectable transmission within the country.

Relevance. Targeted sequencing is becoming an increasingly important tool in the diagnosis of infectious diseases in response to the limitations of conventional diagnostic methods and the high cost and complexity of metagenomic sequencing. Aims. To summarize current approaches for targeted next-generation sequencing (tNGS) in infectious disease diagnostics, to highlight its advantages and limitations in comparison with culture-based and PCR-based methods as well as metagenomic sequencing, and to discuss prospects for its implementation in routine clinical practice and genomic surveillance systems. Conclusion. Targeted sequencing has been shown to substantially improve the sensitivity and specificity of pathogen detection while maintaining turnaround time and cost comparable to conventional diagnostic methods. In addition, it enables accurate pathogen typing and the simultaneous generation of data suitable for genomic surveillance and antimicrobial resistance monitoring. Key technological and organizational barriers are discussed, along with future directions in the development of targeted panels and bioinformatic solutions that may establish tNGS as one of the core tools of infectious disease diagnostics in the coming years.

Introduction. Hepatitis C is a pressing global public health issue. The high variability of the hepatitis C virus (HCV) complicates its whole-genome sequencing; most studies sequence only specific regions of the genome. There is a need for a simple and reliable method for sequencing the whole genome of HCV. Objective. Development and validation of NGS panel for whole-genome sequencing of HCV. Materials and methods. This study presents NGS amplification panel for sequencing the genomes of HCV genotypes 1, 2, and 3. Depending on the genotype, a set of 79, 67, or 89 primers is used. These primers enable amplification of overlapping regions of the HCV genome. Results. The panel was tested on 153 HCV RNA samples isolated from blood plasma specimens (93/6/54 samples of genotypes 1/2/3, respectively). Shannon entropy analysis showed that genetic heterogeneity within the E2 gene is significantly higher than in other parts of viral genome. The frequency of mutations associated with drug resistance was determined. Specifically, for genotype 1, the following mutation detection rates were observed in NS3: Y56F – 37.6%, V170I – 23.7%; in NS5a: R30Q – 8.6%, P58L/S/T – 6.5%, A92T – 4.3%; in NS5b: L159F – 45.2%, S556G/N – 33.3%. Conclusion. The current study describes a method for whole-genome sequencing of HCV genotypes 1, 2, and 3. The HCV sequencing panel shows great potential for use in scientific research and epidemiological monitoring.

Relevance. In 2021, the World Health Assembly called on WHO Member States to strengthen the role of genomic epidemiological surveillance.Objective. To present a revolutionary range of technological tools that determine the success of genomic epidemiological surveillance.Results and discussion. Approaches that can take genomic epidemiological surveillance to a new technological level include rapid nucleic acid amplification methods, including isothermal amplification methods, metagenomic and targeted analysis using high-throughput sequencing technologies, a targeted genome editing system, as well as diagnostic solutions based on it, and the development of genomic sequence databases. In addition, it is necessary to note the importance of developing and implementing a comprehensive approach to the implementation of the genomic epidemiological surveillance system, taking into account the rapid development of a number of fundamental biological sciences related to epidemiology, as well as the wide application of information technologies in the processing of large data sets. Conclusion. Global trends confidently demonstrate a reduction in the time it takes for a technology to transition from scientific development to widespread practical application necessary to protect the population in the context of an epidemic spread of infections caused by previously unknown pathogens. For timely forecasting and prompt response to biological threats and ensuring sanitary and epidemiological well-being, the Russian Federation has successfully applied a triad of technologies: genomic epidemiological surveillance, mobile technologies and big data analytics. The authors consider biotechnological areas and technologies, the improvement of which will ensure the technological leadership of the Russian Federation in the field of genomic epidemiological surveillance.

Aim: determination of alleles of HLA genes associated with autoimmune hepatitis (AIH) and overlap syndrome (OS) in the Russian population.Materials and methods. The study included 160 adult patients with a verified diagnosis of AIH or OS. The control group consisted of 320 conditionally healthy participants. A custom NGS panel was used to type the alleles of the HLA class I and II genes. The statistical analysis was carried out using Pearson’s χ² test with multiple FDR correction (p < 0.05). A logistic regression model was used to evaluate HLA alleles as predictors of the disease.Results. Alleles and haplotypes which frequencies have statistically significant difference in the study and control groups were identified. In the study group, alleles HLA-A*01:01:01 (OR = 2.15; 95 % CI: 1.43–3.23), HLA-B*08:01:01 (OR = 3.38; 95 % CI: 2.10–5.44), HLA-C*07:01:01 (OR = 1.90; 95 % CI: 1.30–2.78), HLA-DPB1*01:01:01 (OR = 3.22; 95 % CI: 1.58–6.55), DQB1*02:01:01 (OR = 3.11; 95 % CI: 2.06–4.70), HLA-DRB1*03:01:01 (OR = 3.03; 95 % CI: 2.02–4.55) were more common. Frequency of occurrence of the DQB1*03:01:01 allele in the study group was lower than in the control group (OR = 0.49; 95 % CI: 0.34–0.71). A logistic regression model was built, which was characterized by an accuracy of 0.688, a sensitivity of 0.487, and a specificity of 0.887.Conclusion. Alleles and haplotypes of HLA genes associated with AIH and OS were identified in a representative sample of the Russian population.