Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for specific well-studied family of viruses. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families. Here, we introduce a virus classification platform, CASTOR, based on machine learning methods. CASTOR is inspired by a well-known technique in molecular biology: restriction fragment length polymorphism (RFLP). It simulates, in silico, the restriction digestion of genomic material by different enzymes into fragments. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of human papillomaviruses (HPV), hepatitis B viruses (HBV) and human immunodeficiency viruses type 1 (HIV-1). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV-1 M subtyping, respectively. Furthermore, CASTOR shows a competitive performance compared to well-known HIV-1 specific classifiers (REGA and COMET) on whole genomes and pol fragments. The performance of CASTOR, its genericity and robustness could permit to perform novel and accurate large scale virus studies. The CASTOR web platform provides an open access, collaborative and reproducible machine learning classifiers. CASTOR can be accessed at http://castor.bioinfo.uqam.ca .

Hepatitis E virus (HEV) is a pathogen that has caused various epidemics and sporadic localized cases. It is considered to be a public health problem worldwide. HEV is a small RNA virus with a significant genetic diversity, a broad host range, and a heterogeneous geographical distribution. HEV is mainly transmitted via the faecal–oral route. However, some animals are considered to be natural or potential reservoirs of HEV, thus elucidating the zoonotic route of transmission via the environment through contact with these animals or consumption of their by-products. Other routes of human-to-human transmission are not negligible. The various human–animal–environment entities, taken under one health approach, show the circulation and involvement of the different species (mainly Paslahepevirus balayani and Rocahepevirus ratti) and genotypes in the spreading of HEV infection. Regarding P. balayani, eight genotypes have been described, of which five genotypes (HEV-1 to 4 and HEV-7) are known to infect humans, while six have been reported to infect animals (HEV-3 to HEV-8). Furthermore, the C1 genotype of the rat HEV strain (HEV-C1) is known to be more frequently involved in human infections than the HEV-C2 genotype, which is known to infect mainly ferrets and minks. Contamination can occur during run-off, flooding, and poor sanitation, resulting in all of these genotypes being disseminated in the environment, contaminating both humans and animals. This systematic review followed the PRISMA guidelines and was registered in PROSPERO 2025 CRD420251071192. This research highlights the importance of investigating the transmission routes and major circulating HEV genotypes in order to adopt a holistic approach for controlling its emergence and preventing future outbreaks. In addition, this article outlines the knowledge of HEV in Africa, underlining the absence of large-scale studies at the environmental, human, and animal levels, which could improve HEV surveillance on the continent.

Introduction: Access to antiretroviral treatment (ART) becomes more and more effective in resource‐limited settings (RLS). However, this global effort would be even more profitable if the access to laboratory services especially in decentralized settings was strengthened. We report the virological outcome and HIV‐1 drug resistance in three West African countries using dried blood spots (DBS) samples.Methods: We included HIV‐1‐infected adults on ART ≥6 months and followed up in capital cities and decentralized sites in Senegal, Mali and Guinea‐Conakry. Patients were consecutively enrolled and DBS were collected in field conditions and kept at ambient temperature before transfer to the reference laboratory. Viral load (VL) was quantified using the NucliSENS EasyQ HIV‐1 v1.2. Genotyping of HIV‐1 pol gene was performed using in‐house protocol.Results: Of the 407 participants, 119, 152 and 136 were from Senegal, Mali and Guinea‐Conakry, respectively. The median treatment duration was 36 months [IQR: 6–136]. Virological failure (VF) (VL≥3log₁₀ copies/mL) was observed in 26% (95% confidence interval (CI), 18–35; n=31), 11% (95% CI, 6–17; n=16) and 24% (95% CI, 17–32; n=33) of patients in Senegal, Mali and Guinea‐Conakry, respectively (p=0.001). Of samples presenting VL≥3log₁₀ copies/mL (n=80), 70 were successfully genotyped. At least one drug resistance mutation (DRM) was detected in the following proportions: 70% (95% CI, 50–86; n=19), 93% (95% CI, 68–100; n=14) and 68% (95% CI, 48–84; n=19) in Senegal, Mali and Guinea‐Conakry, respectively (p=0.22). Twenty‐six per cent (26%; 95% CI, 16–38; n=18) of patients in VF harboured wild‐type viruses, which is likely indicative of weak adherence. Phylogenetic analysis showed the predominance of CRF02_AG subtype (73%; 95% CI, 61–83; n=51).Conclusions: We describe the ART outcome in capital and rural settings of Senegal, Mali and Guinea‐Conakry. Our results in all of the three countries highlight the need to reinforce the ART adherence in order to minimize the occurrence of drug resistance. In addition, these findings provide additional evidence that the use of DBS as a sampling support could assist virological monitoring of patients on ART in remote areas.

In West Africa, research on the hepatitis E virus (HEV) is barely covered, despite the recorded outbreaks. The low level of access to safe water and adequate sanitation is still one of the main factors of HEV spread in developing countries. HEV infection induces acute or sub-clinical liver diseases with a mortality rate ranging from 0.5 to 4%. The mortality rate is more alarming (15 to 25%) among pregnant women, especially in the last trimester of pregnancy. Herein, we conducted a multicentric socio-demographic and seroepidemiological survey of HEV in Senegal among pregnant women. A consecutive and non-redundant recruitment of participants was carried out over the period of 5 months, from March to July 2021. A total of 1227 consenting participants attending antenatal clinics responded to a standard questionnaire. Plasma samples were collected and tested for anti-HEV IgM and IgG by using the WANTAI HEV-IgM and IgG ELISA assay. The overall HEV seroprevalence was 7.8% (n = 96), with 0.5% (n = 6) and 7.4% (n = 91) for HEV IgM and HEV IgG, respectively. One of the participant samples was IgM/IgG-positive, while four were declared indeterminate to anti-HEV IgM as per the manufacturer’s instructions. From one locality to another, the seroprevalence of HEV antibodies varied from 0 to 1% for HEV IgM and from 1.5 to 10.5% for HEV IgG. The data also showed that seroprevalence varied significantly by marital status (p < 0.0001), by the regularity of income (p = 0.0043), and by access to sanitation services (p = 0.0006). These data could serve as a basis to setup national prevention strategies focused on socio-cultural, environmental, and behavioral aspects for a better management of HEV infection in Senegal.