Haruka Abe

Coronavirus (CoV) infections continue to pose a significant challenge to global public health and food security. The COVID-19 pandemic has underscored the importance of One Health approaches and improved surveillance systems. This is due to the considerable potential of CoVs to infect a broad spectrum of hosts and cause respiratory diseases. The present study investigated CoVs circulating in livestock in Vietnam using molecular detection and phylogenetic analysis. A total of 412 samples collected from livestock were analysed for the presence of infectious bronchitis virus (IBV), porcine haemagglutinating encephalomyelitis virus (PHEV), and avian Gamma-CoV. Nearly full-length genomes of IBV and PHEV were obtained. Phylogenetic analysis revealed that the IBV strains detected in this study were GI-13 vaccine-derived. Furthermore, this study provides the first genome sequences of Vietnamese PHEV strains. The viruses were closely related to the respiratory-variant lineage detected in China, suggesting that the viruses may have entered Vietnam from China and subsequently evolved independently within Vietnam. Moreover, avian Gamma-CoVs were inferred to originate from migratory birds, thereby revealing the risk of transmission from migratory birds to livestock. In summary, this study elucidates the diversity of CoVs in livestock in northern Vietnam. Therefore, continuous surveillance is necessary to prevent further spread of CoVs among livestock.

Recently, infections with the H5N1 subtype of highly pathogenic avian influenza virus (H5N1-HPAIV) in mammals have been reported worldwide, including in cows in the United States and successive human cases in Cambodia. In Vietnam, 47 tigers and three leopards died from H5N1-HPAIV infection between August and October 2024. This study aimed to determine the origin of the H5N1 strains that infect tigers in Vietnam and to identify specific mutations associated with mammalian infection. Specimens were collected from tigers that died of suspected H5N1-HPAIV infection in southern Vietnam in September-October 2024. RNA was extracted and subjected to whole-genome sequencing. Time-stamped phylogenetic analysis was performed using H5N1 sequences recently detected in Vietnam and neighbouring countries. Phylogenetic results revealed that the strain found in tigers (Tiger H5N1 strain) belonged to clade 2.3.2.1e and was genetically close to the H5N1-HPAIV lineage responsible for ongoing human infections in Cambodia since 2023. Tiger H5N1 strains harboured several amino acid substitutions associated with mammalian host adaptation or transmissibility, such as E627 K in polymerase basic protein 2, similar to the Cambodian human H5N1 strains. This mammalian-adapted H5N1 lineage should be continuously monitored in poultry and mammals, including humans, in Vietnam to prevent further transmission.

Information on circulating HBV (sub-)genotype, variants, and hepatitis D virus (HDV) coinfection, which vary by geographical area, is crucial for the efficient control and management of HBV. We investigated the genomic characteristics of HBV (with a prevalence of 8.1%) and the prevalence of HDV in Nigeria. We utilised 777 HBV-positive samples and epidemiological data from the two-stage sampled population-based, nationally representative Nigeria HIV/AIDS Indicator and Impact Survey conducted in 2018. We assessed 732 HBV DNA-extracted samples with detectable viral loads (VLs) for (sub-)genotypes and variants by whole-genome pre-amplification, nested PCR of the s-and pol-gene, and BigDye Terminator sequencing. We conducted HDV serology. In total, 19 out of the 36 + 1 states in Nigeria had a high prevalence of HBV (≥8%), with the highest prevalence (10.4%) in the north-central geopolitical zone. Up to 33.2% (95% CI 30.0–36.6) of the participants had detectable VLs of ≥300 copies/mL. The predominant circulating HBV genotype was E with 98.4% (95% CI 97.1–99.1), followed by A with 1.6% (95% CI 0.9–2.9). Drug-resistant associated variants and immune escape variants were detected in 9.3% and 0.4%, respectively. The seroprevalence of HDV was 7.34% (95% CI 5.5–9.2). Nigeria has subtype E as the major genotype with many variants.

Acute respiratory infections are a major global burden in resource-limited countries, including countries in Africa. Although COVID-19 has been well studied since the pandemic emerged in Gabon, Central Africa, less attention has been paid to other respiratory viral diseases, and very little data are available. Herein, we provide the first data on the genetic diversity and detection of 18 major respiratory viruses in Gabon during the COVID-19 pandemic. Of 582 nasopharyngeal swab specimens collected from March 2020 to July 2021, which were SARS-CoV-2 negative, 156 were positive (26%) for the following viruses: enterovirus (20.3%), human rhinovirus (HRV) (4.6%), human coronavirus OC43 (1.2%), human adenovirus (0.9%), human metapneumovirus (hMPV) (0.5%), influenza A virus (IAV) (0.3%), and human parainfluenza viruses (0.5%). To determine the genetic diversity and transmission route of the viruses, phylogenetic analyses were performed using genome sequences of the detected viruses. The IAV strain detected in this study was genetically similar to strains isolated in the USA, whereas the hMPV strain belonging to the A2b subtype formed a cluster with Kenyan strains. This study provides the first complete genomic sequences of HRV, IAV, and hMPV detected in Gabon, and provides insight into the circulation of respiratory viruses in the country.

Herpes B virus (BV) is a zoonotic virus which can be transmitted from macaques to humans, which is often associated with high mortality rates. Because macaques often exhibit asymptomatic infections, individuals who come into contact with these animals face unexpected risks of BV infections. A serological test is widely performed to investigate BV infections. However, the assay’s sensitivity and specificity appeared to be inadequate, and it does not necessarily indicate ongoing viral shedding. Here, we developed LAMP and qPCR assays aiming to detect BVs with a high sensitivity and specificity in various macaque species and validated them using oral swab samples collected from 97 wild cynomolgus macaques living in Thailand. Our LAMP and qPCR assays detected more than 50 and 10 copies of the target sequences per reaction, respectively. The LAMP assay could detect BV within 25 min, indicating its advantages for the rapid detection of BV. Collectively, our findings indicated that both assays developed in this study exhibit advantages and usefulness for BV surveillance and the diagnosis of BV infections in macaques. Furthermore, for the first time, we determined the partial genome sequences of BVs detected in cynomolgus macaques in Thailand. Phylogenetic analysis revealed the species-specific evolution of BV within macaques.

Background: Aedes albopictus and Aedes aegypti are known for their potential as vectors of dengue (DENV) and chikungunya (CHIKV) viruses. However, entomological surveys are mostly carried out during epidemics. In Gabon where outbreaks of both viruses have occurred, there is no vector control program targeting these arboviruses. Therefore, we assessed the presence of Aedes species along a rural–urban gradient in Lambaréné (Gabon) and its surroundings and determined ecological factors associated to their presence. Methods: An entomological survey was conducted in Lambaréné and its surrounding rural areas. Mosquitoes were collected with aspirators around human dwellings, and ecological and environmental data were collected from each study area. Morphological identification keys were used to identify Aedes species. RNA was extracted from pools of female mosquitoes and amplified by RT-qPCR to detect the presence of DENV and CHIKV. Results: Overall, the most common vector collected was Aedes albopictus (97%, 4236/4367 specimens), followed by Aedes aegypti (3%, 131/4367). Albopictus vectors was more abundant in the rural area (Wilcoxon signed-rank test, Z = 627, P = 0.043) than in the urban area. In the urban area, a higher number of mosquitoes (45%) were recorded in the economic zone (zone 3) than in the historical and administrative zones (zone 1 and 2). In the rural area, the proportions of species numbers were significantly higher along the south rural transect (92%) compared to the north rural transect (Wilcoxon signed-rank test, Z = 43, P ˂ 0.016). We also noted a high abundance of vectors in environments characterized by monocultures of Hevea brasiliensis (Hevea) and Manihot esculenta (cassava) (Kruskal–Wallis H-test, H = 25.7, df = 2, P < 0.001). Finally, no mosquito pools were positive for either DENV or CHIKV. Conclusion: Aedes albopictus was the dominant vector across the study sites due to its high invasiveness capacity. This presence re-affirms the potential for local transmission of both DENV and CHIKV, as indicated previously by serological surveys conducted in our study area, even though no transmission was detected during the current study. These findings underscore the need for regular arbovirus surveillance in the study region, with the aim of supporting vector control efforts in the event of outbreaks. Graphical

Herpes B virus (BV) is a zoonotic virus which can be transmitted from macaques to humans, which is often associated with high mortality rates. Because macaques often exhibit asymptomatic infections, individuals who come into contact with these animals face unexpected risks of BV infections. Serological test is widely performed to investigate BV infections. However, the assay’s sensitivity and specificity appeared to be inadequate, and it does not necessarily indicate ongoing viral shedding. Here, we developed LAMP and qPCR assays aiming to detect BVs with high sensitivity and specificity in various macaque species and validated them using oral swab samples collected from 97 wild cynomolgus macaques living in Thailand. Our LAMP and qPCR assays detected more than 50 and 10 copies of the target sequences per reaction, respectively. The LAMP assay could detect BV within 25 min, indicating its advantages for the rapid detection of BV. Collectively, our findings indicated that both assays developed in this study exhibit advantages and usefulness for BV surveillance and diagnosis of BV infections in macaques. Furthermore, for the first time, we determined the partial genome sequences of BVs detected in cynomolgus macaques in Thailand. Phylogenetic analysis revealed the species-specific evolution of BV within macaques.

Viral hepatitis remains one of the largest public health concerns worldwide. Especially in Central Africa, information on hepatitis virus infections has been limited, although the prevalence in this region has been reported to be higher than the global average. To reveal the current status of hepatitis B and C virus (HBV and HCV) infections and the genetic diversity of the viruses, we conducted longitudinal surveillance in Gabon. We detected 22 HBV and 9 HCV infections in 2047 patients with febrile illness. Genetic analyses of HBV identified subgenotype A1 for the first time in Gabon and an insertion generating a frameshift to create an X-preC/C fusion protein. We also revealed that most of the detected HCVs belonged to the “Gabon-specific” HCV subtype 4e (HCV-4e), and the entire nucleotide sequence of the HCV-4e polyprotein was determined to establish the first reference sequence. The HCV-4e strains possessed resistance-associated substitutions similar to those of other HCV-4 strains, indicating that the use of direct-acting antiviral therapy may be complex. These results provide a better understanding of the current situation of hepatitis B and C virus infections in Central Africa and will help public health organizations develop effective countermeasures to eliminate chronic viral hepatitis in this region.