Metagenomics screening of viruses in Arusha, north Tanzania: a one health perspective across wild rodents, domestic dogs and humans

Background: One of the most significant and perilous challenges faced by African societies, including Tanzania, is the public health threat posed by zoonotic viruses. This study aimed to ascertain the presence of viruses in wild rodents, domestic dogs, and humans who shared the same environment.  Methods: A cross-sectional study was conducted in the Ngorongoro district from January to September 2022. Metagenomics next-generation sequencing technologies, including Illumina (MiSeq) and Oxford Nanopore (MinION), were employed to identify viruses in 530 blood samples collected from 200 humans, 230 wild rodents, and 100 domestic dogs. The captured wild rodents belonged to various species: Mastomys spp (n=87), Ratus spp (n=45), Avicanthis spp (n=40), Arcomys spp (n=28), Mus spp (n=16), and Field mice (n=14). The taxonomic classification of viruses was carried out using the Kraken2 program. Results: A total of 20 RNA and 20 DNA viral families were detected. Zoonotic RNA families identified in rodents included Peribunyaviridae, Hantaviridae, Flaviviridae, Coronaviridae, Orthomyxoviridae, Paramyxoviridae, Retroviridae, Picornaviridae, Arenaviridae, Togaviridae, and Tobaniviridae. The zoonotic DNA families detected in rodents were Adenoviridae, Poxviridae, Herpesviridae, Anelloviridae, and Circoviridae. Peribunyaviridae and Hataviridae were identified in both humans and rodents. Unclassified +ssRNA viruses were found in dogs and humans. Herpesviridae was present in all three hosts. When compared to dogs and humans, rodents harbored zoonotic viruses that pose a significant public health safety concern. Conclusion: The study unveiled a noteworthy pattern where the majority of RNA and DNA viruses with zoonotic potential were detected in wild rodents, as opposed to dogs and humans. These findings underscore the pivotal role played by wild rodent populations in the transmission and maintenance of such viruses

Genetic diversity of Brazilian isolates of feline immunodeficiency virus

We isolated Feline immunodeficiency virus (FIV) from three adult domestic cats, originating from two open shelters in Brazil. Viruses were isolated from PBMC following co-cultivation with the feline T-lymphoblastoid cell line MYA-1. All amplified env gene products were cloned directly into pGL8MYA. The nucleic acid sequences of seven clones were determined and then compared with those of previously described isolates. The sequences of all of the Brazilian virus clones were distinct and phylogenetic analysis revealed that all belong to subtype B. Three variants isolated from one cat and two variants were isolated from each of the two other cats, indicating that intrahost diversity has the potential to pose problems for the treatment and diagnosis of FIV infection

Viral outbreak in corals associated with an in situ bleaching event: atypical herpes-like viruses and a new megavirus infecting Symbiodinium

Previous studies of coral viruses have employed either microscopy or metagenomics, but few have attempted to comprehensively link the presence of a virus-like particle (VLP) to a genomic sequence. We conducted transmission electron microscopy imaging and virome analysis in tandem to characterize the most conspicuous viral types found within the dominant Pacific reef-building coral genus Acropora. Collections for this study inadvertently captured what we interpret as a natural outbreak of viral infection driven by aerial exposure of the reef flat coincident with heavy rainfall and concomitant mass bleaching. All experimental corals in this study had high titers of viral particles. Three of the dominant VLPs identified were observed in all tissue layers and budding out from the epidermis, including viruses that were ∼70, ∼120, and ∼150 nm in diameter; these VLPs all contained electron dense cores. These morphological traits are reminiscent of retroviruses, herpesviruses, and nucleocytoplasmic large DNA viruses (NCLDVs), respectively. Some 300–500 nm megavirus-like VLPs also were observed within and associated with dinoflagellate algal endosymbiont (Symbiodinium) cells. Abundant sequence similarities to a gammaretrovirus, herpesviruses, and members of the NCLDVs, based on a virome generated from five Acropora aspera colonies, corroborated these morphology-based identifications. Additionally sequence similarities to two diagnostic genes, a MutS and (based on re-annotation of sequences from another study) a DNA polymerase B gene, most closely resembled Pyramimonas orientalis virus, demonstrating the association of a cosmopolitan megavirus with Symbiodinium. We also identified several other virus-like particles in host tissues, along with sequences phylogenetically similar to circoviruses, phages, and filamentous viruses. This study suggests that viral outbreaks may be a common but previously undocumented component of natural bleaching events, particularly following repeated episodes of multiple environmental stressors

Envelope Determinants of Equine Lentiviral Vaccine Protection

Lentiviral envelope (Env) antigenic variation and associated immune evasion present major obstacles to vaccine development. The concept that Env is a critical determinant for vaccine efficacy is well accepted, however defined correlates of protection associated with Env variation have yet to be determined. We reported an attenuated equine infectious anemia virus (EIAV) vaccine study that directly examined the effect of lentiviral Env sequence variation on vaccine efficacy. The study identified a significant, inverse, linear correlation between vaccine efficacy and increasing divergence of the challenge virus Env gp90 protein compared to the vaccine virus gp90. The report demonstrated approximately 100% protection of immunized ponies from disease after challenge by virus with a homologous gp90 (EV0), and roughly 40% protection against challenge by virus (EV13) with a gp90 13% divergent from the vaccine strain. In the current study we examine whether the protection observed when challenging with the EV0 strain could be conferred to animals via chimeric challenge viruses between the EV0 and EV13 strains, allowing for mapping of protection to specific Env sequences. Viruses containing the EV13 proviral backbone and selected domains of the EV0 gp90 were constructed and in vitro and in vivo infectivity examined. Vaccine efficacy studies indicated that homology between the vaccine strain gp90 and the N-terminus of the challenge strain gp90 was capable of inducing immunity that resulted in significantly lower levels of post-challenge virus and significantly delayed the onset of disease. However, a homologous N-terminal region alone inserted in the EV13 backbone could not impart the 100% protection observed with the EV0 strain. Data presented here denote the complicated and potentially contradictory relationship between in vitro virulence and in vivo pathogenicity. The study highlights the importance of structural conformation for immunogens and emphasizes the need for antibody binding, not neutralizing, assays that correlate with vaccine protection. © 2013 Craigo et al

Preliminary PCR-based screening indicates a higher incidence of Porcine Endogenous Retrovirus subtype C (PERV-C) in feral versus domestic swine

Xenotransplantation is considered a potential alternative to allotransplantation to relieve the current shortage of human organs. Due to their similar size and physiology, the organs of pigs are of particular interest for this purpose. Endogenous retroviruses are a result of integration of retroviral genomes into the genome of infected germ cells as DNA proviruses, which are then carried in all cells of the offspring of the organism. Porcine endogenous retroviruses (PERVs) are of special concern because they are found in pig organs and tissues that might otherwise be used for xenotransplantation. PERV proviruses can be induced to replicate and recombine in pigs, and have been shown to infect human cells in vitro. There are three subtypes of PERVs based on differences in the receptor binding domain of the env protein; PERV-A, PERV-B, and PERV-C. PERVs A and B can infect human cells in vitro and can recombine with PERV-C, resulting in a recombinant virus with a higher rate of replication in pig and human cell lines. In this study, we used a PCR-based analysis of 50 domestic and 35 feral pigs to study the distribution of PERVs A, B, and C in swine raised under domestic conditions, versus feral swine from rural areas. PERV-A and PERV-B were universal in both domestic and feral swine. Feral swine had a higher incidence of PERV-C (85.7%) compared to domestic swine (42.0%). Further studies in other feral swine herds are ongoing to verify this observation

Distribution Of Porcine Endogenous Retrovirus (PERV) Variants In Domestic And Feral Pig

Xenotransplantation is considered an alternative to allotransplantation to relieve the current shortage of human organs. Due to their similar size and physiology, the organs of pigs are of particular interest for this purpose. Endogenous retroviruses are a result of integration of retroviral genomes into the genome of infected germ cells as DNA copies (proviruses), which are then carried in all cells of the offspring of the organism. Porcine Endogenous Retroviruses (PERVs) are of special concern because they are found in pig organs and tissue that might be used for xenotransplantation. PERV proviruses, already incorporated into the pig’s genome, can be induced to replicate and recombine in pigs, and have been shown to infect human cells in vitro. There are three classes of PERVs, namely PERV-A, PERV-B, and PERV-C. PERV-A and PERV-B can infect human cells in vitro and can recombine with PERV-C, resulting in a recombinant virus with a higher rate of replication in pig and human cell lines. In this study, a PCR based analysis of 50 domestic and 35 feral pigs was carried out to study the distribution of PERVs A, B, and C. PERV-A and PERV-B were universal in both domestic and feral pigs. The feral varieties of pigs displayed a higher frequency of 85.67% of PERV-C compared to 42.00% in domestic pigs. However, comparative study of presence of PERVs A, B, and C in different breeds of domestic pigs shows there is variation in distribution among breeds, and among individuals of same breeds. From the results of this study, I hypothesize that presence of endogenized PERV genomes in individuals of the same breed is dependent on genetic properties of individual pigs

Epizootiološke značajke retrovirusnih infekcija mačaka na području grada Zagreba

Feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) are among the most common infectious diseases of cats and have a global impact on the health of domestic cats. Both viruses belong to the Retroviridae family and like other members of this family they are associated with lifelong infection after integration of the proviral DNA into the host cell genome. Prevalence data are necessary to define the risk factors, and prophylactic, management, diagnostic and therapeutic measures for stray and owned sick cats. In this study 324 domestic cats were tested with commercially available assays. The tested cats were divided into two groups, stray and owned sick cats. The overall percentage of seropositives for FIV infection was 18.51% and the prevalence for FeLV infection was 14.50%. FIV prevalence ranged from 13.13% in stray cats up to 20.88% within the sick owned cat group. The prevalence for FeLV infection was 6.06% in stray cats and 18.22% among sick owned cats. Regarding FIV infection, our study confirmed a significantly higher percentage of seropositives for male cats, as well as for sexually intact ones within the sick owned group. Males were significantly more likely to have positive results for both retroviral infections. The study confirmed the high rate of retroviral infections in cats from the Zagreb urban area. Males, sexually intact ones, and territorial aggression are predisposing factors for FIV infection, but not for FeLV. Preventive measures should include identification and segregation of infected cats, castration of outdoor male cats, and vaccination.nfekcije virusom mačje imunodeficijencije i virusom mačje leukemije pripadaju među najčešće zarazne bolesti mačaka i znatno utječu na njihovo zdravlje. Oba virusa pripadaju porodici Retroviridae. Kao i ostali virusi iz iste porodice, uzrokuju perzistentnu infekciju ugradnjom provirusne DNK u genom domaćina. Podaci o proširenosti obiju infekcija nužni su za utvrđivanje čimbenika rizika zaraze, mjera prevencije te dijagnostičkih metoda i postupaka sa zaraženom životinjom. Za potrebe ovog istraživanja pretražena su ukupno 324 uzorka pune krvi mačaka komercijalno dostupnim dijagnostičkim testovima. Pretraživane mačke podijeljene su u dvije skupine, slobodnoživuće mačke i bolesne mačke koje imaju vlasnika. Od ukupnog broja pretraženih mačaka infekciju mačjim virusom imunodeficijencije dokazali smo u 18.51 % mačaka, dok je infekcija virusom mačje leukemije dokazana u 14,50 % pretraženih životinja. Proširenost infekcije mačjim virusom imunodeficijencije potvrđena je u 13,13 % mačaka unutar skupine slobodnoživućih mačaka, dok je 20,88 % bolesnih mačaka koje imaju vlasnika bilo pozitivno na istu zaraznu bolest. S druge strane, 6,06 % slobodnoživućih mačaka te 18,22 % bolesnih mačaka koje imaju vlasnike bilo je zaraženo virusom mačje leukemije. Istraživanje potvrđuje statistički značajnu proširenost virusa mačje imunodeficijencije u muških jedinki posebno onih nekastriranih. Muške jedinke također imaju statistički veću mogućnost zaraze obama retrovirusima. Provedeno istraživanje dokazuje visoku proširenost retrovirusnih infeckcija među mačkama na području grada Zagreba. Utvrđeni čimbenici rizika zaraze virusom imunodeficijencije uključuju muški spol, nekastrirane muške jedinke te slododno držanje mačaka. Ti čimbenici rizika nisu dokazani za infekciju mačjim virusom leukemije. Mjere sprečavanja širenja obiju retrovirusnih bolesti uključuju testiranje mačaka, izdvajanje i izolaciju zaraženih, kastraciju muških mačaka te imunoprofilaksu izloženih jedinki

The efficacy of ELISA commercial kits for the screening of equineinfectious anemia virus infection

El mejor indicador de la infección por el virus de la anemia infecciosa equina (Equine infectious anemia virus, EIAV) es la detección de anticuerpos específicos en el suero del caballo. En el presente trabajo se evaluó la capacidad de detección de anticuerpos contra EIAV de dos equipos de ELISA comerciales utilizando 302 muestras de suero equino, así como las ventajas potenciales de su uso como herramientas de screening. Ambos ensayos de ELISA presentaron 100 % de sensibilidad diagnóstica y una especificidad diagnóstica del orden de 92,3 a 94,3 %. Las muestras discordantes fueron analizadas por inmunoblot. Los resultados mostraron que las dos pruebas ELISA son muy eficientes para detectar animales infectados por EIAV, al permitir identificar un mayor número de animales positivos que la prueba de inmunodifusión en gel de agar, oficialmente aprobada en la República Argentina para la certificación de los animales. Las pruebas de ELISA constituyen herramientas muy útiles en los programas de control y de erradicación de la infección por EIAV.The most used and reliable indicator of equine infectious anemia virus (EIAV) infec-tion is the detection of its specific antibodies in horse serum. In the present study, theperformance of two commercial ELISA tests for the detection of EIAV antibodies as well asthe potential advantages of their use as an EIAV infection screening tool were evaluated in 302horse serum samples. Both ELISA assays showed 100% diagnostic sensitivity, and 92.3-94.3%diagnostic specificity. Discordant results were analyzed by immunoblot. The results showedthat both ELISA tests are very efficient at detecting EIAV infected animals, allowing to identifya higher number of positive horse cases. Thus, ELISA assays can be useful tools in EIA controland eradication.Fil: Alvarez, Irene. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; ArgentinaFil: Cipolini Galarza, Fabiana. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; ArgentinaFil: Wigdorovitz, Andrés. Universidad Nacional del Nordeste. Facultad de Ciencias Veterinarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; ArgentinaFil: Trono, Karina Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; ArgentinaFil: Barrandeguy, María Edith. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Virología; Argentina. Universidad del Salvador. Escuela de Veterinaria; Argentin