Orthohantavirus diversity in Central-East Argentina: Insights from complete genomic sequencing on phylogenetics, Geographic patterns and transmission scenarios.

Hantavirus Pulmonary Syndrome (HPS), characterized by its high fatality rate, poses a significant public health concern in Argentina due to the increasing evidence of person-to-person transmission of Andes virus. Several orthohantaviruses were described in the country, but their phylogenetic relationships were inferred from partial genomic sequences. The objectives of this work were to assess the viral diversity of the most prevalent orthohantaviruses associated with HPS cases in the Central-East (CE) region of Argentina, elucidate the geographic patterns of distribution of each variant and reconstruct comprehensive phylogenetic relationships utilizing complete genomic sequencing. To accomplish this, a detailed analysis was conducted of the geographic distribution of reported cases within the most impacted province of the region. A representative sample of cases was then selected to generate a geographic map illustrating the distribution of viral variants. Complete viral genomes were obtained from HPS cases reported in the region, including some from epidemiologically linked cases. The phylogenetic analysis based on complete genomes defined two separate clades in Argentina: Andes virus in the Southwestern region and Andes-like viruses in other parts of the country. In the CE region, Buenos Aires virus and Lechiguanas virus clearly segregate in two subclades. Complete genomes were useful to distinguish person-to-person transmission from environmental co-exposure to rodent population. This study enhances the understanding of the genetic diversity, geographical spread, and transmission dynamics of orthohantaviruses in Central Argentina and prompt to consider the inclusion of Buenos Aires virus and Lechiguanas virus in the species Orthohantavirus andesense, as named viruses.

Orthohantavirus infections in South America: a systematic review and meta-analysis.

Orthohantaviruses are zoonotic pathogens that cause acute and severe syndromes in humans. This review was performed to estimate the occurrence of human orthohantaviruses in South America between 2010 and 2022. A careful evaluation of the eligibility and quality of the articles was carried out after a systematic bibliographic search of four databases. The pooled frequency of human orthohantaviruses was calculated using a random effects model meta-analysis. The heterogeneity of estimates (resulting from the chi2 test and I2 statistics) was investigated by subgroup analysis and meta-regression. 1,962 confirmed cases of orthohantavirus infections were diagnosed among 35,548 individuals from seven South American countries. The general occurrence of orthohantaviruses was estimated to be 4.4% (95% confidence interval: 2.9-6.2%) based on general pooling of human cases from 32 studies. In a subgroup analysis considering the study design and method of diagnosis, the percentages of diagnosed orthohantavirus infections differed substantially (I2 = 97.8%, p = 0.00) among South American countries. Four genetic variants of orthohantavirus have been identified circulating in Argentina, Brazil, Bolivia, Chile, Colombia, and Peru. Although laboratory diagnosis of orthohantaviruses is not performed in many countries in South America, there is evidence that four different orthohantaviruses are circulating in the region. The pooled occurrence of viral infection was approximately 4.0% in more than half of the South American countries. Updated information on the occurrence of human infections is essential for monitoring the territorial spread and determining the frequency of this zoonosis.

Orthohantaviruses in Misiones Province, Northeastern Argentina.

Few cases of hantavirus pulmonary syndrome have been reported in northeastern Argentina. However, neighboring areas show a higher incidence, suggesting underreporting. We evaluated the presence of antibodies against orthohantavirus in small rodents throughout Misiones province. Infected Akodon affinis montensis and Oligoryzomys nigripes native rodents were found in protected areas of Misiones.

Emerging hantaviruses in Central Argentina: First case of Hantavirus Pulmonary Syndrome caused by Alto Paraguay virus, and a novel orthohantavirus in Scapteromys aquaticus rodent.

Orthohantaviruses are emerging rodent-borne pathogens that cause Hantavirus Pulmonary Syndrome in humans. They have a wide range of rodent reservoir hosts and are transmitted to humans through aerosolized viral particles generated by the excretions of infected individuals. Since the first description of HPS in Argentina, new hantaviruses have been reported throughout the country, most of which are pathogenic to humans. We present here the first HPS case infected with Alto Paraguay virus reported in Argentina. Until now, Alto Paraguay virus was considered a non-pathogenic orthohantavirus since it was identified in a rodent, Holochilus chacarius. In addition to this, with the goal of identifying potential hantavirus host species in the province of Santa Fe, we finally describe a novel orthohantavirus found in the native rodent Scapteromys aquaticus, which differed from other hantaviruses described in the country so far. Our findings implicate an epidemiological warning regarding these new orthohantaviruses circulating in Central Argentina as well as new rodent species that must be considered as hosts from now on.

Development of RT-qPCR and semi-nested RT-PCR assays for molecular diagnosis of hantavirus pulmonary syndrome.

Hantavirus Pulmonary Syndrome is an, often fatal, emerging zoonotic disease in the Americas caused by hantaviruses (family: Hantaviridae). In Brazil, hantavirus routine diagnosis is based on serology (IgM-ELISA) while RT-PCR is often used to confirm acute infection. A Semi-nested RT-PCR and an internally controlled RT-qPCR assays were developed for detection and quantification of four hantaviruses strains circulating in the Brazilian Amazon: Anajatuba (ANAJV) and Castelo dos Sonhos (CASV) strains of Andes virus (ANDV) species; and Rio Mamoré (RIOMV) and Laguna Negra (LNV) strains of LNV species. A consensus region in the N gene of these hantaviruses was used to design the primer sets and a hydrolysis probe. In vitro transcribed RNA was diluted in standards with known concentration. MS2 bacteriophage RNA was detected together with hantavirus RNA as an exogenous control in a duplex reaction. RT-qPCR efficiency was around 100% and the limit of detection was 0.9 copies/µL of RNA for RT-qPCR and 10 copies/µL of RNA for Semi-nested RT-PCR. There was no amplification of either negative samples or samples positive to other pathogens. To assess the protocol for clinical sensitivity, specificity and general accuracy values, both assays were used to test two groups of samples: one comprising patients with disease (n = 50) and other containing samples from healthy individuals (n = 50), according to IgM-ELISA results. A third group of samples (n = 27) infected with other pathogens were tested for specificity analysis. RT-qPCR was more sensitive than semi-nested RT-PCR, being able to detect three samples undetected by conventional RT-PCR. RT-qPCR clinical sensitivity, specificity and general accuracy values were 92.5%, 100% and 97.63%, respectively. Thus, the assays developed in this study were able to detect the four Brazilian Amazon hantaviruses with good specificity and sensitivity, and may become powerful tools in diagnostic, surveillance and research applications of these and possibly other hantaviruses.

Hantavirus host assemblages and human disease in the Atlantic Forest.

Several viruses from the genus Orthohantavirus are known to cause lethal disease in humans. Sigmodontinae rodents are the main hosts responsible for hantavirus transmission in the tropical forests, savannas, and wetlands of South America. These rodents can shed different hantaviruses, such as the lethal and emerging Araraquara orthohantavirus. Factors that drive variation in host populations may influence hantavirus transmission dynamics within and between populations. Landscape structure, and particularly areas with a predominance of agricultural land and forest remnants, is expected to influence the proportion of hantavirus rodent hosts in the Atlantic Forest rodent community. Here, we tested this using 283 Atlantic Forest rodent capture records and geographically weighted models that allow us to test if predictors vary spatially. We also assessed the correspondence between proportions of hantavirus hosts in rodent communities and a human vulnerability to hantavirus infection index across the entire Atlantic Forest biome. We found that hantavirus host proportions were more positively influenced by landscape diversity than by a particular habitat or agricultural matrix type. Local small mammal diversity also positively influenced known pathogenic hantavirus host proportions, indicating that a plasticity to habitat quality may be more important for these hosts than competition with native forest dwelling species. We found a consistent positive effect of sugarcane and tree plantation on the proportion of rodent hosts, whereas defaunation intensity did not correlate with the proportion of hosts of potentially pathogenic hantavirus genotypes in the community, indicating that non-defaunated areas can also be hotspots for hantavirus disease outbreaks. The spatial match between host hotspots and human disease vulnerability was 17%, while coldspots matched 20%. Overall, we discovered strong spatial and land use change influences on hantavirus hosts at the landscape level across the Atlantic Forest. Our findings suggest disease surveillance must be reinforced in the southern and southeastern regions of the biome where the highest predicted hantavirus host proportion and levels of vulnerability spatially match. Importantly, our analyses suggest there may be more complex rodent community dynamics and interactions with human disease than currently hypothesized.

First outbreak of Oropouche Fever reported in a non-endemic western region of the Peruvian Amazon: Molecular diagnosis and clinical characteristics.

INTRODUCTION: Oropouche fever is an under-reported and emerging infectious disease caused by Oropouche virus (OROV). Its incidence is under-estimated mainly due to clinical similarities with other endemic arboviral diseases and the lack of specific diagnostic tests. We report the first outbreak of Oropouche fever in a western region of the Peruvian Amazon in Huanuco, Peru. METHODS: A transversal study was carried out during an outbreak in the western Region of Huanuco, Peru between January and July of 2016. Blood samples of 268 patients with acute febrile syndrome were collected and analyzed for OROV via RT- PCR and genetic sequencing. RESULTS: Of all 268 patients, 46 (17%) cases tested positive for OROV. The most common symptoms reported were headache with a frequency of 87% (n = 40) followed by myalgia with 76% (n = 35), arthralgia with 65.2% (n = 30), retro-ocular pain 60.8% (n = 28) and hyporexia with 50% (n = 23). Some patients showed a clinical presentation suggestive of severe OROV infection, of which 4.3% (n = 2) had low platelet count, 8.6% (n = 4) had intense abdominal pain, and 2.1% (n = 1) had a presentation with thoracic pain. CONCLUSION: This study reports an outbreak of OROV in a region where this virus was not previously identified. The disease caused by OROV is an emerging, underdiagnosed infection that requires further research to determine its virulence, pathogenesis, host range and vectors involved in the urban and sylvatic cycles as well as identifying new genotypes to implement sensitive and specific diagnostic tools that can be applied to endemic regions.

The mystery of the phylogeographic structural pattern in rodent-borne hantaviruses.

Hantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of hantaviruses through virus-reservoir interactions, it is important to know how the radiation and diversity of hantaviruses occurred. In this paper, we evaluate the pattern of hantavirus diversification based on a complete S segment representing major groups of hantaviruses found in the Americas. Phylogenetic analyses revealed a high degree of phylogeographic structure and a surprising pattern of geographical distribution of New World hantaviruses. The available data suggest that hantaviruses related to the Arvicolinae rodent subfamily in North America probably emerged and initially adapted from a shared common ancestor of the Tula virus. The first clade of hantaviruses associated with Neotominae occupied a stem lineage, especially those that emerged in Central America or Mexico. Hantaviruses from Central America and Mexico found in Neotominae rodents spread northward and probably gave rise to the first phylogroup of hantaviruses associated with Sigmodontinae in North America. Two preferential host-switching transmissions in hantaviruses apparently gave rise to two different paraphyletic group in Neotominae and Sigmodontinae. Our study supports a probable epicenter of diversification in Central America and/or Mexico for hantaviruses related to both the Neotominae and Sigmodontinae subfamilies.

Natural infection of Neotropical bats with hantavirus in Brazil.

Bats (Order: Chiroptera) harbor a high diversity of emerging pathogens presumably because their ability to fly and social behavior favor the maintenance, evolution, and dissemination of these pathogens. Until 2012, there was only one report of the presence of Hantavirus in bats. Historically, it was thought that these viruses were harbored primarily by rodent and insectivore small mammals. Recently, new species of hantaviruses have been identified in bats from Africa and Asia continents expanding the potential reservoirs and range of these viruses. To assess the potential of Neotropical bats as hosts for hantaviruses and its transmission dynamics in nature, we tested 53 bats for active hantaviral infection from specimens collected in Southeastern Brazil. Part of the hantaviral S segment was amplified from the frugivorous Carollia perspicillata and the common vampire bat Desmodus rotundus. DNA sequencing showed high similarity with the genome of Araraquara orthohantavirus (ARQV), which belongs to one of the more lethal hantavirus clades (Andes orthohantavirus). ARQV-like infection was detected in the blood, urine, and organs of D. rotundus. Therefore, we describe a systemic infection in Neotropical bats by a human pathogenic Hantavirus. We also propose here a schematic transmission dynamics of hantavirus in the study region. Our results give insights to new, under-appreciated questions that need to be addressed in future studies to clarify hantavirus transmission in nature and avoid hantavirus outbreaks.

Co-circulation of Araraquara and Juquitiba Hantavirus in Brazilian Cerrado.

Hantavirus cardiopulmonary syndrome is an emerging serious disease in the Americas, transmitted from wild rodents to humans through inhalation of aerosol containing virus. Herein, we characterized two distinct hantaviruses circulating in rodent species form Central Plateau, Midwestern region of Brazil in the Cerrado (savanna-like) biome, an area characterized by small trees and grasses adapted to climates with long dry periods. In this study, we identified the co-circulation of the Araraquara virus and a possible new lineage of the Juquitiba virus (JUQV) in Oligoryzomys nigripes. The implications of co-circulation are still unknown, but it can be the key for increasing viral diversity or emergence of new species through spillover or host switching events leading to co-infection and consequently recombination or reassortment between different virus species. Phylogenetic analyses based on the complete S segment indicated that, alongside with Oligoryzomys mattogrossae rodents, O. nigripes species could also have a whole as JUQV reservoir in the Cerrado biome. Although these rodents' species are common in the Cerrado biome, they are not abundant demonstrating how complex and different hantavirus enzootic cycles can be in this particular biome.

Hantavirus Pulmonary Syndrome Caused by Maripa Virus in French Guiana, 2008-2016.

We report 5 human cases of hantavirus pulmonary syndrome found during surveillance in French Guiana in 2008-2016; of the 5 patients, 4 died. This pathogen should continue to be monitored in humans and rodents in effort to reduce the occurrence of these lethal infections in humans stemming from ecosystem disturbances.

[Hantavirus pulmonary syndrome in Buenos Aires, 2009-2014]. / Síndrome pulmonar por hantavirus en Buenos Aires, 2009-2014.

Andes virus is the causative agent of hantavirus pulmonary syndrome (HPS) in Argentina and neighboring countries. In our country four different areas are affected: Northwest, Southwest, Central and Northeast, where distinct Andes virus genotypes were characterized. Three genotypes were described in Buenos Aires province (Central area): AND-Buenos Aires, AND-Lechiguanas and AND-Plata. In this work, we considered all HPS cases confirmed by ELISA and real time RT-PCR during the period 2009-2014 in Buenos Aires province. The annual distribution, fatality rate and geographic distribution were analyzed. We also analyzed the genotypes involved by RT-PCR and nucleotide sequencing. Finally we evaluated epidemiological data in order to establish the route of transmission. We analyzed 1386 suspect cases of hantavirus infection from Buenos Aires province and we confirmed 88 cases of Hantavirus Pulmonary Syndrome during 2009-2014. The overall average was 14.3 cases per year. The occurrence of a HPS outbreak was confirmed in Buenos Aires province during 2013, showing a 3 fold increase in case number compared to the annual average between 2009 and 2012, tending to normalize during 2014. The overall lethality was 25.6%, with a maximum value of 45.5% in 2011. Genotype analysis was performed in 30.7% of confirmed cases, AND-BsAs show the highest incidence, it was characterized in 72% of the studied cases. Epidemiological data and results of viral genome comparison strongly suggest person-to-person transmission in the three clusters of two cases described in our study.

Síndrome pulmonar por hantavirus en Buenos Aires, 2009-2014 / Hantavirus pulmonary syndrome in Buenos Aires, 2009-2014

El virus Andes es el agente causante del síndrome pulmonar por hantavirus en Argentina y países limítrofes. Existen varios genotipos característicos en las cuatro regiones endémicas del país. En la provincia de Buenos Aires, zona central, co-circulan tres genotipos: AND-BsAs, AND-Lechiguanas y AND-Plata. A partir de los casos confirmados por ELISA y PCR en tiempo real durante el período 2009-2014 en Buenos Aires, se evaluó la distribución anual, la letalidad y la distribución geográfica dentro de la provincia; mediante RT-PCR y secuenciación nucleotídica se analizaron los genotipos implicados. También se estudió la evidencia epidemiológica para determinar la ruta de infección en casos agrupados. Se analizaron 1386 muestras de casos sospechosos de la provincia de Buenos Aires, confirmándose 88 casos de Síndrome Pulmonar por Hantavirus durante el período 2009-2014. El promedio general fue de 14.3 casos por año. El análisis del genotipo viral se realizó en el 30.7% de los casos confirmados, AND-BsAs fue el de mayor incidencia, caracterizado en el 72% de los casos estudiados. Se confirmó la ocurrencia de un brote de síndrome pulmonar por hantavirus Buenos Aires durante el año 2013, con un registro de casos 3 veces mayor respecto al promedio anual del período 2009-2012, con tendencia a normalizarse durante 2014. La letalidad general fue del 25.6%, con un valor máximo de 45.5% en 2011. Se evaluaron los datos epidemiológicos y los resultados obtenidos del análisis de comparación de genomas virales en 3 agrupamientos de 2 casos cada uno, sugiriendo fuertemente transmisión persona a persona.

Andes virus is the causative agent of hantavirus pulmonary syndrome (HPS) in Argentina and neighboring countries. In our country four different areas are affected: Northwest, Southwest, Central and Northeast, where distinct Andes virus genotypes were characterized. Three genotypes were described in Buenos Aires province (Central area): AND-Buenos Aires, AND-Lechiguanas and AND-Plata. In this work, we considered all HPS cases confirmed by ELISA and real time RT-PCR during the period 2009-2014 in Buenos Aires province. The annual distribution, fatality rate and geographic distribution were analyzed. We also analyzed the genotypes involved by RT-PCR and nucleotide sequencing. Finally we evaluated epidemiological data in order to establish the route of transmission. We analyzed 1386 suspect cases of hantavirus infection from Buenos Aires province and we confirmed 88 cases of Hantavirus Pulmonary Syndrome during 2009-2014. The overall average was 14.3 cases per year. The occurrence of a HPS outbreak was confirmed in Buenos Aires province during 2013, showing a 3 fold increase in case number compared to the annual average between 2009 and 2012, tending to normalize during 2014. The overall lethality was 25.6%, with a maximum value of 45.5% in 2011. Genotype analysis was performed in 30.7% of confirmed cases, AND-BsAs show the highest incidence, it was characterized in 72% of the studied cases. Epidemiological data and results of viral genome comparison strongly suggest person-to-person transmission in the three clusters of two cases described in our study.

Phylogenetic Relationship of Necoclí Virus to Other South American Hantaviruses (Bunyaviridae: Hantavirus).

The results of a previous study suggested that Cherrie's cane rat (Zygodontomys cherriei) is the principal host of Necoclí virus (family Bunyaviridae, genus Hantavirus) in Colombia. Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences in this study confirmed that Necoclí virus is phylogenetically closely related to Maporal virus, which is principally associated with the delicate pygmy rice rat (Oligoryzomys delicatus) in western Venezuela. In pairwise comparisons, nonidentities between the complete amino acid sequence of the nucleocapsid protein of Necoclí virus and the complete amino acid sequences of the nucleocapsid proteins of other hantaviruses were ≥8.7%. Likewise, nonidentities between the complete amino acid sequence of the glycoprotein precursor of Necoclí virus and the complete amino acid sequences of the glycoprotein precursors of other hantaviruses were ≥11.7%. Collectively, the unique association of Necoclí virus with Z. cherriei in Colombia, results of the Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences, and results of the pairwise comparisons of amino acid sequences strongly support the notion that Necoclí virus represents a novel species in the genus Hantavirus. Further work is needed to determine whether Calabazo virus (a hantavirus associated with Z. brevicauda cherriei in Panama) and Necoclí virus are conspecific.

Detection of different South American hantaviruses.

Hantaviruses are the etiologic agents of Hemorrhagic Fever with Renal Syndrome (HFRS) in Old World, and Hantavirus Pulmonary Syndrome (HPS)/Hantavirus Cardiopulmonary Syndrome (HCPS), in the New World. Serological methods are the most common approach used for laboratory diagnosis of HCPS, however theses methods do not allow the characterization of viral genotypes. The polymerase chain reaction (PCR) has been extensively used for diagnosis of viral infections, including those caused by hantaviruses, enabling detection of few target sequence copies in the sample. However, most studies proposed methods of PCR with species-specific primers. This study developed a simple and reliable diagnostic system by RT-PCR for different hantavirus detection. Using new primers set, we evaluated human and rodent hantavirus positive samples of various regions from Brazil. Besides, we performed computational analyzes to evaluate the detection of other South American hantaviruses. The diagnostic system by PCR proved to be a sensible and simple assay, allowing amplification of Juquitiba virus, Araraquara virus, Laguna Negra virus, Rio Mamore virus and Jabora virus, beyond of the possibility of the detecting Andes, Anajatuba, Bermejo, Choclo, Cano Delgadito, Lechiguanas, Maciel, Oran, Pergamino and Rio Mearim viruses. The primers sets designed in this study can detect hantaviruses from almost all known genetics lineages in Brazil and from others South America countries and also increases the possibility to detect new hantaviruses. These primers could easily be used both in diagnosis of suspected hantavirus infections in humans and also in studies with animals reservoirs.

Preferential host switching and its relation with Hantavirus diversification in South America.

In recent years, the notion of co-speciation between Hantavirus species and their hosts was discarded in favour of a more likely explanation: preferential host switching. However, the relative importance of this last process in shaping the evolutionary history of hantaviruses remains uncertain, given the present limited knowledge not only of virus-host relationships but also of the pathogen and reservoir phylogenies. In South America, more than 25 hantavirus genotypes were detected; several of them act as aetiological agents of hantavirus pulmonary syndrome (HPS). An understanding of the diversity of hantaviruses and of the processes underlying host switching is critical since human cases of HPS are almost exclusively the result of human-host interactions. In this study, we tested if preferential host switching is the main process driving hantavirus diversification in South America, by performing a co-phylogenetic analysis of the viruses and their primary hosts. We also suggest a new level of amino acid divergence to define virus species in the group. Our results indicate that preferential host switching would not be the main process driving virus diversification. The historical geographical proximity among rodent hosts emerges as an alternative hypothesis to be tested.

Co-circulation in a single biome of the Juquitiba and Araraquara hantavirus detected in human sera in a sub-tropical region of Brazil.

Hantaviruses is an emerging infectious disease. Although HCPS has been reported in several regions of Brazil, more cases of HCPS have recently been reported in Minas Gerais than in any other state. In 2009, we analyzed 27 samples presenting antibodies against hantaviruses. These samples originated from 688 symptomatic patients, as determined based on the Hemorrhagic Fever Protocol. A subsequent SYBR Green-based real-time RT-PCR demonstrated the presence of the virus in 22 of the samples. Among the RT-PCR-positive samples, 17 were analyzed using DNA sequencing; these sequences were compared with others deposited in GenBank and showed similarity with the Araraquara and Juquitiba virus clusters. This work describe the detection of Juquitiba virus, including three fatal cases, in Minas Gerais state, furthermore, showed that it is feasible to characterize the circulating strains using a small fragment of S segment. Finally, the results suggest the co-circulation of Araraquara and Juquitiba virus in a single biome in Minas Gerais state.

Person-to-person household and nosocomial transmission of andes hantavirus, Southern Chile, 2011.

Andes hantavirus (ANDV) causes hantavirus cardiopulmonary syndrome in Chile and is the only hantavirus for which person-to-person transmission has been proven. We describe an outbreak of 5 human cases of ANDV infection in which symptoms developed in 2 household contacts and 2 health care workers after exposure to the index case-patient. Results of an epidemiologic investigation and sequence analysis of the virus isolates support person-to-person transmission of ANDV for the 4 secondary case-patients, including nosocomial transmission for the 2 health care workers. Health care personnel who have direct contact with ANDV case-patients or their body fluids should take precautions to prevent transmission of the virus. In addition, because the incubation period of ANDV after environmental exposure is longer than that for person-to-person exposure, all persons exposed to a confirmed ANDV case-patient or with possible environmental exposure to the virus should be monitored for 42 days for clinical symptoms.