Novel Oliveros-like Clade C Mammarenaviruses from Rodents in Argentina, 1990-2020.

Following an Argentine Hemorrhagic Fever (AHF) outbreak in the early 1990s, a rodent survey for Junín virus, a New World Clade B arenavirus, in endemic areas of Argentina was conducted. Since 1990, INEVH has been developing eco-epidemiological surveillance of rodents, inside and outside the Argentine Hemorrhagic Fever endemic area. Samples from rodents captured between 1993 and 2019 that were positive for Arenavirus infection underwent Sanger and unbiased, Illumina-based high-throughput sequencing, which yielded 5 complete and 88 partial Mammarenaviruses genomes. Previously, 11 genomes representing four species of New World arenavirus Clade C existed in public records. This work has generated 13 novel genomes, expanding the New World arenavirus Clade C to 24 total genomes. Additionally, two genomes exhibit sufficient genetic diversity to be considered a new species, as per ICTV guidelines (proposed name Mammarenavirus vellosense). The 13 novel genomes exhibited reassortment between the small and large segments in New World Mammarenaviruses. This work demonstrates that Clade C Mammarenavirus infections circulate broadly among Necromys species in the Argentine Hemorrhagic Fever endemic area; however, the risk for Clade C Mammarenavirus human infection is currently unknown.

Optimal reference genes for RNA tissue analysis in small animal models of hemorrhagic fever viruses.

Reverse-transcription quantitative polymerase chain reaction assays are frequently used to evaluate gene expression in animal model studies. Data analyses depend on normalization using a suitable reference gene (RG) to minimize effects of variation due to sample collection, sample processing, or experimental set-up. Here, we investigated the suitability of nine potential RGs in laboratory animals commonly used to study viral hemorrhagic fever infection. Using tissues (liver, spleen, gonad [ovary or testis], kidney, heart, lung, eye, brain, and blood) collected from naïve animals and those infected with Crimean-Congo hemorrhagic fever (mice), Nipah (hamsters), or Lassa (guinea pigs) viruses, optimal species-specific RGs were identified based on five web-based algorithms to assess RG stability. Notably, the Ppia RG demonstrated stability across all rodent tissues tested. Optimal RG pairs that include Ppia were determined for each rodent species (Ppia and Gusb for mice; Ppia and Hrpt for hamsters; and Ppia and Gapdh for guinea pigs). These RG pair assays were multiplexed with viral targets to improve assay turnaround time and economize sample usage. Finally, a pan-rodent Ppia assay capable of detecting Ppia across multiple rodent species was developed and successfully used in ecological investigations of field-caught rodents, further supporting its pan-species utility.

cis-Acting Element at the 5' Noncoding Region of Tacaribe Virus S RNA Modulates Genome Replication.

Tacaribe virus (TCRV) is the prototype of New World mammarenaviruses, a group that includes several members that cause hemorrhagic fevers in humans. The TCRV genome comprises two RNA segments, named S (small) and L (large). Both genomic segments contain noncoding regions (NCRs) at their 5' and 3' ends. While the 5'- and 3'-terminal 19-nucleotide sequences are known to be essential for promoter function, the role of their neighboring internal noncoding region (iNCR) sequences remains poorly understood. To analyze the relevance of the 5' and 3' iNCRs in TCRV S RNA synthesis, mutant S-like minigenomes and miniantigenomes were generated. Using a minireplicon assay, Northern blotting, and reverse transcription-quantitative PCR, we demonstrated that the genomic 5' iNCR is specifically engaged in minigenome replication yet is not directly involved in minigenome transcription, and we showed that the S genome 3' iNCR is barely engaged in this process. Analysis of partial deletions and point mutations, as well as total or partial substitution of the 5' iNCR sequence, led us to conclude that the integrity of the whole genomic 5' iNCR is essential and that a local predicted secondary structure or RNA-RNA interactions between the 5' and 3' iNCRs are not strictly required for viral S RNA synthesis. Furthermore, we employed a TCRV reverse genetic approach to ask whether manipulation of the S genomic 5' iNCR sequence may be suitable for viral attenuation. We found that mutagenesis of the 5' promoter-proximal subregion slightly impacted recombinant TCRV virulence in vivo. IMPORTANCE The Mammarenavirus genus of the Arenaviridae family includes several members that cause severe hemorrhagic fevers associated with high morbidity and mortality rates, for which no FDA-approved vaccines and limited therapeutic resources are available. We provide evidence demonstrating the specific involvement of the TCRV S 5' noncoding sequence adjacent to the viral promoter in replication. In addition, we examined the relevance of this region in the context of an in vivo infection. Our findings provide insight into the mechanism through which this 5' viral RNA noncoding region assists the L polymerase for efficient viral S RNA synthesis. Also, these findings expand our understanding of the effect of genetic manipulation of New World mammarenavirus sequences aimed at the rational design of attenuated recombinant virus vaccine platforms.

First study of Seoul virus (SEOV) in urban rodents from newly urbanized areas of Gran La Plata, Argentina.

Alterations of ecosystems have deep effects on the distribution of parasites. Big cities of Argentina present structural features that favor the presence of synanthropic species, acting as source of zoonotic diseases, for example in urban rodents: the Norway rat (Rattus norvegicus) and the black rat (R. rattus). One of the important zoonotic pathogens related are the RNA virus Hantavirus, with high prevalence rates in South America. The aim of this study was to explore and identify the presence of Hantavirus in urban rodents from Gran La Plata, Argentina. The presence of anti-hantavirus IgG antibodies was determined by the Enzyme-Linked Immunosorbent Assay. Six samples turned out positive for Seoul virus (SEOV, p = 14.3%). These are the first records of SEOV in urban rodents in Gran La Plata. It represents the first report in R. rattus in Argentina, and in America. This situation underscores the inequality and historical forgetfulness of a portion of society, calling for urgent action to be taken in this regard.

First study of Seoul virus (SEOV) in urban rodents from newly urbanized areas of Gran La Plata, Argentina

Abstract Alterations of ecosystems have deep effects on the distribution of parasites. Big cities of Argentina present structural features that favor the presence of synanthropic species, acting as source of zoonotic diseases, for example in urban rodents: the Norway rat (Rattus norvegicus) and the black rat (R. rattus). One of the important zoonotic pathogens related are the RNA virus Hantavirus, with high prevalence rates in South America. The aim of this study was to explore and identify the presence of Hantavirus in urban rodents from Gran La Plata, Argentina. The presence of anti-hantavirus IgG antibodies was determined by the Enzyme-Linked Immunosorbent Assay. Six samples turned out positive for Seoul virus (SEOV, p= 14.3%). These are the first records of SEOV in urban rodents in Gran La Plata. It represents the first report in R. rattus in Argentina, and in America. This situation underscores the inequality and historical forgetfulness of a portion of society, calling for urgent action to be taken in this regard.

Chapare Hemorrhagic Fever and Virus Detection in Rodents in Bolivia in 2019.

BACKGROUND: In June 2019, the Bolivian Ministry of Health reported a cluster of cases of hemorrhagic fever that started in the municipality of Caranavi and expanded to La Paz. The cause of these cases was unknown. METHODS: We obtained samples for next-generation sequencing and virus isolation. Human and rodent specimens were tested by means of virus-specific real-time quantitative reverse-transcriptase-polymerase-chain-reaction assays, next-generation sequencing, and virus isolation. RESULTS: Nine cases of hemorrhagic fever were identified; four of the patients with this illness died. The etiologic agent was identified as Mammarenavirus Chapare mammarenavirus, or Chapare virus (CHAPV), which causes Chapare hemorrhagic fever (CHHF). Probable nosocomial transmission among health care workers was identified. Some patients with CHHF had neurologic manifestations, and those who survived had a prolonged recovery period. CHAPV RNA was detected in a variety of human body fluids (including blood; urine; nasopharyngeal, oropharyngeal, and bronchoalveolar-lavage fluid; conjunctiva; and semen) and in specimens obtained from captured small-eared pygmy rice rats (Oligoryzomys microtis). In survivors of CHHF, viral RNA was detected up to 170 days after symptom onset; CHAPV was isolated from a semen sample obtained 86 days after symptom onset. CONCLUSIONS: M. Chapare mammarenavirus was identified as the etiologic agent of CHHF. Both spillover from a zoonotic reservoir and possible person-to-person transmission were identified. This virus was detected in a rodent species, O. microtis. (Funded by the Bolivian Ministry of Health and others.).

Assessing cross-reactivity of Junín virus-directed neutralizing antibodies.

Arenaviruses cause several viral hemorrhagic fevers endemic to Africa and South America. The respective causative agents are classified as biosafety level (BSL) 4 pathogens. Unlike for most other BSL4 agents, for the New World arenavirus Junín virus (JUNV) both a highly effective vaccination (Candid#1) and a post-exposure treatment, based on convalescent plasma transfer, are available. In particular, neutralizing antibodies (nAbs) represent a key protective determinant in JUNV infection, which is supported by the correlation between successful passive antibody therapy and the levels of nAbs administered. Unfortunately, comparable resources for the management of other closely related arenavirus infections are not available. Given the significant challenges inherent in studying BSL4 pathogens, our goal was to first assess the suitability of a JUNV transcription and replication-competent virus-like particle (trVLP) system for measuring virus neutralization under BSL1/2 conditions. Indeed, we could show that infection with JUNV trVLPs is glycoprotein (GP) dependent, that trVLP input has a direct correlation to reporter readout, and that these trVLPs can be neutralized by human serum with kinetics similar to those obtained using authentic virus. These properties make trVLPs suitable for use as a proxy for virus in neutralization assays. Using this platform we then evaluated the potential of JUNV nAbs to cross-neutralize entry mediated by GPs from other arenaviruses using JUNV (strain Romero)-based trVLPs bearing GPs either from other JUNV strains, other closely related New World arenaviruses (e.g. Tacaribe, Machupo, Sabiá), or the distantly related Lassa virus. While nAbs against the JUNV vaccine strain are also active against a range of other JUNV strains, they appear to have little or no capacity to neutralize other arenavirus species, suggesting that therapy with whole plasma directed against another species is unlikely to be successful and that the targeted development of cross-specific monoclonal antibody-based resources is likely needed. Such efforts will be supported by the availability of this BSL1/2 screening platform which provides a rapid and easy means to characterize the potency and reactivity of anti-arenavirus neutralizing antibodies against a range of arenavirus species.

Orthohantavirus genotype Lechiguanas in Oligoryzomys nigripes (Rodentia: Cricetidae): New evidence of host-switching.

To identify and predict situations of increased risk of orthohantavirus infection in humans, it is necessary to study the relationships between the virus and its rodent hosts. The present study investigated orthohantavirus infection in an assemblage of wild Sigmodontinae rodents of the Paraná Delta, Argentina, and providing new evidence of host-switching events. Rodents belonging to the species Oxymycterus rufus (n = 187), Akodon azarae (n = 82), Oligoryzomys flavescens (n = 80), Oligoryzomys nigripes (n = 47), Scapteromys aquaticus (n = 38), Deltamys kempi (n = 7) and Holochilus brasiliensis (n = 2) were captured at 4 sampling sites during 20 trapping sessions. Blood samples were analyzed by IgG ELISA and livers by a nested reverse transcription PCR for the diagnosis of orthohantavirus infection. The amplified products of the S and M orthohantavirus genomes were sequenced and analyzed to determine similarities with species of the Orthohantavirus genus. The species of the Oligoryzomys positive to the virus were confirmed by amplifying and sequencing the complete cyt b gene. Of the 443 serum samples analyzed by IgG ELISA, A. azarae presented the highest host-specific prevalence value (10/82, 12.2%) followed by Ol. nigripes (4/47, 8.5%) and Ox. rufus (1/187, 0.5%). All the sero-positive Ol. nigripes (n = 4) were positive to the amplification of the S and M segments of the Lechiguanas genotype (98% nucleotide identity for both segments). This is surprising given that Ol. nigripes has been previously associated with Juquitiba genotype, not Lechiguanas. The latter is generally associated with Ol. flavescens, which in our study were all sero-negative. In addition, the association Ox. rufus - Pergamino genotype found here is, to our knowledge, novel and another potential evidence of host-switching considering that Pergamino has been originally associated with A. azarae. These findings contribute to the building evidence that contradicts the one-genotype-one-reservoir species premise in the association between rodent reservoirs and orthohantaviruses, and supports the hypothesis that the community structure of sympatric host species may contribute to orthohantavirus dynamics.

[Outbreak of hantavirus pulmonary syndrome in Tucumán, Argentina]. / Brote de síndrome pulmonar por hantavirus, Tucumán, Argentina.

We describe an outbreak of hantavirus pulmonary syndrome in the Burruyacú Department, Province of Tucumán. The detection in 2016 of a case of hantavirosis affecting a 23-year-old woman, considered at that time to be the first case occurred in that province, promoted a thorough epidemiological study. The investigation allowed the retrospective detection of another case occurred one month earlier in a 5-year-old child in the same Department. In both cases, the infection was confirmed by serology (case 1 at days 4 and 7 of disease onset, case 2 at day 4) and the viral genotype was characterized as HU39694. The contacts of both cases were serologically negative for hantavirus. The rodents captured in the area belonged to genus Akodon, genus Calomys and species Mus musculus. Oligoryzomys, the known reservoir for this viral genotype, was not found. Specific anti-hantavirus antibodies were not detected in the captured rodents. Given that the patients had not visited hantavirus endemic areas and their contacts were negative for hantavirus, we infer that the patients were locally exposed to fluids of infected rodents during their usual social or recreational outdoor activities. In conclusion, we demonstrate that hantavirus HU39694 -a genotype until now considered to be restricted to the Central Pampas of the country- is circulating in the North Western province of Tucumán. The endemic area of hantavirosis is thus expanded to this province but the viral reservoir in the area has not yet been identified.

[Autochthonous case of spotted fever caused by Rickettsia parkeri in Ensenada, Buenos Aires]. / Caso autóctono de fiebre manchada por Rickettsia parkeri en Ensenada, Buenos Aires.

We present a case of spotted fever occurred in an adult residing in Ensenada, Buenos Aires province in February 2016. The patient presented with an acute febrile syndrome associated with a skin necrotic lesion on the left leg secondary to a tick bite. The general symptoms were a maculopapular rash, headache, myalgia, and arthralgias. Seroconversion of anti-Rickettsia specific IgG antibodies confirmed recent infection. The nucleotidic and aminoacidic sequences of a gltA gen fragment matched 100% the sequences of R. parkeri strains from Argentina and other countries of America. The patient responded well to treatment with doxycycline.

Caso autóctono de fiebre manchada por Rickettsia parkeri en Ensenada, Buenos Aires / Autochthonous case of spotted fever caused by Rickettsia parkeri in Ensenada, Buenos Aires

Se comunica un caso autóctono de fiebre manchada por Rickettsia parkeri en un adulto residente en Ensenada, Provincia de Buenos Aires ocurrido en el verano de 2016. El cuadro, secundario a una mordedura de garrapata en la pierna izquierda, se presentó como un síndrome febril agudo con deterioro del estado general, cefalea, mialgias, artralgias y exantema maculopapular. El sitio de la mordedura presentaba una úlcera con escara necrótica. El diagnóstico se confirmó por conversión serológica IgG anti-antígenos del género Rikettsia. La secuencia de un fragmento del gen gltA amplificado a partir de la lesión de piel presentó 100% identidad nucleotídica con las secuencias de cepas de R. parkeri aisladas en Argentina y en varios países de América. El paciente evolucionó favorablemente al tratamiento con doxiciclina.

We present a case of spotted fever occurred in an adult residing in Ensenada, Buenos Aires province in February 2016. The patient presented with an acute febrile syndrome associated with a skin necrotic lesion on the left leg secondary to a tick bite. The general symptoms were a maculopapular rash, headache, myalgia, and arthralgias. Seroconversion of anti-Rickettsia specific IgG antibodies confirmed recent infection. The nucleotidic and aminoacidic sequences of a gltA gen fragment matched 100% the sequences of R. parkeri strains from Argentina and other countries of America. The patient responded well to treatment with doxycycline.

Brote de síndrome pulmonar por hantavirus, Tucumán, Argentina / Outbreak of hantavirus pulmonary syndrome in Tucumán, Argentina

Se describe un brote de síndrome pulmonar por hantavirus en el departamento de Burruyacú, provincia de Tucumán. La detección en 2016 de un caso de hantavirosis en una joven de 23 años -en ese momento considerado el primero ocurrido en dicha provincia- promovió un estudio epidemiológico exhaustivo, que permitió detectar retrospectivamente otro caso ocurrido en un niño de 5 años, un mes antes, en el mismo departamento. La infección fue confirmada por serología en ambos casos (caso 1 en muestras de 4 y 7 días de evolución, caso 2 en muestra a los 4 días). En ambos casos el genotipo viral fue caracterizado como HU39694 y los contactos fueron serológicamente negativos. En las áreas fueron identificados roedores pertenecientes a los géneros Akodon y Calomys y a la especie Mus musculus, pero no a Oligoryzomys, el reservorio habitual del genotipo HU39694. Tampoco se detectaron anticuerpos anti-hantavirus en suero de los roedores capturados. La ausencia de registro de viajes a área endémica de este genotipo y los hábitos recreacionales de los pacientes, sumados a los resultados serológicos negativos para hantavirus en los contactos, permiten inferir la posible exposición de los pacientes a fluidos de roedores infectados durante actividades recreativas o sociales al aire libre en sus respectivas áreas de residencia. En conclusión, se demuestra la circulación en Tucumán del genotipo viral HU39694, hasta ahora considerado restringido a la región pampeana central. Se extiende así a Tucumán el área endémica de hantavirosis, pero no se identificó el reservorio en el área.

We describe an outbreak of hantavirus pulmonary syndrome in the Burruyacú Department, Province of Tucumán. The detection in 2016 of a case of hantavirosis affecting a 23-year-old woman, considered at that time to be the first case occurred in that province, promoted a thorough epidemiological study. The investigation allowed the retrospective detection of another case occurred one month earlier in a 5-year-old child in the same Department. In both cases, the infection was confirmed by serology (case 1 at days 4 and 7 of disease onset, case 2 at day 4) and the viral genotype was characterized as HU39694. The contacts of both cases were serologically negative for hantavirus. The rodents captured in the area belonged to genus Akodon, genus Calomys and species Mus musculus. Oligoryzomys, the known reservoir for this viral genotype, was not found. Specific anti-hantavirus antibodies were not detected in the captured rodents. Given that the patients had not visited hantavirus endemic areas and their contacts were negative for hantavirus, we infer that the patients were locally exposed to fluids of infected rodents during their usual social or recreational outdoor activities. In conclusion, we demonstrate that hantavirus HU39694 -a genotype until now considered to be restricted to the Central Pampas of the country- is circulating in the North Western province of Tucumán. The endemic area of hantavirosis is thus expanded to this province but the viral reservoir in the area has not yet been identified.