Fast surveillance response reveals the introduction of a new yellow fever virus sub-lineage in 2021, in Minas Gerais, Brazil.

BACKGROUND: In Brazil, the yellow fever virus (YFV) is maintained in a sylvatic cycle involving wild mosquitoes and non-human primates (NHPs). The virus is endemic to the Amazon region; however, waves of epidemic expansion reaching other Brazilian states sporadically occur, eventually causing spillovers to humans. OBJECTIVES: To report a surveillance effort that led to the first confirmation of YFV in NHPs in the state of Minas Gerais (MG), Southeast region, in 2021. METHODS: A surveillance network was created, encompassing the technology of smartphone applications and coordinated actions of several research institutions and health services to monitor and investigate NHP epizootics. FINDINGS: When alerts were spread through the network, samples from NHPs were collected and YFV infection confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and genome sequencing at an interval of only 10 days. Near-complete genomes were generated using the Nanopore MinION sequencer. Phylogenetic analysis indicated that viral genomes were related to the South American genotype I, clustering with a genome detected in the Amazon region (state of Pará) in 2017, named YFVPA/MG sub-lineage. Fast YFV confirmation potentialised vaccination campaigns. MAIN CONCLUSIONS: A new YFV introduction was detected in MG 6 years after the beginning of the major outbreak reported in the state (2015-2018). The YFV strain was not related to the sub-lineages previously reported in MG. No human cases have been reported, suggesting the importance of coordinated surveillance of NHPs using available technologies and supporting laboratories to ensure a quick response and implementation of contingency measures to avoid YFV spillover to humans.

Occurrence of Colletotrichum musicola causing anthracnose on Manihot esculenta.

Cassava (Manihot esculenta) is one of the main food sources of energy in developing countries owing to its starch-rich roots (Pinweha et al., 2015). Anthracnose is considered the most destructive disease of the aerial part of this crop (Bragança et al., 2016; Liu et al., 2019), and it is caused by species such as Colletotrichum plurivorum, C. karstii, C. fructicola, C. siamense (Liu et al., 2019), and C. theobromicola (Oliveira et al, 2016). In 2019, leaves with irregular necrotic spots, typical symptoms of anthracnose, were collected in Pará, Brazil. Commercial sampled fields showed 20% of incidence of anthracnose. Colletotrichum strains were isolated and cultured on potato dextrose agar at 25 ºC with a 12-h light photoperiod from surface-disinfected (70% alcohol and 1% sodium hypochlorite) lesion transition area. Five of the obtained isolates exhibited brown colonies on the upper and lower surfaces. Conidia were hyaline, cylindrical and aseptate, 12.82-15.23 µm × 3.52-5.25 µm in size. These phenotypic characters were similar to those belonging to C. orchidearum sensu lato (Damm et al. 2019). Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), ß-tubulin (TUB2), chitin synthase 1(CHS-1), and histone HIS3 partial gene were amplified and sequenced for one representative isolate (UFT/Coll89). Sequences were deposited in GenBank [Accession numbers: MT396235 (GAPDH), MT800856 (TUB2), MT800870 (CHS-1), and MT856672 (HIS3)]. BLASTn searches of CHS-1 and HIS3 sequences showed 100% identity to C. musicola. Maximum Likelihood Phylogenetic analysis, including previously published sequences of closely related species, placed the isolate from Cassava in the C. musicola clade with 100% support, and confidently it assigned to this species. Pathogenicity was proven with inoculations by spraying a conidial suspension (106 conida mL-1) on 3-month-old cassava plants (three unwounded leaves per plant). The plants were placed in a humid chamber at 25 °C for 48h, and a 12-h photoperiod. The negative control was represented by plants inoculated with sterile distilled water. The experiment was repeated twice. The same symptoms observed in the field were reproduced only in inoculated leaves, from which the pathogen was reisolated lesions fulfilling Koch's postulates. No symptoms were observed on the negative control. To our knowledge, this is the first report of C. musicola joining a group of new and emergent species of Colletotrichum causing anthracnose in cassava producing regions around the world. The identification of this species causing cassava anthracnose is crucial to improve the disease control strategies and resistance breeding programs.

First report of Colletotrichum chrysophillum causing cassava anthracnose in Brazil.

Cassava (Manihot esculenta Crantz) has significant socioeconomic relevance in Brazil and other developing countries, as one of the main sources of carbohydrates for human and animal consumption (De Oliviera et al., 2011). Among the cassava crop diseases, anthracnose is one of the main limiting factors for production and may be caused by species like Colletotrichum plurivorum, C. karstii, C. fructicola, and C. siamense (Bragança et al., 2016; Liu et al., 2019; Oliveira et al., 2016; Sangpueak; Phansak; Buensanteai, 2018). Severity in the field is variable, depending on the resistance of the variety used and is also highly influenced by the climate, being the most severe disease under high humidity and high temperature. Under these conditions, it can cause losses of up to 100%. In 2019, cassava leaves presenting dark brown necrotic injuries of different sizes and irregular borders-typical anthracnose symptoms- were collected from commercial plantations in the states of Pará and Tocantins, Brazil. Symptomatic tissue fragments were superficially disinfected, placed in plates with potato dextrose agar (PDA), and incubated under 25 ± 2 °C for seven days. In the 56 isolates used in the morphological identification, the colonies were white and gray at the top and dark gray in the bottom with sector formation. The conidia were hyaline, cylindrical, and aseptic, 10.04 to 17.83 µm long × 3.29 to 5.75 µm wide. These phenotypical characteristics were similar to those of C. gloeosporioides lato sensu species (Weir et al., 2012). Genomic DNA was extracted from two representative isolates (UFT/Coll69, collected in the municipality of Casa de Tábua-PA; UFT/Coll82, collected in Pau Darco-PA) and the APN2 / MAT-IGS, DNA lyase (Apn2), and glyceraldehyde-3-phosphate dehydrogenase-IGS (GAP2-IG) intergenic spacers were amplified and sequenced. The nucleotide sequences were deposited in the GenBank (accession numbers: MT409462, MT396231, MT759633, MT396239, MT396232, MT800846). The BLASTn (Basic Local Alignment Search Tool) showed a 99 to 100% similarity with Colletotrichum chrysophillum. The maximum likelihood phylogenetic analysis grouped the isolates in the C. chrysophillum clade, with a high bootstrap value (98%). Based on morphocultural characteristics and the phylogenetic analysis, the isolates associated with M. esculenta anthracnose were identified as C. chrysophillum, with a frequency of 6.67% among Colletotrichum colonies isolated from cassava leaves. The inoculation of three isolates was carried out in three plants, three leaves for each plant, by spraying spore solution with a concentration of 1×106 conidia / ml, without wounding the leaves and placed in a humid chamber at 25 ° C for ten days. Control plants were inoculated with sterile distilled water. From the 2nd day after inoculation, small irregular necrotic lesions appeared that increased in size over time, while control plants remained asymptomatic. Both were pathogenic and the symptoms caused after inoculation were similar to each other and to those observed in the field. In Brazil, anthracnose by C. chrysophillum was reported in cashew (Veloso et al., 2018) and banana trees (Vieira et al., 2017). To our knowledge, this is the first report of cassava anthracnose disease by C. chrysophillum.

Genome sequence of bubaline alphaherpesvirus 1 (BuHV1) isolated in Australia in 1972.

Bubaline alphaherpesvirus 1 (BuHV1) is a member of the family Herpesviridae, subfamily Alphaherpesvirinae, genus Varicellovirus. To date, no full genome sequence of BuHV has been published. Here, we report the complete genome sequence of bubaline alphaherpesvirus 1 (BuHV1) strain b6 (BuHV1-b6), isolated from a water buffalo (Bubalus bubalis) in 1972 in Australia. The virus was multiplied in MDBK cells, and the DNA was extracted and subjected to high-throughput sequencing. The reads were aligned and combined into a single genome sequence, with bovine alphaherpesvirus 5 (BoHV5) strain SV507/99 (accession number NC005261) as a reference. The BuHV1-b6 genome is a linear double-stranded DNA molecule, 137,452 bp long, with a GC content of 76.8%. The genome consists of two unique sequences: a long, or UL, sequence (103,818 bp) and a short, or US, sequence (9,586 bp), with the latter being flanked by inverted IR and TR elements of 12,024 bp each. The arrangement is typical of herpesvirus genomes of the D-type. The overall sequence has a 92.2% similarity at the nucleotide level to the reference BoHV5 strain. Our report provides a significant landmark in the history of herpesviruses, represented by the genome sequence of this 44-year-old virus isolate.

Molecular detection and characterization of BK and JC polyomaviruses in urine samples of renal transplant patients in Southern Brazil.

The human polyomaviruses JC (JCPyV) and BK (BKPyV) are widespread in the human population. Following the primary infection, virus reactivation may lead to nephropathy and graft rejection in renal transplant patients. This study was carried out to access the presence of BKPyV and JCPyV DNA in urine samples collected from renal transplant patients (n = 92) and healthy individuals (n = 88) in Porto Alegre, Rio Grande do Sul. The samples were submitted to a nested PCR. A significantly higher frequency (P < 0.001) of BKPyV was found in renal transplant patients (65.2%) in comparison to the control group (32.9%). JCPyV was detected equally in both groups. Phylogenetic analysis of both BKPyV and JCPyV amplicons demonstrates the presence of the BKPyV subtypes I and II, whereas for JCPyV, four different groups are found (1, 2, 3, and 4).

Diverse gammacoronaviruses detected in wild birds from Madagascar.

To date, infectious bronchitis virus (IBV) is potentially found in wild birds of different species. This work reports the survey of coronaviruses in wild birds from Madagascar based on the targeting of a conserved genome sequence among different groups of CoVs. Phylogenetic analyses revealed the presence of gammacoronaviruses in different species of Gruiformes, Passeriformes, Ciconiiformes, Anseriformes, and Charadriiformes. Furthermore, some sequences were related to various IBV strains. Aquatic and migratory birds may play an important role in the maintenance and spread of coronaviruses in nature, highlighting their possible contribution in the emergence of new coronavirus diseases in wild and domestic birds.

Prevalence, under-reporting, and epidemiological surveillance of COVID-19 in the Araguaína City of Brazil.

Asymptomatic and underreported individuals remain a source of coronafig disease 2019 (COVID-19) transmission to others. Data on the prevalence and epidemiological factors influencing transmission are fundamental for establishing control measures, especially in vulnerable regions such as the Amazon. This study aimed to determine the point prevalence and active infection of COVID-19 among the population in Araguaína, a Brazilian city located in the Amazon region, analyzed the socioeconomic and behavioral variables of a statistically representative sample of this population using an epidemiological survey, and identify the viral genomic diversity in the region. During the sixth epidemiological week of 2021 (February 8 to 12), samples of 497 inhabitants of the municipality asymptomatic for respiratory syndromes underwent reverse transcription-quantitative polymerase chain reaction and serological tests (immunoglobulin M and immunoglobulin G). A questionnaire collated data on socioeconomic factors, prevention measures, and health status history. The active infection rate was 6.2%, and the prevalence was 13.5% of the study population. Active infection cases were under-reported; each reported positive case represented 14-28 under-reported cases. Lineages P.2, P.1, and B.1.1 were detected. Working from home was a protective factor against the infection, and clinical signs of fever, dry cough, and loss of taste or smell were associated with testing positive (p <0.05). A descriptive analysis of the indicators revealed that the entire population was susceptible to the disease. Intensified vaccination strategies are required regardless of socioeconomic factors, health conditions, and preventive measures. Implementation of objective, comprehensive, and efficient management tools to minimize the spread of COVID-19 in this municipality can serve as a model for other regions of Brazil.

High Frequencies of kdr Mutation and Chikungunya Infection in Aedes aegypti Population from Minas Gerais, Brazil.

The Chikungunya virus (CHIKV) presents global health challenges, with Brazil experiencing outbreaks since its introduction in 2014. In 2023, following a CHIKV outbreak in Minas Gerais (MG), social media was used to optimize an entomological survey aimed at identifying vectors and viral lineages and assessing insecticide resistance. Following Instagram posts, residents with suspected CHIKV infection were able to schedule mosquito aspirations. In total, 421 mosquitoes (165 Aedes aegypti and 256 Culex quinquefasciatus) were captured from 40 households in Salinas city (MG) and tested for the Dengue, Zika, and Chikungunya viruses through RT-qPCR. Twelve of 57 pools (10 Ae. aegypti and two Cx. quinquefasciatus) tested positive for CHIKV RNA. Viral RNA was also detected in the heads of nine Ae. aegypti, indicating viral dissemination but not in Cx. quinquefasciatus. Genome sequencing yielded the first near-complete genome from the 2023 outbreak, unveiling that the CHIKV strain belonged to the East/Central/South African (ECSA) genotype. Additionally, genetic analyses revealed high frequencies of kdr alleles, including in CHIKV-infected mosquitoes, suggesting resistance to pyrethroid insecticides in this Ae. aegypti population. Social media was important for guiding mosquito-capture efforts in CHIKV transmission hotspots, thus optimizing the opportunity for viral detection. These findings emphasize the urgent need for innovative vector studies and control strategies, as well as interdisciplinary approaches in public health interventions.

Detection of Alphacoronavirus in velvety free-tailed bats (Molossus molossus) and Brazilian free-tailed bats (Tadarida brasiliensis) from urban area of Southern Brazil.

A survey was carried out in search for bat coronaviruses in an urban maternity roost of about 500 specimens of two species of insectivorous bats, Molossus molossus and Tadarida brasiliensis, in Southern Brazil. Twenty-nine out of 150 pooled fecal samples tested positive by reverse transcription-PCR contained fragments of the RNA-dependent RNA polymerase gene of coronavirus-related viruses. The sequences clustered along with bat alphacoronaviruses, forming a subcluster within this group. Our findings point to the need for risk assessment and continued surveillance of coronavirus infections of bats in Brazil.

Multiplex PCR followed by restriction length polymorphism analysis for the subtyping of bovine herpesvirus 5 isolates.

BACKGROUND: Several types and subtypes of bovine herpesviruses 1 and 5 (BoHV-1 and BoHV-5) have been associated to different clinical conditions of cattle, making type/subtype differentiation essential to understand the pathogenesis and epidemiology of BoHV infections. BoHV-5 subtyping is currently carried out by BstEII restriction enzyme analysis (REA) of the complete virus genome. This method allowed the description of three subtypes, one of which is the most widespread while the remaining two have so far only been found in South America. The present work describes a multiplex PCR followed by REA for BoHV-5 subtyping. RESULTS: The method consists in the simultaneous amplification of glycoprotein B and UL54 gene fragments of 534 and 669 base pairs (bp), respectively, BstEII digestion of amplicons, separation of products in 1% agarose gels, and analysis of fragment length polymorphims. The multiplex PCR detected up to 227 BoHV-5 genome copies and 9.2 × 105 BoHV-5 genome copies when DNA was extracted from purified virus or infected tissue homogenates, respectively. The applicability of multiplex PCR-REA was demonstrated on 3 BoHV-5 reference strains. In addition, subtyping of two new isolates and seventeen previously reported ones (17 BHV-5a and 2 BHV-5b) by this method gave coincident results with those obtained with the classic BstEII REA assay. CONCLUSIONS: Multiplex PCR-REA provides a new tool for the fast and simple diagnosis and subtyping of BoHV-5.

Detection of vanC1 gene transcription in vancomycin-susceptible Enterococcus faecalis.

Here we report the presence and expression levels of the vanC1 and vanC(2/3) genes in vancomycin-susceptible strains of Enterococcus faecalis. The vanC1 and vanC(2/3) genes were located in the plasmid DNA and on the chromosome, respectively. Specific mRNA of the vanC1 gene was detected in one of these strains. Additionally, analysis of the vanC gene sequences showed that these genes are related to the vanC genes of Enterococcus gallinarum and Enterococcus casseliflavus. The presence of vanC genes is useful for the identification of E. gallinarum and E. casseliflavus. Moreover, this is the first report of vanC mRNA in E. faecalis.

Surveillance, Prevention, Evolution and Control of Emerging Viruses: A 2022 Editorial Update.

The Special Issue "Emerging Viruses: Surveillance, Prevention, Evolution and Control" has been published annually by Viruses, since 2019, highlighting the increasing effort of the scientific community for the surveillance and further research of new emerging or re-emerging viruses [...].

Recovery of complete genomes of canine parvovirus from clinical samples.

Canine parvovirus (CPV) is a highly pathogenic virus that affects dogs, especially puppies. CPV is believed to have evolved from feline panleukopenia virus (FPV), eventually giving rise to three antigenic types, CPV-2a, 2b, and 2c. CPV-2 is recognized for its resilience in contaminated environments, ease of transmission among dogs, and pathogenicity for puppies. Despite the relevance of the virus, complete genome sequences of CPV available at GenBank, to date, are scarce. In the current study, we have developed a methodology to allow the recovery of complete CPV-2 genomes directly from clinical samples. For this, seven fecal samples from Gurupi, Tocantins, North Brazil, were collected from puppies with clinical signals of viral enteritis, and submitted to viral DNA isolation and amplification. Two multiplex PCR strategies were designed including primers targeting fragments of 400 base pairs (bp) and 1,000 bp along the complete genome. Sequencing was performed with the Nanopore® technology and results obtained with the two approaches were compared. Genome assembly revealed that the 400 bp amplicons generated larger numbers of reads, allowing a more reliable coverage of the whole genome than those attained with primers targeting the larger (1000 bp) amplicons. Nevertheless, both enrichment methodologies were efficient in amplification and sequencing. Viral genome sequences were of high quality and allowed more precise typing and subtyping of viral genomes compared to the commonly employed strategy relying solely on the analysis of the VP2 region, which is limited in scope. The CPV-2 genomes recovered in this study belong to the CPV2a and CPV-2c subtypes, closely related to isolates from the neighboring Amazonian region. In conclusion, the technique reported here may contribute to increase the number of full CPV genomes available, which is essential for understanding the genetic mechanisms underlying the evolution and spread of CPV-2.

Circulation of Dengue Virus Serotype 1 Genotype V and Dengue Virus Serotype 2 Genotype III in Tocantins State, Northern Brazil, 2021-2022.

In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of cases of arboviral disease, particularly Dengue virus (DENV). This study aimed to deepen the knowledge on DENV circulation within that state by conducting full genome sequencing of viral genomes recovered from 61 patients between June 2021 and July 2022. There were a total of 8807 and 20,692 cases in 2021 and 2022, respectively, as reported by the state's Secretary of Health. Nucleotide sequencing confirmed the circulation of DENV serotype 1, genotype V and DENV serotype 2, genotype III in the State. Younger age groups (4 to 43 years old) were mostly affected; however, no significant differences were detected regarding the gender distribution of cases in humans. Phylogenetic analysis revealed that the circulating viruses belong to DENV-1 genotype V American and DENV-2 genotype III Southeast Asian/American. The Bayesian analysis of DENV-1 genotype V genomes sequenced here are closely related to genomes previously sequenced in the state of São Paulo. Regarding the DENV-2 genotype III genomes, these clustered in a distinct, well-supported subclade, along with previously reported isolates from the states of Goiás and São Paulo. The findings reported here suggest that multiple introductions of these genotypes occurred in the Tocantins state. This observation highlights the importance of major population centers in Brazil on virus dispersion, such as those observed in other Latin American and North American countries. In the SNP analysis, DENV-1 displayed 122 distinct missense mutations, while DENV-2 had 44, with significant mutations predominantly occurring in the envelope and NS5 proteins. The analyses performed here highlight the concomitant circulation of distinct DENV-1 and -2 genotypes in some Brazilian states, underscoring the dynamic evolution of DENV and the relevance of surveillance efforts in supporting public health policies.

Neutralizing antibodies to bovine and bubaline alphaherpesviruses in water buffaloes (Bubalus bubalis).

Water buffaloes (Bubalus bubalis) have been introduced in many regions of the world as a source of animal protein. In many instances, bubaline cattle are reared close to or mixed with bovine or zebuine cattle. However, little is known about infectious diseases of bubaline and the interactions that may arise involving the microbiota of those species. Alphaherpesviruses of ruminants (bovine alphaherpesviruses types 1 and 5, BoHV-1, BoHV-5; bubaline alphaherpesvirus 1, BuHV-1) are highly cross-reactive in serological assays performed with bovine or zebuine sera. However, the profile of reactivity of bubaline cattle sera to alphaherpesviruses remains unknown. As such, it is not known which virus strain (or strains) would be most appropriate to be used as the challenge virus in the laboratory in search for alphaherpesvirus-neutralizing antibodies. In this study, the profile of neutralizing antibodies to alphaherpesviruses in bubaline sera was determined against different types/subtypes of bovine and bubaline alphaherpesviruses. Sera (n=339) were screened in a 24-h serum neutralization test (SN) against 100 TCID50 of each of the challenge viruses. From those, 159 (46.9 %) neutralized at least one of the viruses assayed; 131 (38.6%) sera neutralized the three viral strains used for screening. The viral strain that was neutralized by the largest number of sera was BoHV-5b A663 (149/159; 93.7%). A few sera neutralized only one of the challenge viruses: four sera neutralized BoHV-1 LA only; another neutralized BoHV-5 A663 only and four others neutralized BuHV-1 b6 only. SN testing with two additional strains gave rise to similar results, where maximum sensitivity (defined here as the largest number of sera that neutralized the challenge viruses) was obtained by adding positive results attained with three of the challenge strains. Differences in neutralizing antibody titers were not significant to allow inferences on which would be the most likely virus that induced the antibody responses detected here.

Arbovirus surveillance in mosquitoes: Historical methods, emerging technologies, and challenges ahead.

Arboviruses cause millions of infections each year; however, only limited options are available for treatment and pharmacological prevention. Mosquitoes are among the most important vectors for the transmission of several pathogens to humans. Despite advances, the sampling, viral detection, and control methods for these insects remain ineffective. Challenges arise with the increase in mosquito populations due to climate change, insecticide resistance, and human interference affecting natural habitats, which contribute to the increasing difficulty in controlling the spread of arboviruses. Therefore, prioritizing arbovirus surveillance is essential for effective epidemic preparedness. In this review, we offer a concise historical account of the discovery and monitoring of arboviruses in mosquitoes, from mosquito capture to viral detection. We then analyzed the advantages and limitations of these traditional methods. Furthermore, we investigated the potential of emerging technologies to address these limitations, including the implementation of next-generation sequencing, paper-based devices, spectroscopic detectors, and synthetic biosensors. We also provide perspectives on recurring issues and areas of interest such as insect-specific viruses.

An indirect ELISA to detect antibodies to the gC of bovine alphaherpesvirus 1 (BoAHV1) displaying no crossreactivity with antibodies induced by bovine alphaherpesvirus 5 (BoAHV5).

Seroprevalence of bovine alphaherpesvirus type 1 (BoAHV1) infections may be contaminated by crossreactive antibodies to bovine alphaherpesvirus type 5 (BoAHV5). To avoid such crossreactivity, an indirect enzyme-linked immunosorbent assay prepared with a recombinant glycoprotein C (gC) antigen (ELISA-gC1) was developed, aiming the detection of antibodies to BoAHV1, with no crossreactivity with BoAHV5 antibodies. The antigen for the ELISA-gC1 was the product of the expression of 219 bp from the N-terminal portion of the BoAHV1 gC gene, which bears low homology between the two virus types. The test was validated on 131 bovine serum samples, including 26 sera from BoAHV1-experimentally immunized, 38 sera from BoAHV5-experimentally infected or immunized calves, and 67 sera from calves seronegative for both BoAHV1 and BoAHV5, as determined by serum neutralization (SN). When compared to SN for BoAHV1, the ELISA-gC1 presented 100% sensitivity, 95.5 % specificity, 100 % negative predictive value, 89.6 % positive predictive value, 98.8 % precision, and a kappa correlation coefficient (κ) 0.95. None of the 38 BoAHV5-seropositive calves was detected by the ELISA-gC1. The ELISA-gC1 proved highly effective for the identification of BoAHV1-positive sera, with no crossreactivity with anti-BoAHV5 antibodies, thus able to distinguish serological responses from BoAHV1- and BoAHV5-seropositive cattle. Its capacity to detect BoAHV1-specific antibodies should allow the determination of the actual BoAHV1 prevalence in herds, which cannot be serologically determined in countries where BoAHV5 is also prevalent due to antibody crossreactivity. Apart from recognizing exclusively BoAHV1-infected cattle, the ELISA-gC1 may also be used in support of BoAHV5 epidemiological studies by allowing the exclusion of BoAHV1-seropositive animals.

An ELISA to Detect Antibodies to Bovine Alphaherpesviruses 1 and 5 and Bubaline Alphaherpesvirus 1 in Cattle Sera.

Bovine alphaherpesvirus 1 (subtypes 1.1, 1.2a, and 1.2b), type 5 (subtypes 5a, 5b, and 5c), and bubaline herpesvirus 1 (BuHV-1) induce highly, though not fully cross-reactive serological responses. Most types and subtypes of these viruses circulate particularly in countries of the southern hemisphere, notably Brazil and Argentina. Therefore, the detection of infected animals is important in defining prevention and control strategies, particularly when flocks are destined for international trade. Identification of infected herds is most often achieved by assays that detect antibodies, such as enzyme immunoassays (ELISAs). However, to date, no ELISA has been evaluated in its capacity to detect antibodies to these alphaherpesviruses. Here, an ELISA was developed to detect antibodies to all currently recognized BoAHV-1, BoAHV-5, and BuAHV-1 types/subtypes, and its sensitivity and specificity were determined. Six hundred bovine sera were screened in serum neutralization tests (SN) against the seven viruses. ELISAs prepared with each of the viruses were compared to SN. Subsequently, a combined assay with multiple antigens LISA was prepared by mixing five viral antigens, chosen for their highest sensitivity in the preparative assays. In comparison to SN, the mAgELISA sensitivity was 96.5% with 96.1% specificity (κ = 0.93; PPV = 95.0%; NPV = 97.3%). The findings reveal that the mAgELISA developed here is highly suitable for the detection of antibodies, comparable in sensitivity and specificity to that of SN when performed with all known types and subtypes of bovine and bubaline alphaherpesviruses.

Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil.

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modeling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centers in the Southeast. Phylodynamic analysis unraveled the circulation of three distinct lineages and provided proof of the directionality of a known spatial corridor that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.

The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub.

Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.