Biology subjects

Bispo de Filippis, A. M.

Publications and source records attributed to Bispo de Filippis, A. M..

6 recordsLinked to original sources

bioRxiv2026

Infection of neotropical non-human primates with bat deltaviruses

Background & Aims: The origin of hepatitis D virus (HDV) and related deltaviruses remains elusive. Contrarily, hepatitis B virus, HDV's helper virus, and related hepadnaviruses display long-term association with primates. Current data suggest cross-order host shifts as a common mechanism in deltavirus ecology, but corroborative evidence is lacking. Here, we aimed to elucidate the genealogy of primate deltaviruses. Methods: We screened 961 non-human primate (NHP) liver specimens obtained in Brazil between 2017-2023 for deltaviruses and hepadnaviruses. Complete deltaviral genomes were obtained via overlapping nested RT-PCR, cloned, expressed in vitro and analyzed via immunoblot and immunofluorescence analysis. Anti-deltaviral antibodies in NHP and vampire bats were detected via immunofluorescence analysis. Results: We detected deltaviruses in two NHP. Complete deltaviral genomes exhibited common features including high self-complementarity, genomic and antigenomic ribozymes, and a delta antigen open reading frame. NHP deltaviruses were phylogenetically related to viruses found in common vampire bats. The NHP deltaviruses replicated in vitro without the expression of a large delta antigen. We did not detect anti-deltaviral antibodies in NHP sera (0/249), in contrast to sera from common vampire bats (7/112; 6.2%, 95% CI: 1.8-10.7), indicating viral circulation in bats. Ancestral state reconstruction suggested a bat origin of NHP deltaviruses. Targeted screening excluded a coinfecting hepadnavirus in the deltavirus-positive animals but led to the discovery of a hepadnavirus, corroborating a non-recent introduction of hepadnaviruses into the primate stem-lineage. Conclusions: Our data are consistent with deltaviral cross-order host shifts and suggestive of the susceptibility of primates to reservoir-bound deltaviruses, lending credibility to a zoonotic origin of HDV.

microbiology↗

bioRxiv2021

Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil

The Northeast region of Brazil registered the second highest incidence proportion of chikungunya fever in 2019. In that year an outbreak consisting of patients presented with febrile disease associated with joint pain were reported by the public primary health care service in the city of Natal, Rio Grande do Norte state, in March 2019. At first, the aetiological agent of the disease was undetermined. Since much is still unknown about chikungunya virus (CHIKV) genomic diversity and evolutionary history in this northeasternmost state, we used a combination of portable whole genome sequencing, molecular clock, and epidemiological analyses that revealed the re-introduction of the CHIKV East-Central-South-African (ECSA) lineage into Rio Grande do Norte. We estimated CHIKV ECSA lineage was first introduced into Rio Grande do Norte in early June 2014, while the 2019 outbreak clade diverged around April 2018 during a period of increased chikungunya incidence in the Southeast region, which might have acted as a source of virus dispersion towards the Northeast region. Together, these results confirm the ECSA lineage continues to spread across the country through interregional importation events likely mediated by human mobility. HIGHLIGHTSCHIKV ECSA lineage introduction into Rio Grande do Norte state, Northeast Brazil, was estimated to early June 2014 At least two CHIKV importation events occurred in Rio Grande do Norte state, Brazil The 2019 chikungunya outbreak in Rio Grande do Norte was likely caused by a second event of CHIKV introduction imported from Rio de Janeiro state.

genomics↗

bioRxiv2020

A systematic evaluation of IgM and IgG antibody assay accuracy in diagnosing acute Zika Virus infection in Brazil; lessons relevant to emerging infections

Accurate diagnostics underpin effective public health responses to emerging viruses. For viruses, such as Zika virus (ZIKV), where the viremia clears quickly, antibody-based (IgM or IgG) diagnostics are recommended for patients who present seven days after symptom onset. However, cross-reactive antibody responses can complicate test interpretation among populations where closely related viruses circulate. We examined the accuracy (proportion of samples correctly categorized as Zika-positive or negative) for antibody-based diagnostics among Brazilian residents (Rio de Janeiro) during the ZIKV outbreak. Four ZIKV ELISAs (IgM and IgG Euroimmun, IgM Novagnost and CDC MAC), two dengue ELISAs (IgM and IgG Panbio), and the ZIKV plaque reduction neutralization test (PRNT) were evaluated. Positive samples were ZIKV PCR confirmed clinical cases collected in 2015-2016 (n=169); Negative samples (n=236) were collected before ZIKV was present in Brazil ([≤]2013). Among serum samples collected [≥]7 days from symptom onset, PRNT exhibited the highest accuracy (93.7%), followed by the Euroimmun IgG ELISA (77.9%). All IgM assays exhibited lower accuracy (<74%). IgG was detected more consistently than IgM among ZIKV cases using Euroimmun ELISAs (68% versus 22%). Anti-DENV IgM ELISA was positive in 41.1% of confirmed ZIKV samples tested. The Euroimmun IgG assay, although misdiagnosing 22% of samples, provided the most accurate ELISA. Anti-ZIKV IgG was detected more reliably than IgM among ZIKV patients, suggesting a secondary antibody response to assay antigens following ZIKV infection. Antibody ELISAs need careful evaluation in their target population to optimise use and minimise misdiagnosis, prior to widespread deployment, particularly where related viruses co-circulate.

microbiology↗

bioRxiv2019

Yellow fever virus spread in Rio de Janeiro and Espirito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies

The recent re-emergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the virus rapid dissemination in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil we generated 18 complete and near-complete genomes from the peak of the epidemic curve from non-human primates (NHPs) and human infected cases across Espirito Santo and Rio de Janeiro states. Genomic sequencing of 18 YFV genomes revealed the timing, source and likely routes of yellow fever virus transmission and dispersion during the one of the largest outbreaks ever registered in Brazil. We showed that the recent YFV epidemic spillover southwards several times from Minas Gerais to Espirito Santo and Rio de Janeiro states in 2016 to 2019. The quick production and analysis of data from portable sequencing could identify the corridor of spread of YFV. These findings reinforce that real-time and continued genomic surveillance strategies can assist in the monitoring and public health responses of arbovirus epidemics.\n\nIMPORTANCEArbovirus infections in Brazil including Yellow Fever, Dengue, Zika and Chikungunya result in considerable morbidity and mortality and are pressing public health concerns. However, our understanding of these outbreaks is hampered by limited availability of real time genomic data. In this study, we investigated the genetic diversity and spatial distribution of YFV during the current outbreak in southeastern Brazil. To gain insights into the routes of YFV introduction and dispersion, we tracked the virus by sequencing YFV genomes sampled from non-human primates and infected patients from the southeastern region. Our study provides an understanding of how YFV initiates transmission in new Brazilian regions and illustrates that near-real time genomics in the field can augment traditional approaches to infectious disease surveillance and control.

microbiology↗

bioRxiv2019

Re-introduction of dengue virus serotype 2 in the State of Rio de Janeiro after almost a decade of epidemiological silence

The Asian/American genotype of dengue virus serotype 2 (DENV-2) has been introduced in Brazil through the state of Rio de Janeiro around 1990, and since then it has been spreading and evolving, leading to several waves of dengue epidemics throughout the country that cause a major public health problem. Of particular interest has been the epidemic of 2008, whose highest impact was evidenced in the state of Rio de Janeiro, with a higher number of severe cases and mortality rate, compared to previous outbreaks. Interestingly, no circulation of DENV-2 was witnessed in this region during the preceding 9-year period. By early 2010, phylogenetic analysis of the 2008 epidemic strain revealed that the outbreak was caused by a new viral lineage of the Asian/American genotype, which was pointed as responsible for the outbreak severity as well. The same scenario is repeating in 2019 in this state; however, only a few cases have been detected yet. To provide information that helps to the understanding of DENV-2 dynamics in the state of Rio de Janeiro, and thereafter contribute to public health control and prevention actions, we employed phylogenetic studies combined with temporal and dynamics geographical features to determine the origin of the current viral strain. To this effect, we analyzed a region of 1626 nucleotides entailing the Envelope/NS1 viral genes. Our study reveals that the current strain belongs to the same lineage that caused the 2008 outbreak, however, it is phylogenetically distant from any Brazilian strain identified so far. Indeed, it seemed to be originated in Puerto Rico around 2002 and has been introduced into the state in late 2018. Taking into account that no DENV-2 case was reported over the last decade in the state (representing a whole susceptible children generation), and the fact that a new viral strain may be causing current dengue infections, these results will be influential in strengthening dengue surveillance and disease control, mitigating the potential epidemiological consequences of virus spread.\n\nAuthor SummaryBy the time dengue virus serotype 2 (DENV-2) was introduced into Brazil through the state of Rio de Janeiro in 1990, the first dengue hemorrhagic cases started to evidence as well. Years of seasonal outbreaks were followed by almost ten years oy epidemiological silence in the state. However, in 2007 this serotype was re-introduced into the state causing one of the worst dengue epidemics ever described in the country. The same viral genotype was involved, however, a different viral lineage was detected and pointed as responsible for the outbreak severity. This same scenario could repeat nowadays in the state of Rio de Janeiro. Since new DENV-2 cases are being detected in this region, we analyzed the identity and origin of the viral strain obtained from two infected patients. Phylogeny combined with temporal and geographical analyses of viral sequences demonstrated that the strain causing 2019s dengue cases belonged to the same lineage as the one causing the outbreak in 2008, but to a different subgroup, and might have originated in Puerto Rico and entered the state in recent times. These results may represent a crucial starting point for strengthening Brazilian surveillance systems and disease control, helping to reduce the impact of a potential epidemic of great magnitude.

microbiology↗

bioRxiv2018

Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection

Brazil, which is hyperendemic for dengue virus (DENV), has had recent Zika (ZIKV) and (CHIKV) Chikungunya virus outbreaks. Since March 2016, CHIKV is the arbovirus infection most frequently diagnosed in Rio de Janeiro. In the analysis of 1835 syndromic patients, screened by real time RT-PCR, 56.4% of the cases were attributed to CHIKV, 29.6% to ZIKV, and 14.1% to DENV-4. Sequence analyses of CHIKV from sixteen samples revealed that the East-Central-South-African (ECSA) genotype of CHIKV has been circulating in Brazil since 2013 [95% bayesian credible interval (BCI): 03/2012-10/2013], almost a year before it was detected by arbovirus surveillance program. Brazilian cases are related to Central African Republic sequences from 1980s. To the best of our knowledge, given the available sequence published here and elsewhere, the ECSA genotype was likely introduced to Rio de Janeiro early on 2014 (02/2014; BCI: 07/2013-08/2014) through a single event, after primary circulation in the Bahia state at the Northestern Brazil in the previous year. The observation that the ECSA genotype of CHIKV was circulating undetected underscores the need for improvements in molecular methods for viral surveillance.

genomics↗