Beyond pathogens: the intriguing genetic legacy of endogenous retroviruses in host physiology.

The notion that viruses played a crucial role in the evolution of life is not a new concept. However, more recent insights suggest that this perception might be even more expansive, highlighting the ongoing impact of viruses on host evolution. Endogenous retroviruses (ERVs) are considered genomic remnants of ancient viral infections acquired throughout vertebrate evolution. Their exogenous counterparts once infected the host's germline cells, eventually leading to the permanent endogenization of their respective proviruses. The success of ERV colonization is evident so that it constitutes 8% of the human genome. Emerging genomic studies indicate that endogenous retroviruses are not merely remnants of past infections but rather play a corollary role, despite not fully understood, in host genetic regulation. This review presents some evidence supporting the crucial role of endogenous retroviruses in regulating host genetics. We explore the involvement of human ERVs (HERVs) in key physiological processes, from their precise and orchestrated activities during cellular differentiation and pluripotency to their contributions to aging and cellular senescence. Additionally, we discuss the costs associated with hosting a substantial amount of preserved viral genetic material.

Human endogenous retroviruses and the inflammatory response: A vicious circle associated with health and illness.

Human Endogenous Retroviruses (HERVs) are derived from ancient exogenous retroviral infections that have infected our ancestors' germline cells, underwent endogenization process, and were passed throughout the generations by retrotransposition and hereditary transmission. HERVs comprise 8% of the human genome and are critical for several physiological activities. Yet, HERVs reactivation is involved in pathological process as cancer and autoimmune diseases. In this review, we summarize the multiple aspects of HERVs' role within the human genome, as well as virological and molecular aspects, and their fusogenic property. We also discuss possibilities of how the HERVs are possibly transactivated and participate in modulating the inflammatory response in health conditions. An update on their role in several autoimmune, inflammatory, and aging-related diseases is also presented.

First case report of monkeypox in Brazil: clinical manifestations and differential diagnosis with sexually transmitted infections.

In 2022, an outbreak of monkeypox is being reported in non-endemic areas, with unusual clinical manifestations. The detailed clinical description of the first patient that received the diagnosis of monkeypox in Brazil is reported here, whose clinical manifestations can easily lead to misdiagnosis of sexually transmitted infections. A 41 years old male presented to an emergency room with a vesicular rash with eight days of evolution. He had traveled to Portugal and Spain and reported non-penetrative sexual involvement with three different male individuals. On the third day of symptoms, he sought medical care and received empirical treatment directed to sexually transmitted infections. As the symptoms did not improve, he sought medical attention at an infectious disease referral center presenting, on admission, an ulcerated penile lesion with central necrotic crusts, a disseminated pleomorphic skin rash and an oropharyngeal ulcer. The monkeypox diagnosis was suspected due to the characteristics of the lesions and the history of intimate contact with casual partners, and it was later confirmed by sequencing the almost complete monkeypox genome. The patient was hospitalized for pain control, which required opiate administration. He developed a secondary bacterial infection on the penile lesions, which were treated with oral antibiotics. He was discharged after 14 days, with lesions in process of re-epithelialization. Given the current outbreak, we must consider the possibility of monkeypox in patients with suggestive lesions, anywhere on the body (including the genitals), added to an epidemiological link or history of intimate contact with strangers or casual partners.

Characterization of insect-specific Culex flavivirus (Flaviviridae) nucleotide sequences in mosquitoes from urban parks in São Paulo, Brazil.

BACKGROUND: Despite their worldwide occurrence, the distribution and role of insect-specific flaviviruses (ISFs) remain unclear. METHODS: We evaluated the presence of ISFs in mosquitoes collected in São Paulo, Brazil, using reverse transcription and semi-nested polymerase chain reaction (PCR). Some of the positive samples were subjected to nanopore sequencing. RESULTS: Twelve mosquito pools (2.8%) tested positive for flavivirus infection. Nanopore sequencing was successfully performed on six samples. Phylogenetic analysis grouped these sequences into genotype 2 of Culex flavivirus (CxFV). CONCLUSIONS: The identification of CxFV genotype 2 at new locations in São Paulo highlights the importance of understanding the role of ISFs in mosquito vector competence.

SARS-CoV-2 BA.1 and BA.2 coinfection detected by genomic surveillance in Brazil, January 2022.

In January 2022, our genomic surveillance network identified a SARS-CoV-2 BA.1 and BA.2 coinfection in a sample from a patient residing in Brazil. Our results suggest that the true number of SARS-CoV-2 coinfections remains largely underestimated.

Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil.

The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the "third wave" of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta sub-lineages emerged, including the globally spread AY.101 and AY.99.2. In this study we performed a detailed analysis of the COVID-19 scenario in Brazil from April to December 2021 by using data collected by the largest private medical diagnostic company in Latin America (Dasa), and SARS-CoV-2 genomic sequences generated by its SARS-CoV-2 genomic surveillance project (GENOV). For phylogenetic and Bayesian analysis, SARS-CoV-2 genomes available at GISAID public database were also retrieved. We confirmed that the Brazilian AY.99.2 and AY.101 were the most prevalent lineages during this period, overpassing the Gamma variant in July/August. We also estimated that AY.99.2 likely emerged a few weeks after the entry of the B.1.617.2 in the country, at some point between late April and May and rapidly spread to other countries. Despite no increased fitness described for the AY.99.2 lineage, a rapid shift in the composition of Delta SARS-CoV-2 lineages prevalence in Brazil took place. Understanding the reasons leading the AY.99.2 to become the dominant lineage in the country is important to understand the process of lineage competitions that may inform future control measures.

Low frequency of SARS-CoV2 infection in daycare centers during the reopening of school activities in the Southeast's poor area of Brazil.

SARS-Cov2 has already infected over 482 million people and caused more than 6.1 million deaths. The beginning of the pandemic has led the health authorities of several countries to adopt non-pharmacological preventive measures such as daycare closures. The reopening took place when the country had the highest rates of infection and mortality (mainly due to the gamma variant (P.1) outbreak) and the beginning of the vaccination program. Therefore, we aimed to investigate the prevalence of SARS-CoV2 in daycare after educational activities resumed. The study was conducted in seven childcare facilities. Swab samples from the nasopharynx were collected from children and staff members. The viral RNA was obtained through PureLink RNA extraction kit purification and SARS-CoV2 presence was detected using the All plex SARS-CoV2 kit. The study population included 201 participants, including daycare workers and children. The average age of the workers and children is 40 and 3 years old, respectively. Among the children, 47.5% are female and among the workers, 91.4%. One (0.5%) test came out positive for the presence of SARS-CoV-2, which was from a sample of an asymptomatic childcare worker, and no secondary infections were detected. Considering that the return to daycare activities occurred during a period with a high number of deaths and a lack of vaccines throughout the country, the small number of cases indicates the effectiveness of the several preventive measures used by daycare centers in preventing SARS-CoV2 transmission.

Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.

Use of saliva and RT-PCR screening for SARS-CoV-2 variants of concern: Surveillance and monitoring.

Genomic surveillance has been applied since the beginning of the COVID-19 pandemic to track the spread of the virus, leading to the characterization of multiple SARS-CoV-2 variants, including variants of concern (VOC). Although sequencing is the standard method, a rapid molecular test for screening and surveillance of VOC is considered for detection. Furthermore, using alternative saliva as specimen collection facilitates the implementation of a less invasive, self-collected sample. In this study, we applied a combinatory strategy of saliva collection and reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 VOC detection. Saliva samples from patients attending a tertiary hospital with suspected COVID-19 were collected and SARS-CoV-2 RNA was detected using SARS-CoV-2 RT-qPCR reagent kit (PerkinElmer). Positive saliva samples were screened for SARS-CoV-2 VOC with previously described RT-PCR for Alpha, Beta, and Gamma variants. Saliva samples were positive in 171 (53%) of 324 tested. A total of 108 (74%) from positive samples were also positive for VOC by RT-PCR screening. Those samples were found between January and August 2021. This approach allowed us to successfully use an alternative and complementary tool to genomic surveillance to monitor the circulation of SARS-CoV-2 VOC in the studied population.

First case report of monkeypox in Brazil: clinical manifestations and differential diagnosis with sexually transmitted infections

ABSTRACT In 2022, an outbreak of monkeypox is being reported in non-endemic areas, with unusual clinical manifestations. The detailed clinical description of the first patient that received the diagnosis of monkeypox in Brazil is reported here, whose clinical manifestations can easily lead to misdiagnosis of sexually transmitted infections. A 41 years old male presented to an emergency room with a vesicular rash with eight days of evolution. He had traveled to Portugal and Spain and reported non-penetrative sexual involvement with three different male individuals. On the third day of symptoms, he sought medical care and received empirical treatment directed to sexually transmitted infections. As the symptoms did not improve, he sought medical attention at an infectious disease referral center presenting, on admission, an ulcerated penile lesion with central necrotic crusts, a disseminated pleomorphic skin rash and an oropharyngeal ulcer. The monkeypox diagnosis was suspected due to the characteristics of the lesions and the history of intimate contact with casual partners, and it was later confirmed by sequencing the almost complete monkeypox genome. The patient was hospitalized for pain control, which required opiate administration. He developed a secondary bacterial infection on the penile lesions, which were treated with oral antibiotics. He was discharged after 14 days, with lesions in process of re-epithelialization. Given the current outbreak, we must consider the possibility of monkeypox in patients with suggestive lesions, anywhere on the body (including the genitals), added to an epidemiological link or history of intimate contact with strangers or casual partners.

Characterization of insect-specific Culex flavivirus (Flaviviridae) nucleotide sequences in mosquitoes from urban parks in São Paulo, Brazil

ABSTRACT Background: Despite their worldwide occurrence, the distribution and role of insect-specific flaviviruses (ISFs) remain unclear. Methods: We evaluated the presence of ISFs in mosquitoes collected in São Paulo, Brazil, using reverse transcription and semi-nested polymerase chain reaction (PCR). Some of the positive samples were subjected to nanopore sequencing. Results: Twelve mosquito pools (2.8%) tested positive for flavivirus infection. Nanopore sequencing was successfully performed on six samples. Phylogenetic analysis grouped these sequences into genotype 2 of Culex flavivirus (CxFV). Conclusions: The identification of CxFV genotype 2 at new locations in São Paulo highlights the importance of understanding the role of ISFs in mosquito vector competence.

Low frequency of SARS-CoV2 infection in daycare centers during the reopening of school activities in the Southeast's poor area of Brazil

ABSTRACT SARS-Cov2 has already infected over 482 million people and caused more than 6.1 million deaths. The beginning of the pandemic has led the health authorities of several countries to adopt non-pharmacological preventive measures such as daycare closures. The reopening took place when the country had the highest rates of infection and mortality (mainly due to the gamma variant (P.1) outbreak) and the beginning of the vaccination program. Therefore, we aimed to investigate the prevalence of SARS-CoV2 in daycare after educational activities resumed. The study was conducted in seven childcare facilities. Swab samples from the nasopharynx were collected from children and staff members. The viral RNA was obtained through PureLink RNA extraction kit purification and SARS-CoV2 presence was detected using the All plex SARS-CoV2 kit. The study population included 201 participants, including daycare workers and children. The average age of the workers and children is 40 and 3 years old, respectively. Among the children, 47.5% are female and among the workers, 91.4%. One (0.5%) test came out positive for the presence of SARS-CoV-2, which was from a sample of an asymptomatic childcare worker, and no secondary infections were detected. Considering that the return to daycare activities occurred during a period with a high number of deaths and a lack of vaccines throughout the country, the small number of cases indicates the effectiveness of the several preventive measures used by daycare centers in preventing SARS-CoV2 transmission.

Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022

ABSTRACT Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.

NS1-based ELISA test efficiently detects dengue infections without cross-reactivity with Zika virus.

OBJECTIVES: The aim of this study was to achieve greater specificity of dengue virus (DENV) serological tests based on a recombinant antigen derived from non-structural protein 1 (ΔNS1) with regard to cross-reactive Zika virus (ZIKV) anti-NS1 antibody responses. This is of relevance in endemic regions for the serological discrimination of both DENV and ZIKV, such as Brazil and other tropical countries. METHODS: The ΔNS1 proteins were obtained as recombinant antigens and were evaluated as solid-phase-bound antigens in the ELISA test to detect anti-NS1 IgG antibodies. The performance of the ∆NS1-based DENV IgG ELISA was assessed with both mouse and human serum samples previously exposed to DENV or ZIKV. RESULTS: The ∆NS1-based DENV IgG ELISA detected anti-DENV NS1 IgG without cross-reactivity with ZIKV-positive serum samples. The sensitivity and specificity of the assay determined using samples previously characterized by real-time PCR (qRT-PCR) or plaque reduction neutralization assay (PRNT) were 82% and 93%, respectively. CONCLUSION: The ∆NS1-based DENV IgG ELISA conferred enhanced diagnostic specificity for anti-DENV serological tests and may be particularly useful for serological analyses in endemic regions for both DENV and ZIKV transmission.

SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil.

Reinfection by the severe acute respiratory syndrome coronavirus type 2 (SARS-COV-2) has been reported in many countries, suggesting that the virus may continue to circulate among humans despite the possibility of local herd immunity due to massive previous infections. The emergence of variants of concern (VOC) that are more transmissible than the previous circulating ones has raised particular concerns on the vaccines effectiveness and reinfection rates. The P.1 lineage was first identified in December 2020 in Manaus city and is now globally spread. We report the first case of reinfection of SARS-CoV-2 caused by the P.1 variant outside of Manaus. The potential of these new variants to escape naturally and vaccine- induced immunity highlights the need for a global vigilance.

Dynamics of SARS-CoV-2 Variants of Concern in Brazil, Early 2021.

Brazil is the country with the second-largest number of deaths due to the coronavirus disease-2019 (COVID-19). Two variants of concern (VOCs), Alpha (B.1.1.7) and Gamma (P.1), were first detected in December 2020. While Alpha expanded within an expected rate in January and February 2021, its prevalence among new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases started to decrease in March, which coincided with the explosion of Gamma variant incidence all over the country, being responsible for more than 95% of the new cases over the following months. A significantly higher viral load [i.e., mean cycle threshold (Ct) values] for Gamma in comparison to non-VOC samples was verified by the analysis of a large data set of routine reverse transcription-PCR (RT-PCR) exams. Moreover, the rate of reinfections greatly increased from March 2021 onward, reinforcing the enhanced ability of Gamma to escape the immune response. It is difficult to predict the outcomes of competition between variants since local factors like frequency of introduction and vaccine coverage play a key role. Genomic surveillance is of uttermost importance for the mitigation of the pandemic.

Anti-Zika virus activity of several abietane-type ferruginol analogues.

Abietane diterpenoids are naturally occurring plant metabolites with a broad spectrum of biological effects including antibacterial, antileishmanial, antitumor, antioxidant, as well as antiinflammatory activities. Recently, we found that some analogues of natural ferruginol ( 2 ) actively inhibited dengue virus 2 (DENV-2) replication. Due to the similarity with DENV, we envisaged that abietane diterpenoids would also be active against Zika virus (ZIKV). Six selected semi-synthetic abietane derivatives of (+)-dehydroabietylamine ( 3 ) were tested. Cytotoxicity was determined by MTT assay in Vero cells. In vitro anti-ZIKV (clinical isolate, IMT17) activity was evaluated by plaque assay. Interestingly, these molecules showed potential as anti-ZIKV agents, with EC50 values ranging from 0.67 to 18.57 µM, and cytotoxicity (CC50 values) from 2.56 to 35.09 µM. The 18-Oxoferruginol (8) (EC50 = 2.60 µM, SI = 13.51) and 12-nitro-N-benzoyldehydroabietylamine (9) (EC50= 0.67 µM, SI = 3.82) were the most active compounds, followed by 12-hydroxy-N-tosyldehydroabietylamine ( 7 ) (EC50 = 3.58 µM, SI = 3.20) and 12-hydroxy-N,N-phthaloyldehydroabietylamine ( 5 ) (EC50 = 7.76 µM, SI = 1.23). To the best of our knowledge, this is the first report on anti-Zika virus properties of abietanes.