Faecal-oral transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is yet to be validated, but it is a critical issue and additional research is needed to elucidate the risks of ...the novel coronavirus in sanitation systems. This is the first study that investigates the potential health risks of SARS-CoV-2 in sewage to wastewater treatment plant (WWTP) workers. A quantitative microbial risk assessment (QMRA) is applied for three COVID-19 scenarios (moderate, aggressive and extreme) to study the effects of different stages of the pandemic in terms of percentage of infected population on the probability of infection to WWTP workers. A dose-response model for SARS-CoV-1 (as a surrogate pathogen) is assumed in the QMRA for SARS-CoV-2 using an exponential model with k = 4.1 × 102. Literature data are incorporated to inform assumptions for calculating the viral load, develop the model, and derive a tolerable infection risk. Results reveal that estimates of viral RNA in sewage at the entrance of WWTPs ranged from 4.14 × 101 to 5.23 × 103 GC·mL−1 (viable virus concentration from 0.04 to 5.23 PFU·mL−1, respectively). In addition, estimated risks for the aggressive and extreme scenarios (2.6 × 10−3 and 1.3 × 10−2, respectively) were likely to be above the derived tolerable infection risk for SARS-CoV-2 of 5.5 × 10−4 pppy, thus reinforcing the concern of sewage systems as a possible transmission pathway of SARS-CoV-2. These findings are helpful as an early health warning tool and in prioritizing upcoming risk management strategies, such as Emergency Response Plans (ERPs) for water and sanitation operators during the COVID-19 and future pandemics.
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•Viral loads and infectivity of SARS-CoV-2 in sewage affluent to WWTPs were estimated.•QMRA estimated the risk of infection for WWTP workers in three COVID-19 scenarios.•QMRA risk estimates will provide critical input for risk management decisions.•Wastewater operators can benefit from QMRA-informed Emergency Response Plans.
We evaluated epidemiologic and molecular characteristics of monkeypox virus (MPXV) infections sampled from 2 healthcare nurses. Five days after collecting samples from an infected patient, the nurses ...showed typical MPXV manifestations; quantitative PCR and whole-genome sequencing confirmed MPXV infection, most likely transmitted through contact with fomites.
COVID-19, para onde seguir? Spilki, Fernando Rosado
Revista Thema,
07/2020, Volume:
18, Issue:
ESPECIAL
Journal Article
Peer reviewed
Open access
“Nunca estivemos de fato tão longe uns dos outros, não pela quarentena, mas por um conjunto de convicções extremadas que já se apresentava desde bem antes de 2020. E nesse momento em que o caos já ...vinha instalado nas relações humanas, com reflexos evidentes na política e economia, chega o SARS-CoV-2, vírus causador da COVID-19, um pequeníssimo meteoro, produzindo abismos inimagináveis.“
With the arrival of coronavirus disease 2019 (COVID‐19) in Brazil in February 2020, several preventive measures were taken by the population aiming to avoid severe acute respiratory syndrome ...coronavirus 2 (SARS‐CoV‐2) infection including the use of masks, social distancing, and frequent hand washing then, these measures may have contributed to preventing infection also by other respiratory viruses. Our goal was to determine the frequencies of Influenza A and B viruses (FLUAV/FLUBV), human mastadenovirus C (HAdV‐C), Enterovirus 68 (EV‐68), and rhinovirus (RV) besides SARS‐CoV‐2 among hospitalized patients suspect of COVID‐19 with cases of acute respiratory disease syndrome (ARDS) in the period of March to December 2020 and to detect possible coinfections among them. Nucleic acid detection was performed using reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR) in respiratory samples using naso‐oropharyngeal swabs and bronchoalveolar lavage. A total of 418 samples of the 987 analyzed (42.3%) were positive for SARS‐CoV‐2, 16 (1.62%) samples were positive for FLUAV, no sample was positive for FLUBV or EV‐68, 67 (6.78%) samples were positive for HAdV‐C, 55 samples were positive for RV 1/2 (26.3%) and 37 for RV 2/2 (13.6%). Coinfections were also detected, including a triple coinfection with SARS‐CoV‐2, FLUAV, and HAdV‐C. In the present work, a very low frequency of FLUV was reported among hospitalized patients with ARDS compared to the past years, probably due to preventive measures taken to avoid COVID‐19 and the high influenza vaccination coverage in the region in which this study was performed.
Omicron has become the dominant variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since first reported in November 2021. From the initially detected Wuhan lineage, sublineages ...BA.2, BA.4, BA.5, BQ, XAG, and XBB have emerged over time and are dominant in many countries. Therefore, the aim is to evaluate which variants are circulating and the clinical characteristics of inpatients infected with the Omicron variant.
This retrospective cohort study selected hospitalized patients admitted with respiratory symptoms to a hospital in the state of Rio Grande do Sul, Brazil, between June and July 2022. SARS-CoV-2 results were analyzed together with clinical outcomes and vaccination status. A viral genome library was prepared and forwarded to the Illumina MiSeq Platform for sequencing.
In total, 37 genomes were sequenced. Concerning the Omicron sublineages, our study detected: BA.1 (21 K), BA.2 (21 L), BA.4 (22A), BA.5 (22B), BA.2.12.1 (22C), BQ.1 (22E), XBB (22F), and XAG recombinant. Omicron BA.5 (30%), BA.2 (19%), and BQ.1 (19%) were the most frequent sublineages, respectively. In total, 38% of patients present hypertension, and the most common symptoms were coughing (62%). Analyzing the COVID-19 vaccination, 30% of patients were fully vaccinated, 49% had a partial vaccination status, and 21% were unvaccinated (no dose).
BA.5 was the most prevalent sublineage in our study and surpassed the predominance of BA.2, as reported by the national genomic surveillance program. BQ.1 was diagnosed earlier in this study than it was officially reported in the state. Current data have demonstrated that the Omicron variant causes less severe infections, with the high rate of transmissibility and mutational landscape causing the rapid emergence of new sublineages.
Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand ...the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Esteio (Southern Brazil) using phylogenetics and phylodynamics inferences from 21 new genomes in global and regional context. Importantly, the case fatality rate (CFR) in Esteio (3.26%) is slightly higher compared to the Rio Grande do Sul (RS) state (2.56%) and the entire Brazil (2.74%).
We provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. Lineages containing this substitution must be subject of intense surveillance due to its association with immune evasion. We also found two epidemiologically-related clusters, including one from patients of the same neighborhood. Phylogenetics and phylodynamics analysis demonstrates multiple introductions of the Brazilian most prevalent lineages (B.1.1.33 and B.1.1.248) and the establishment of Brazilian lineages ignited from the Southeast to other Brazilian regions.
Our data show the value of correlating clinical, epidemiological and genomic information for the understanding of viral evolution and its spatial distribution over time. This is of paramount importance to better inform policy making strategies to fight COVID-19.
•Emergence, dispersion, and consolidation of the Delta variant in South Brazil.•Gamma variant was completely replaced by Delta variant in five months.•Most sequences generated were classified as ...AY.99.2, AY.99.2-like, and AY.101.
The emergence of Variants of Concern (VOC) presenting an unusual number of new mutations is one of the most remarkable features of SARS-CoV-2. The Delta variant, since its appearance, replaced the VOC Gamma, which was responsible for the major COVID-19 wave in Brazil. In this study, we performed a Delta whole-genome sequencing of 183 samples as part of a major genomic surveillance study performed since the beginning of the pandemic. Here, we showed an emergence, widespread dispersion and consolidation of the Delta variant in Rio Grande do Sul State, completely replacing the Gamma variant in a four to five months period. Performing the phylogenetic and phylodynamic analysis, the majority of the sequences generated herein were classified as AY.99.2, AY.99.2-like and AY.101. AY.99.2 Delta-related lineage has been widely reported in Brazil and in the Americas as well. Altogether, our findings provided a mutational profile of the sequences and presented high substitutions per site in the root-to-tip phylogenetic tree, corroborating studies that show the high mutational rate of SARS-CoV-2 over time.
The year 2020 was profoundly marked by the emergence and spread of SARS-CoV-2, causing COVID-19, which represents the greatest pandemic of the 21st century until now, and a major challenge for ...virologists in the scientific and medical communities. Increased numbers of SARS-CoV-2 infection all over the world imposed social and travel restrictions, including avoidance of face-to-face scientific meetings. Therefore, for the first time in history, the 2020 edition of the Brazilian Society of Virology (SBV) congress was totally online. Despite the challenge of the new format, the Brazilian society board and collaborators were successful in virtually congregating more than 921 attendees, which was the greatest SBV participant number ever reached. Seminal talks from prominent national and international researchers were presented every night, during a week, and included discussions about environmental, basic, animal, human, plant and invertebrate virology. A special roundtable debated exclusively new data and perspectives regarding COVID-19 by some of the greatest Brazilian virologists. Women scientists were very well represented in another special roundtable called "Young Women Inspiring Research", which was one of the most viewed and commented section during the meeting, given the extraordinary quality of the presented work. Finally, SBV offered the Helio Gelli Pereira award for one graduate and one undergraduate student, which has also been a fruitful collaboration between the society and
journal. The annual SBV meeting has, therefore, reached its goals to inspire young scientists, stimulate high-quality scientific discussion and to encourage global collaboration between virologists.
Adenoviruses (AdV) are related to respiratory and gastrointestinal diseases in animals and human beings. Their wide genetic diversity in water bodies and their resistance to environmental conditions ...allow the use of AdV as a reliable marker for detection of fecal contamination. In this work, the diversity of AdV along Belo Stream - in the city of Caxias do Sul, Rio Grande do Sul, Brazil - was evaluated. Samples were compared in both concentrated and unconcentrated forms. The identification of different AdV species was performed by amplifying a partial sequence of the DNA polymerase gene. AdV was detected in 24 out of 55 concentrated samples (43.6%) and the following species were identified: human adenovirus (HAdV) species C (4/55; 7.2%), D (6/55; 10.9%), E (2/55; 3.6%), and F (9/55; 16.3%). AdV related to other mammalian hosts, such as bovine adenovirus (1/55, 1.8%) and murine adenovirus (2/55, 3.6%), have also been identified; 23.6% (13/55) of the unconcentrated samples were positive, and identified as HAdV species C (6/55, 10.9%), D (1/55, 1.8%), and F (6/55, 10.9%). Results obtained evidenced the presence and the great diversity of AdV, mainly of human origin, circulating in Belo Stream. As expected, the concentration step performed helped to detect AdV in more samples.
Along the coastal zone of the State of São Paulo, Brazil, diffuse discharges that flow directly to tourist beaches are responsible for introducing various pathogens into recreational waters. The ...objective of this study was to analyze, for the first time, the presence of protozoa (Cryptosporidium ssp and Giardia ssp), as well as human mastadenoviruses (HAdV–species C and F) and other species of adenoviruses (AdV) in beach drainage channels of Enseada and Perequê, municipality of Guarujá, São Paulo, Brazil. Protozoa were not detected in any sample over the course of the 11‐month study. In relation to HAdVs, 100% (n = 22) of the water samples presented contamination by at least one type of virus (C, D, or F species), suggesting potential risks to the public health following recreational exposure of beach users to these waters.
Practitioner points
First report on the presence of human adenoviruses in urban drainage channels in the coast of São Paulo State, Brazil.
Urban surface water runoff is responsible for introducing human adenoviruses linked to disease outbreaks in areas of intense recreation.
Cryptosporidium oocysts and Giardia cysts were below the limit of detection for all analyzed samples.
However, all sites were positive for at least one of the viral species (HAdV–C, HAdV–D, or HAdV–F).
Viral loads found in the water were similar to those commonly found in the wastewater.
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