SARS-CoV-2 Spillback to Wild Coatis in Sylvatic-Urban Hotspot, Brazil.

We tested coatis (Nasua nasua) living in an urban park near a densely populated area of Brazil and found natural SARS-CoV-2 Zeta variant infections by using quantitative reverse transcription PCR, genomic sequencing, and serologic surveillance. We recommend a One Health strategy to improve surveillance of and response to COVID-19.

No molecular evidence for influenza A virus and coronavirus in bats belonging to the families Phyllostomidae, Vespertilionidae, and Molossidae in the state of São Paulo, Brazil.

This study aimed to evaluate, by molecular methods, the presence of influenza A virus (IAV) and coronavirus in non-hematophagous bats collected in the state of São Paulo, Brazil. Samples of lung tissue and small intestine from 105 bats belonging to three families (Phyllostomidae, Vespertilionidae, and Molossidae) were collected in 22 municipalities in the state of São Paulo. Genetic identification of bats species was performed by amplification and sequencing of a fragment of 710 bp of the mitochondrial COI gene. In the detection of IAV, genomes were performed by RT-PCR, aiming at the amplification of a 245-bp fragment of the IAV matrix (M) protein gene. For coronaviruses, two fragments of 602 and 440 bp corresponding to segments along the gene encoding the RNA-dependent RNA polymerase (RdRp) were targeted. The detection limit for each of the PCRs was also determined. All samples analyzed here were negative for both viruses, and the lower limit of detection of the PCRs for the amplification of influenza virus A and coronavirus was estimated at 3.5 × 103 and 4.59 genomic copies per microliter, respectively. Although bats have been shown to harbor a large number of pathogens, the results of the present study support the theory that virus circulation in bats in the wild often occurs at low viral loads and that our understanding of the complex infectious dynamics of these viruses in wild conditions is still limited.

Fast inactivation of coronavirus in filtering-facepiece respirators in a reflective cylindrical UV-C chamber.

Objective: We report on the development and characterization of a UV-C (λ  =  200 - 280 nm, λpeak = 254 nm) chamber designed for the rapid disinfection of N95 class filtering-facepiece respirators contaminated with SARS-CoV-2 coronaviruses. The device was evaluated against Betacoronavirus strain MHV-3 and its virucidal capacity was evaluated as a function of different applied UV-C doses (UV-C exposure times of 60 s, 120 s, 180 s, and 240 s) using two types of respirators geometry (shell and two-panel shapes, 3M 8801 H and 9920 H, respectively), at eight points of the respirators. Background: Most chemical disinfection methods are not recommended for N95 masks. UV-C light provided by UVGI lamps (254 nm) is an effective physical agent against viruses and bacteria due to direct photochemical harming effect on DNA/RNA, and can provide rapid disinfection for personal protective equipment such as N95/PFF2 masks. Results: The device reached a mean elimination rate of 99.9999% of MHV-3 inoculated into all the assessed different points on the tested PFF2 respirator models in a UV-C cycle of just 60 s. Statistical analysis performed through Person´s chi-square test showed no correlation between the viral infectivity reduction and the viral inoculation point (p = 0.512) and the tested respirator models (p = 0.556). However, a correlation was found between the exposure time and the viral infectivity reduction (p = 0.000*), between UV-C and no UV-C exposure. All the tested UV-C exposure times (60 s, 120 s, 180 s, and 240 s) provided the same reduction in infection rates. Therefore, 60 s was confirmed as the minimum exposure time to achieve a 99.9999% or 6 Log reduction in MHV-3 coronavirus infection rates in the PFF2 samples tested in the device. Conclusions: We conclude that the assessed UV-C chamber for the inactivation of MHV-3 coronavirus in N95/PFF2 standard masks can be a promising tool for effective and rapid disinfection of coronaviruses, including SARS-CoV-2 virus.

Virucidal PVP-Copper Salt Composites against Coronavirus Produced by Electrospinning and Electrospraying.

Electrospinning technology was used to produced polyvinylpyrrolidone (PVP)-copper salt composites with structural differences, and their virucidal activity against coronavirus was investigated. The solutions were prepared with 20, 13.3, 10, and 6.6% w/v PVP containing 3, 1.0, 0.6, and 0.2% w/v Cu (II), respectively. The rheological properties and electrical conductivity contributing to the formation of the morphologies of the composite materials were observed by scanning electron microscopy (SEM). SEM images revealed the formation of electrospun PVP-copper salt ultrafine composite fibers (0.80 ± 0.35 µm) and electrosprayed PVP-copper salt composite microparticles (1.50 ± 0.70 µm). Energy-dispersive X-ray spectroscopy (EDS) evidenced the incorporation of copper into the produced composite materials. IR spectra confirmed the chemical composition and showed an interaction of Cu (II) ions with oxygen in the PVP resonant ring. Virucidal composite fibers inactivated 99.999% of coronavirus within 5 min of contact time, with moderate cytotoxicity to L929 cells, whereas the virucidal composite microparticles presented with a virucidal efficiency of 99.999% within 1440 min of exposure, with low cytotoxicity to L929 cells (mouse fibroblast). This produced virucidal composite materials have the potential to be applied in respirators, personal protective equipment, self-cleaning surfaces, and to fabric coat personal protective equipment against SARS-CoV-2, viral outbreaks, or pandemics.

High genetic diversity of alphacoronaviruses in bat species (Mammalia: Chiroptera) from the Atlantic Forest in Brazil.

Bat coronaviruses (Bat-CoVs) represent around 35% of all virus genomes described in bats. Brazil has one of the highest mammal species diversity, with 181 species of bats described so far. However, few Bat-CoV surveillance programmes were carried out in the country. Thus, our aim was to jevaluate the Bat-CoV diversity in the Atlantic Forest, the second biome with the highest number of bat species in Brazil. We analysed 456 oral and rectal swabs and 22 tissue samples from Atlantic Forest bats, detecting Alphacoronavirus in 44 swab samples (9.6%) targeting the RdRp gene from seven different bat species, three of which have never been described as Bat-CoV hosts. Phylogenetic analysis of the amino acid (aa) sequences coding the RdRp gene grouped the sequences obtained in our study with Bat-CoV previously detected in identical or congeneric bat species, belonging to four subgenera, with high aa identity (over 90%). The RdRp gene was also detected in three tissue samples from Diphylla ecaudata and Sturnira lilium, and the partial S gene was successfully sequenced in five tissues and swab samples of D. ecaudata. The phylogenetic analysis based on the partial S gene obtained here grouped the sequence of D. ecaudata with CoV from Desmodus rotundus previously detected in Peru and Brazil, belonging to the Amalacovirus subgenus, with aa identity ranging from 73.6% to 88.8%. Our data reinforce the wide distribution of Coronaviruses in bats from Brazil and the novelty of three bats species as Bat-CoV hosts and the co-circulation of four Alphacoronavirus subgenera in Brazil.

Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution.

Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of previously unreported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: (i) the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution, and (ii) a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains.

Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil.

Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory; it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins; (ii) analyze them phylogenetically against global SARS-CoV-2 sequences; and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially São Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil.

Prompt Inactivation of Coronavirus Using a 280 nm Light-Emitting Diode Cluster Device.

Objective: We report on the development and characterization of a UV-C light-emitting diode (LED) 280 nm cluster prototype device designed for the rapid disinfection of SARS-CoV-2 coronaviruses. The device was evaluated against the Betacoronavirus mouse hepatitis virus-3 strain, and its virucidal capacity was probed as a function of different applied UV-C doses versus different situations concerning irradiation distances. Background: UV-C LEDs are light emitters that offer advantages over low-pressure mercury lamps, such as quasimonochromaticity, lower electrical power consumption, instant on/off with the instant full-power operation, unlimited on/off cycles for disinfection schemes, and a much longer lifetime operation, in addition to portability aspects, as well as UV-C LEDs do not contain heavy metal in its composition such as mercury, found in ultraviolet germicidal irradiation (UVGI) lamps. Results: This novel device reached a 99.999% elimination rate at a distance of 9 cm at all the tested irradiation times (dose dependence), demonstrating that it took only 30 sec to achieve this inactivation rate. Its virucidal effectivity in rapid virus inactivation was demonstrated. Conclusions: We conclude that the HHUVCS cluster device (λp = 280 nm) provides a rapid virucidal effect against the SARS-CoV-2 coronavirus. The current research should encourage further advances in UV-C LED-based devices designed for the inactivation of SARS-CoV-2 virus on surfaces, in air, and in liquids.

Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil

Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory;it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins;(ii) analyze them phylogenetically against global SARS-CoV-2 sequences;and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially São Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil.

Ultraviolet germicidal irradiation is effective against SARS-CoV-2 in contaminated makeup powder and lipstick.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is mainly transmitted by airborne droplets generated by infected individuals. Since this and many other pathogens are able to remain viable on inert surfaces for extended periods of time, contaminated surfaces play an important role in SARS-CoV-2 fomite transmission. Cosmetic products are destined to be applied on infection-sensitive sites, such as the lips and eyelids. Therefore, special biosafety precautions should be incorporated into the routine procedures of beauty parlors and shops. Indeed, innovative cosmetics companies are currently searching for disinfection protocols that ensure the customers' safety in makeup testing. Here, we propose an ultraviolet germicidal irradiation (UVGI) strategy that can be used to reduce the odds of COVID-19 fomite transmission by makeup testers. It is well-known that UVGI effectively inactivates pathogens on flat surfaces and clear fluids. However, ultraviolet-C (UVC) radiation at 254 nm penetrates poorly in turbid and porous materials, such as makeup and lipstick formulations. Thus, we investigated the virucidal effect of UVGI against SARS-CoV-2 deposited on such substrates and compared their performance to that of flat polystyrene surfaces, used as controls. Concentrated infectious SARS-CoV-2 inoculum (106 PFU/mL) deposited on lipstick and makeup powder was completely inactivated (>5log10 reduction) following UVC exposures at 1,260 mJ/cm2, while flat plastic surfaces required 10 times less exposure (126 mJ/cm2) to reach the same microbicidal performance. We conclude that UVGI comprises an effective disinfection strategy to promote biosafety for cosmetics testers. However, appropriate UVC dosimetry must be implemented to overcome inefficiencies caused by the optical properties of turbid materials in lipsticks and makeup powders.