The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.

The objective of this study was to evaluate the immunoglobulin G (IgG) absorption by Santa Ines lambs under two colostrum management systems usually used by producers. Twenty-seven Santa Ines newborn lambs received two meals of 250 ml of bovine colostrum from Holstein cows (BC group) or ovine colostrum from Santa Ines ewes (OC group) at 0 and 6 h of life. Pools of BC and OC were analyzed by radial immunodiffusion to quantify IgG. Results are expressed as least-square means and standard errors of mean (means ± s.e.m.). The concentration of IgG in bovine and ovine pools averaged 115.7 ± 20.5 and 48.1 ± 5.0 mg/ml, respectively, levels of concentration found in similar regular colostrum managements. The efficiency of IgG absorption was evaluated under two aspects, maximum apparent efficiency of absorption and total apparent efficiency of absorption (AEAmax and AEAtotal, respectively). The AEAmax was calculated taking into account the mass of IgG ingested just in the first meal of colostrum at birth and the serum IgG concentration at 6 h while the AEAtotal took into account the serum IgG concentration at 24 h of life that reflects the first colostrum offered at birth and the second meal at 6 h. The IgG and apparent efficiency of absorption results were transformed into the square root and log base 10, respectively, and were presented as geometric least-square means. In BC, lower (P < 0.05) AEAmax and AEAtotal were verified (14.2% and 15.6%, respectively), in relation to OC (23.6% and 24.4%, respectively). Serum IgG concentrations at 24 h were significantly higher (P < 0.05) in BC (31.4 mg/ml, respectively) compared with OC (22.2 mg/ml, respectively). The results in this study confirm that there is a limitation to the process of IgG absorption by the enterocytes of newborn lambs, which determined a nonlinear behavior of passive immunity acquisition. Similar values of AEAmax and AEAtotal for the two sources of colostrum reveal that the process of IgG absorption from the first and second meals during the first 6 h of life did not change and indicates that the ingestion of a second feeding of quality colostrum can enhance the acquisition of immune protection of newborn lambs.

Bovine colostrum (BC) has been used for nutraceutical purposes for animals and humans. Bovine colostrum is a complex heterogeneous product and its antimicrobial activity, antioxidant potential, and growth factors can vary depending on age and species of the cow as well as their environment. Bovine colostrum preparation in skimmed or whey fractions can also alter properties of BC. Our goal was to compare cumulative anti-inflammatory, antioxidant, and adipogenic properties of natural (whole) versus whey BC. We compared properties of whole and whey BC in 3T3-L1 preadipocytes permanently transfected with reporters responding to changes in inflammatory (NfκbRE/green fluorescent protein), anti-inflammatory (Nrf2/YFP), and adipogenic (Fabp4/cyan fluorescent protein) status in cells. Interleukin-6 secretion in these cells was measured by ELISA. Whole and whey BC induce IL-6 secretion from 3T3-L1 fibroblasts; however, whey preparation stimulated less IL-6 secretion. Cumulative inflammatory nuclear factor (NF)κB activation in the presence of lipopolysaccharide was reduced by both whole (-27%) and whey BC (-22%) compared with lipopolysaccharide-treated cells (100%). Treatment with whole BC was more effective in the reduction of NFκB activation compared with whey BC and occurred in a dose-dependent manner. In consonance with decreased NFκB activation, the Nrf2 promoter activity was also reduced in response to whole (-27%) and whey (-13%) treatments compared with nontreated cells (100%). Whole and whey BC suppressed adipogenesis, measured as induction of Fabp4, by -27 and -13%, respectively, compared with nontreated 3T3-L1 fibroblasts (100%). Our results showed distinct differences in properties of whey and whole BC that could be used to attain reduced adipogenic or cumulative inflammatory responses.