No abstract

Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10 . Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses.

Case Report A 26‐year‐old woman with sickle cell disease (SCD) on chronic transfusion therapy complained of severe arthralgia, myalgia, abdominal pain, headache, and fever 24 hours after transfusion of a red blood cells (RBCs). Dengue virus (DENV) infection was suspected and the patient was hospitalized for clinical support and RBC transfusion, to lower the hemoglobin S to less than 30%. The patientʼs clinical condition improved approximately 8 days after the onset of symptoms. Results DENV type 2 (DENV‐2) TaqMan real‐time polymerase chain reaction was negative in the patient's pretransfusion sample while the posttransfusion sample was positive (Ct, 27.8), suggesting a high viral load and an acute infection. To investigate DENV transfusion transmission (TT‐DENV) the stored donor serum was tested and was also positive (Ct, 25.8). Molecular typing confirmed the presence of DENV‐2. The phylogenetic analysis of the DENV‐2 strains obtained from both donor and patient samples were classified as the Southeast Asia‐American genotype (Genotype III) and demonstrated 100% genomic identity, indicating TT‐DENV. Conclusion This is the first description of TT‐DENV in a SCD patient. A presumed high viral load in the transfused RBC unit probably determined the early clinical manifestation. In endemic regions dengue fever should be considered as differential diagnosis in SCD patients with fever and acute pain crisis, mainly during DENV outbreaks.

To metagenomically analyse blood units originating from the Brazilian Amazon and positive for parenterally transmitted infections (human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-lymphotropic virus (HTLV), Chagas disease or syphilis). Methods: Twenty plasma samples (35% HBV-positive, 10% HIV-positive, 10% HCV-positive, 20% positive for syphilis, 20% for Chagas disease, and 5% for HTLV) assembled in pools were analysed by metagenomic next-generation sequencing. The obtained raw sequencing data were submitted to a bioinformatic pipeline set up for identification of emerging viruses. The viral reads of interest were phylogenetically analysed and confirmed by PCR in the individual samples. Results: The metagenomic analysis identified contigs belonging to the emerging human Gemykibivirus-2 (HuGkV-2) in two pools. The HuGkV-1 phylogeny demonstrated that the Amazonian isolate formed a separate cluster with other HuGkV-2 strains obtained from human hosts. The PCR confirmation detected HuGkV-1 DNA in three individual samples (15%). Conclusions: HuGkV-2 is an emerging virus with unknown clinical impact. The detection of HuGkV-2 DNA in blood donations positive for parenterally transmitted infections showed that HuGkV-2 can be considered as an opportunistic viral agent with a hypothetic parenteral transmission route.