Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2.

The emergence of SARS-CoV-2 and the subsequent pandemic have prompted extensive diagnostic and clinical efforts to mitigate viral spread. However, these strategies have largely overlooked the presence of other respiratory viruses. Acute respiratory diseases in pediatric patients can be caused by a diverse range of viral agents, and metagenomics represents a powerful tool for their characterization. This study aimed to investigate the viral abundance in pediatric patients with acute respiratory symptoms who tested negative for SARS-CoV-2 during the Omicron pandemic wave. To achieve this, viral metagenomics and next-generation sequencing were employed on 96 nasopharyngeal swab samples, which were organized into 12 pools, with each pool consisting of eight individual samples. Metagenomic analysis revealed that the most prevalent viruses associated with acute disease in pediatric patients were respiratory syncytial virus (detected in all pools) and enteroviruses, which are known to cause significant morbidity and mortality in children. Additionally, clinically significant viruses such as mumps orthorubulavirus, human metapneumovirus, influenza A, and a wide array of human herpesviruses (1, 3-7) were identified. These findings highlight the extensive potential of viral metagenomics in identifying viruses other than SARS-CoV-2 that contribute to acute infections in children. Consequently, this methodology should garner clinical attention in terms of differential diagnosis and the development of public policies to address such conditions in the global pediatric population.

Merkel cell polyomavirus (MCPyV) DNA prevalence in Brazilian blood donors.

Merkel cell polyomavirus (MCPyV) is an oncogenic virus that has been etiologically linked to Merkel cell carcinoma. Low levels of MCPyV DNA have been detected in blood donors with unclear impact on transfusion. The prevalence of MCPyV DNA in Brazilian blood donors is unclear. Therefore, the objective of this study was to evaluate the MCPyV DNA prevalence among Brazilian blood donors. We examined the presence of MCPyV DNA by real-time PCR (qPCR) in a total of 450 serum samples obtained from blood donors from three Brazilian regions (North, Central-West and South). The overall estimated MCPyV DNA prevalence was 1.1% (CI = 95%, 0.16-2.06%). Divided by region, in North Brazil (city of Macapa, state of Amapá) and South Brazil (city of Santa Maria, state of Rio Grande do Sul), the MCPyV prevalence was the same: 1.33% (CI = 95%, range 0.0-3.14%). In Central-West Brazil (city of Brasilia), the MCPyV prevalence was 0.6% (CI = 95%, 0.0-1.96%). All MCPyV positive samples showed a high cycle threshold (median Ct = 35.5), most probably related to the low viral load. More studies are necessary to unveil the impact of this oncogenic virus on transfusion medicine and if such exists, especially in regards of its infectivity and transmission potential.

Molecular identification of the emerging Human Gemykibivirus-2 (HuGkV-2) among Brazilian blood donors.

Human gemykibivirus-2 (HuGkV-2) belonging to the Gemykibivirus genus (Genomoviridae family) is an emerging DNA virus which has been described as a component of the virome of a wide variety of samples including clinical ones. So far, the HuGkV-2 DNA prevalence in the human population as well as its clinical impact are completely unknown. The objective of this study was to investigate the HuGkV-2 DNA prevalence among Brazilian healthy blood donors from three different geographic regions. A total of 450 blood samples were screened for HuGkV-2 DNA (150 samples were from the Brazilian Amazon, 150 from Midwest Brazil and 150 from South Brazil). The overall HuGkV-2 DNA prevalence was 7.8 %. Considering the examined regions, the highest prevalence was observed in the Brazilian Amazon (city of Macapa, state of Amapa), 15.3 %, followed by the Midwest Brazil (city of Brasilia, Federal District) (6.0 %) and South Brazil (city of Santa Maria, Rio Grande do Sul State) (2.0 %). This study gives preliminary insights on the molecular prevalence of HuGkV-2 DNA among Brazilian blood donors, highlighting that the highest HuGkV-2 prevalence was recorded in the Brazilian Amazon. However, more studies regarding the prevalence, transmission routes and any possible clinical effects appear to be crucial in order to understand the impact of this emerging viral agent.

Molecular identification of the emerging human Gemykibivirus-2 (HuGkV-2) among Brazilian blood donors

Human gemykibivirus-2 (HuGkV-2) belonging to the Gemykibivirus genus (Genomoviridae family) is an emerging DNA virus which has been described as a component of the virome of a wide variety of samples including clinical ones. So far, the HuGkV-2 DNA prevalence in the human population as well as its clinical impact are completely unknown. The objective of this study was to investigate the HuGkV-2 DNA prevalence among Brazilian healthy blood donors from three different geographic regions. A total of 450 blood samples were screened for HuGkV-2 DNA (150 samples were from the Brazilian Amazon, 150 from Midwest Brazil and 150 from South Brazil). The overall HuGkV-2 DNA prevalence was 7.8 %. Considering the examined regions, the highest prevalence was observed in the Brazilian Amazon (city of Macapa, state of Amapa), 15.3 %, followed by the Midwest Brazil (city of Brasilia, Federal District) (6.0 %) and South Brazil (city of Santa Maria, Rio Grande do Sul State) (2.0 %). This study gives preliminary insights on the molecular prevalence of HuGkV-2 DNA among Brazilian blood donors, highlighting that the highest HuGkV-2 prevalence was recorded in the Brazilian Amazon. However, more studies regarding the prevalence, transmission routes and any possible clinical effects appear to be crucial in order to understand the impact of this emerging viral agent.

Metavirome composition of Brazilian blood donors positive for the routinely tested blood-borne infections.

Viral metagenomics is widely applied to characterize emerging viral pathogens but it can also reveal the virome composition in health and disease. The evaluation of the virome in healthy blood donors can provide important knowledge on possible transfusion threats. Currently, there is still a paucity of information regarding the virome of blood donors who test positive for routinely tested blood-borne infections. Such analysis may reveal co-infections which in turn appear to be crucial for transfusion medicine and for patient management. The aim of this study was to evaluate the metavirome in blood donors who tested positive for routinely tested blood-borne infections, the information for which is important for transfusion medicine and blood donor management. For this purpose, we analyzed 18 blood donations obtained from HIV and HBV-infected blood donors from the Brazilian Amazon (Amapa state) and 11 HIV, HBV, HCV, syphilis and Chagas disease - positive blood donations obtained from blood donors sampled in South Brazil (Rio Grande do Sul state). We additionally included a control group of 20 blood donors obtained from Southeast Brazil (State of São Paulo). Samples were assembled in pools and sequenced by the Illumina NovaSeq 6000 platform. To link a given virus with geographic region or type of blood donor, we performed supervised machine learning classification (fingerprint analysis). The virome of both locations was predominantly composed of commensal viruses. However, in HBV-infected blood donors from the Brazilian Amazon, the Human Pegivirus-1 (HPgV-1) reads were prevailing, while in HIV-infected donors from the same location, the torque teno virus (TTV) reads expressive abundance. In blood donors from South Brazil, the most abundant reads were classified as Human endogenous retrovirus K (HERV-K). Putative emerging viruses like the Human gemykibivirus-2 (HuGkV-2) were exclusively identified in samples from the Brazilian Amazon. The fingerprint analysis demonstrated that the HERV-K, TTV-7, 13, and 15 were statistically important for the infected blood donors, while TTV-5, 12 and 20 were linked to geographic localization. Our study revealed differences in the viral composition among blood donors who tested positive for routinely tested blood-borne infections from two different Brazilian regions and indicated the presence of putative emerging viruses in samples obtained from the Amazon. Together our results show that the presence of specific commensal viruses may be related donor infection status but additional investigations including larger study groups and samples from other Brazilian regions are needed to confirm this hypothesis.