Genomic Surveillance of SARS-CoV-2: Study of Cases Intradomiciliary Infection in Brazilian Amazonia

Abstract

Studies have shown that the family environment is very favorable for SARSCOV- 2 transmission, making family groups susceptible to intra-household infection because they maintain direct contact with an infected person. We screened a cohort of 416 individuals who tested positive for SARS-CoV-2 from June to October 2021 for intradomiciliary infection. Twenty-two families with an average of 2 to 4 members were located in 12 municipalities in the state of Rondônia. Nasopharyngeal samples were collected, extracted using the QIAamp viral RNA mini kit and genomic sequencing was performed using samples with ct<25 by Illumina platform, the sequences were analyzed for phylogeny, mutations, and lineages. Among the samples analyzed 72.72% matched for VOC Delta and 27.27% for Gamma variant. The median viral load for both variants was 6.95. The main symptoms presented were cough, headache, and fever. No hospitalizations or deaths were reported. We observed that among the positive individuals, 24% were immunized with the 1st and 2nd dose, 40% were partially immunized, and 36% were not immunized. For each strain, subvariants were identified, being P.1.4 and P.1.14 for the Gamma variant and AY.43, AY.99.2 and AY.122 for Delta. The mutations mostly behaved as lineage-defining, with only eight families showing point mutations. In conclusion, it was observed that despite the low adherence to immunization, household cases were equally expressed in viral characteristics and in the low rate of hospital evolution for COVID-19, and this may be a factor associated with the permanence of infection in an isolated family environment.