IMPORTANCEThere is an urgent need to assess the feasibility of COVID-19 surveillance measures in educational settings. OBJECTIVETo assess whether young children can feasibly self-collect SARS-CoV-2 samples for surveillance testing over the course of an academic year.

Background The limited variation observed among SARS-CoV-2 consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference. Methods We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from four prospective studies with household membership data, a proxy for transmission linkage. Results Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 SNPs; range, 0-40). Most (83.1%, 255/307) samples harbored at least one intrahost single nucleotide variant (iSNV; median: 117; IQR: 17-208), above a minor allele frequency threshold of 0.2%. Pairs in the same household shared significantly more iSNVs (mean: 1.20 iSNVs; 95% CI: 1.02-1.39) than did pairs in different households infected with the same viral clade (mean: 0.31 iSNVs; 95% CI: 0.28-0.34), a signal that decreases with increasingly stringent minor allele frequency thresholds. The number of shared iSNVs was significantly associated with an increased odds of household membership (aOR: 1.35; 95% CI: 1.23 -1.49). However, the poor concordance of iSNVs detected across sequencing replicates (24.8% and 35.0% above a 0.2% and 1% threshold), confirms technical concerns that current sequencing and bioinformatic workflows do not consistently recover low frequency within-host variants. Conclusions Shared within-host variation may augment the information in consensus sequences for predicting transmission linkages. Improving sensitivity and specificity of within-host variant identification will improve the informativeness of within-host variation.

Background In order to mitigate the spread of SARS-CoV-2 and the COVID-19 pandemic, public health officials have recommended self-isolation, self-quarantine of exposed household contacts (HHC), and mask use to limit viral spread within households and communities. While household transmission of SARS-CoV-2 is common, risk factors for HHC transmission are poorly understood. Methods In this prospective cohort study, we enrolled 37 households with at least one reverse transcription polymerase chain reaction-confirmed (RT-PCR) COVID-19 index case from March 2020 - March 2021, in order to calculate secondary attack rates (SAR) and define risk factors for secondary infections. Participants were tested daily for SARS-CoV-2 via RT-PCR, using self-collected lower nasal samples. Households were followed until all members tested negative for seven consecutive days. We collected demographics, medical conditions, relationship to index case, and socioeconomic indicators. Subgroup data analysis was conducted and stratified by positivity status. Results Of 99 enrolled participants, 37 were index cases and 62 were household contacts (HHC), of whom 25 HHC were infected (40.3%). Secondary attack rate (SAR) was highest among adults caring for a parent (n=4/4, 100%) and parents of index cases (5/10, 50%). Households whose income came from service work had greater risk of transmission compared to households whose primary income was technology (n=5/7; 71.4% vs 3/8; 37.5% respectively). Pediatric contacts were at lower risk of infection when compared to adult contacts (n=5/18, 27.8% vs n=20/44, 45.5% respectively). Conclusion This study suggests that household transmission represents a key source of community-based infection of SARS-CoV-2. Allocating resources for education/training regarding prevention among infected individuals and their close contacts will be critical for control of future outbreaks of SARS-CoV-2. Disclosures All Authors: No reported disclosures

Background: The limited variation observed among SARS-CoV-2 consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference. Methods: We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples from four prospective studies and combined sequence data with household membership data, a proxy for transmission linkage. Results: Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 SNPs; range, 0-40). Most (83.1%, 255/307) samples harbored at least one intrahost single nucleotide variant (iSNV; median: 117; IQR: 17-208), when applying a liberal minor allele frequency of 0.5% and prior to filtering. A mean of 15.4% of within-host iSNVs were recovered one day later. Pairs in the same household shared significantly more iSNVs (mean: 1.20 iSNVs; 95% CI: 1.02-1.39) than did pairs in different households infected with the same viral clade (mean: 0.31 iSNVs; 95% CI: 0.28-0.34), a signal that increases with increasingly liberal thresholds. Conclusions: Although only a subset of within-host variation is consistently shared across likely transmission pairs, shared iSNVs may augment the information in consensus sequences for predicting transmission linkages.

Background Breath samples collected from patients infected with respiratory viruses are necessary for viral detection using breath analyzer devices. Given the highly transmissible nature of many of these illnesses, sample collection requires a multi-layered approach to ensure the safety of the research staff responsible for obtaining and transporting these samples. Our team established a protocol to minimize exposure to and transmission of COVID-19 when collecting breath samples. Methods We collected breath samples from 64 participants, of which 31 (48.4%) were positive for SARS-CoV-2 at the time of their visit. Before we started sample collection, biosafety inspection was conducted. We used a five-pronged approach to enhance safety and minimize transmission. First, we collected specimens in an outdoor space while the patients were seated in their vehicles. Second, we used a disposable mouthpiece and a one-way valve to fill a 1L TEDLAR bag. Third, patients were instructed to close the valve tightly before returning it to the staff. Fourth, we placed the bag in secondary containers which were placed in tertiary containers to minimize any contact with aerosols in the TEDLAR bag. In the last step, we placed a portable HEPA filter near the indoor sample processing unit to minimize exposure and air contamination with the samples. Study staff donned all forms of necessary personal protective equipment, including gloves, gowns, N95 respirators, and protective eyewear, during sample collection and transportation. Results A total of 64 breath samples were collected from 64 adult participants from February to March 2022. A total of 30 participants (46.9%) were within 7 days of their initial diagnosis. All participants were able to successfully collect samples without additional resources or attempts. All samples were able to be transported successfully into the lab. No staff contracted COVID-19 during the study period. Conclusion Layered safety measures, including protective equipment, physical barriers, and well-ventilated environments mitigated the risks associated with breath sample collections from infected participants. Disclosures Yvonne A. Maldonado, MD, Pfizer: Grant/Research Support|Pfizer: Member, DSMB, Pfizer Meningococcal Vaccine clinical trial.