Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of selection along a transmission chain. While increased force of infection, receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here we compare the transmission bottleneck of non-VOC SARS-CoV-2 lineages to those of Alpha, Delta, and Omicron. We sequenced viruses from 168 individuals in 65 households. Most virus populations had 0–1 single nucleotide variants (iSNV). From 64 transmission pairs with detectable iSNV, we identify a per clade bottleneck of 1 (95% CI 1–1) for Alpha, Delta, and Omicron and 2 (95% CI 2–2) for non-VOC. These tight bottlenecks reflect the low diversity at the time of transmission, which may be more pronounced in rapidly transmissible variants. Tight bottlenecks will limit the development of highly mutated VOC in transmission chains, adding to the evidence that selection over prolonged infections may drive their evolution.

Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of natural selection along a transmission chain. Many viruses exhibit tight bottlenecks, and studies of early SARS-CoV-2 lineages identified a bottleneck of 1-3 infectious virions. While increased force of infection, host receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here, we compare the transmission bottleneck of non-variant-of-concern (non-VOC) SARS-CoV-2 lineages to those of the Alpha, Delta, and Omicron variants. We sequenced viruses from 168 individuals in 65 multiply infected households in duplicate to high depth of coverage. In 110 specimens collected close to the time of transmission, within-host diversity was extremely low. At a 2% frequency threshold, 51% had no intrahost single nucleotide variants (iSNV), and 42% had 1-2 iSNV. In 64 possible transmission pairs with detectable iSNV, we identified a bottleneck of 1 infectious virion (95% CI 1-1) for Alpha, Delta, and Omicron lineages and 2 (95% CI 2-2) in non-VOC lineages. The latter was driven by a single iSNV shared in one non-VOC household. The tight transmission bottleneck in SARS-CoV-2 is due to low genetic diversity at the time of transmission, a relationship that may be more pronounced in rapidly transmissible variants. The tight bottlenecks identified here will limit the development of highly mutated VOC in typical transmission chains, adding to the evidence that selection over prolonged infections in immunocompromised patients may drive their evolution.

Background: Approximately two-thirds of children aged <5 years receive out-of-home child care. Childcare attendees have an increased risk of infections compared to children not in childcare settings, possibly due to their close contact in a shared environment. As multidrug-resistant organisms (MDROs) increasingly move from healthcare-associated to community settings, childcare can provide a venue for further transmission of these pathogens. Our objective was to evaluate the bioburden of pathogens present on fomites in childcare centers and how surface contamination changes over time. Methods: The study was conducted in the single-room play area of an Ypsilanti, Michigan, childcare center caring for children aged 3–5 years. Polyester swabs were used to collect surface samples from 16 locations in the room, including (1) laminate, wood and plastic tabletops and furniture; (2) a stainless steel sink and adjacent plastic trash bin; and (3) wood, metal and plastic toys. A water sample was also collected at a 17th site. Samples were collected twice weekly for 5 of 6 weeks, followed by 1 additional collection (September–October 2019). Tryptic soy agar was used for standard plate counts and selective media were used to identify methicillin-resistant Staphylococcus aureus (MRSA), Vvancomycin-resistant Enterococcus (VRE), and extended-spectrum β-lactamase (ESBL)–producing Enterobacteriaceae. Single-plex RT-PCR was used to detect norovirus and adenovirus. Results: Among 175 samples collected on 11 days, MRSA and ESBL-producing Enterobacteriaceae were detected from 10.3% (18 of 175) and 8.0% (14 of 175), respectively, of environmental specimens. No specimens were positive for VRE or norovirus. Adenovirus was detected in 20 of 175 specimens (11.4%). Median bioburden by site ranged from 85 CFU/mL to 2,510 CFU/mL. The highest median bioburden was observed at the sink (2,510 CFU/mL), followed by the plastic building block table (1,620 CFU/mL), the small wood blocks (1,565 CFU/mL) and water from a water play area and an adjacent tabletop (1,260 and 1,100 CFU/mL respectively). The highest single day bioburden was 273,000 CFU/mL at the sink. Conclusion: The presence of MDROs on childcare center fomites raised concern for exposure to these pathogens among vulnerable populations. More study is needed to determine the degree to which these contaminated fomites drive transmission between children. We found the highest bioburdens on sites where children played or washed with water, identifying potential targets for more frequent cleaning.Funding: NoneDisclosures: Emily T. Martin reports a consulting from Pfizer.

BackgroundOut-of-home child care (CC) is a risk factor for viral acute respiratory infection (ARI) in young children. Little is known, however, about differences in frequencies of viral infection between CC children and those cared for exclusively at home.MethodsUsing surveillance data from the HIVE household cohort in southeast Michigan from 2014–2018 (4 seasons), we analyzed 1022 illness cases from 354 children aged 0–6 years. Age groups were dichotomized as infants (aged <2 years) and toddlers/preschoolers (aged 2–6 years). Households were prospectively enrolled and nasal respiratory swabs were collected from children upon report of acute illness symptoms. We used real-time RT–PCR to test for 18 respiratory viruses.ResultsWe detected at least one virus in 855 illness cases (83% of all illnesses reported). Age at first illness onset in all four seasons was significantly younger among CC children than homecare children (P < 0.001) across all 4 years (average difference = 1.25 years). CC children <2 years had slightly lower odds of viral detection during illness (OR = 0.89, 95% CI [0.49, 1.61]) but higher odds at ages 2–6y (1.07 [0.65, 1.76]); neither was statistically significant. Neither CC nor homecare children were significantly more or less at risk for any particular pathogen—expect for rhinovirus in the <2-year group, where odds of rhinovirus infection were 58% lower (OR = 0.42) in CC children compared with homecare counterparts (95% CI, 0.21–0.83). Conversely, CC attendees under 3 more frequently had influenza, RSV, hMPV, parainfluenza, and coronavirus; however, none of these associations were significant. Odds of coinfection (> 1 virus detected) were higher among CC children, but not significant (OR = 1.4 [0.63, 2.96] and 1.2 [0.77, 1.88] in <2 year and 2–6 year age groups, respectively). Among all children <7 year, the mean number of pathogens detected was not different between CC and homecare individuals (1.20 vs. 1.23, P = 0.16).ConclusionAs expected, results indicated that CC attendees aged 0–6y experienced illness episodes earlier in life compared with homecare children. Our analysis also indicated that, compared with children cared for at home, CC children were less at risk for rhinovirus infection when young but could potentially be at higher risk for viruses of greater clinical concern.Disclosures All authors: No reported disclosures.