RESUMO
Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over one thousand COVID-19 cases among residents and visitors. Most cases were fully vaccinated, many of whom were also symptomatic, prompting a comprehensive public health response, motivating changes to national masking recommendations, and raising questions about infection and transmission among vaccinated individuals. To characterize the outbreak and the viral population underlying it, we combined genomic and epidemiological data from 467 individuals, including 40% of known outbreak-associated cases. The Delta variant accounted for 99% of sequenced outbreak-associated cases. Phylogenetic analysis suggests over 40 sources of Delta in the dataset, with one responsible for a single cluster containing 83% of outbreak-associated genomes. This cluster was likely not the result of extensive spread at a single site, but rather transmission from a common source across multiple settings over a short time. Genomic and epidemiological data combined provide strong support for 25 transmission events from, including many between, fully vaccinated individuals; genomic data alone provides evidence for an additional 64. Together, genomic epidemiology provides a high-resolution picture of the Provincetown outbreak, revealing multiple cases of transmission of Delta from fully vaccinated individuals. However, despite its magnitude, the outbreak was restricted in its onward impact in MA and the US, likely due to high vaccination rates and a robust public health response.
RESUMO
SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.
RESUMO
BackgroundTransmission of COVID-19 from people without symptoms poses considerable challenges to public health containment measures. The distribution of viral loads in individuals with and without symptoms remains uncertain. Comprehensive cross-sectional screening of all individuals in a given setting provides an unbiased way to assess viral loads independent of symptoms, which informs transmission risks. COVID-19 cases initially peaked in Massachusetts in mid-April 2020 before declining through June, and congregate living facilities were particularly affected during this early surge. We performed a retrospective analysis of data from a large public health-directed outbreak response initiative that involved comprehensive screening within nursing homes and assisted living facilities in Massachusetts to compare nasopharyngeal (NP) viral loads (as measured by RT-PCR cycle threshold (Ct) levels) in residents and staff to inform our ability to detect SARS-CoV-2 in individuals with or without symptoms in the population. MethodsBetween April 9 and June 9, 2020, we tested NP swabs from 32,480 unique individuals comprising staff and residents of the majority of nursing homes and assisted living facilities in Massachusetts. Under the direction of the MA Department of Public Health (MDPH), symptomatology at the time of sampling and demographic information was provided by each facility for each individual to facilitate reporting to health officials. NP swabs were collected, RNA extracted, and SARS-CoV-2 testing performed using quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). ResultsThe nursing home and assisted living facilities resident cohort (N =16,966) was 65% female with a mean age of 82 years (SD 13 yrs). The staff cohort (N = 15,514) was 76% female with a median age of 45 (SD 15 yrs). A total 2654 residents (15.5%) and 624 staff (4.1%) tested positive for SARS-CoV-2. 12.7% of residents and 3.7% of staff without symptoms tested positive for SARS-CoV-2, compared to 53.1% of residents and 18.2% of staff with symptoms. Of the individuals who tested positive, 70.8% of residents and 92.4% of staff lacked symptoms at the time of testing. In aggregate, the distributions of Cts for viral probes used in the qRT-PCR assay were very similar, with a statistically but not meaningfully different mean ({Delta}Ct 0.71 cycles, p = 0.006) and a similar range (12-38 cycles), between populations with and without symptoms over the entire time period, across all sub-categories examined (age, race, ethnicity, sex, resident/staff). Importantly, the Ct mean values and range were indistinguishable between the populations by symptom class during the peak of the outbreak in Massachusetts, with a Ct gap appearing only later in the survey period, reaching >3 cycles (p [≤] 0.001) for facilities sampled during the last two weeks of the study. ConclusionsIn a large cohort of individuals screened for SARS-CoV-2 by qRT-PCR, we found strikingly similar distributions of viral load in patients with or without symptoms at the time of testing during the local peak of the epidemic; as the epidemic waned, individuals without symptoms at the time of testing had lower viral loads. The size of the study population, including both staff and residents spanning a wide range of ages, provides a comprehensive cross-sectional point prevalence measurement of viral burden in a study spanning 2 months. Because the distributions of viral loads in infected individuals irrespective of symptomatology are very similar, existing testing modalities that have been validated for detection of SARS-CoV-2 RNA in symptomatic patients should perform similarly in individuals without symptoms at the time of testing.
