ABSTRACT
Background. International travel facilitates SARS-CoV-2 spread globally. Early detection of variants among arriving international travelers could provide viral information about introduction of variants with differing infectivity, virulence, and vaccine effectiveness, enabling adjustments to treatment and prevention strategies. We initiated a genomic surveillance program at 4 US airports to detect SARS-CoV-2 variants among arriving international travelers. Methods. Between November 29, 2021-April 24, 2022, we enrolled arriving air travelers (>=18 years) from flights originating in 16 countries on 5 continents. At four airports, participants self-collected nasal swab samples that were pooled with 5-25 other samples by country of flight. Participants were also given a take-home saliva collection kit;saliva was collected 3-5 days after arrival and mailed back to the laboratory. SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) was performed on all samples at the laboratory. Positives underwent whole genome sequencing. Demographic, clinical, and travel information was collected. Results. We enrolled 28,656 travelers;median age was 42 years (interquartile range 31-55), 48% were female, and 99.4% self-reported COVID-19 vaccination. Overall, 19%(504/2,666) of pooled and 7.5%(285/3804) of individual samples were positive for SARS-CoV-2. Highest pool positivity of 46% occurred during January 3-10, 2022 (Figure 1).Omicron variant accounted for 97%of sequences (Figure 2).We detected the earliest reporting of Omicron sub-lineages BA.2 and BA.3 (7 and 43 days earlier than reported elsewhere) in the United States and North America, respectively. During April 4-18, we detected an increasing trend of pool positivity among travelers on South African flights, detecting one of the first US-reported BA.4 sub-lineages consistent with early surge of cases in South Africa. Weekly pooled positivity for travelers on South African flights aligned with World Health Organization (WHO)-reported 7-day COVID-19 incidence rates over the same period (Figure 3). ] Conclusion. This genomic sequencing surveillance platform is a model for traveler-based SARS-CoV-2 genomic surveillance that can be used as an early warning system to detect future outbreaks and pandemics. (Figure Presented).
ABSTRACT
This report focuses on the emergence of the B.1.1.7 variant in the United States. As of 12 January, 2021, neither the B.1.351 nor the P.1 variants have been detected in the United States. For information about emerging SARS-CoV-2 variants of concern, CDC maintains a webpage dedicated to providing information on emerging SARS-CoV-2 variants. The B.1.1.7 variant has a mutation in the S protein that affects the binding domain of the receptor. It also has 13 other lineage-defining variants that are related to the S protein. These variants, which include a deletion at position 69 and 70, have been known to cause S-gene target failure. Multiple lines of evidence show that B.1.1.7 is a more efficiently transmitted variant of SARS-CoV-2 than other variants. In the UK, infections with this variant were more common than those with other variants. The potential increase in the number of cases of B.1.1.7 in the U.S. could affect the trajectory of the pandemic. A simple two-variant compartmental model has been developed to model this phenomenon. The potential impact of vaccinations was simulated assuming that 1 million doses were administered each day starting in 2021. It was estimated that 95% immunity was achieved 14 to 30 days after receiving 2 doses, and although B.1.1.7 is still the dominant strain, its transmission was significantly reduced after becoming the dominant variant. Currently, there is no evidence that the COVID-19 variants cause better clinical outcomes than the SARS-CoV-2 strains. However, a higher transmission rate increases the number of patients requiring hospitalisation, which could result in more deaths. The experiences of the UK and the B.1.1.7 variant illustrate the importance of having a coordinated and comprehensive approach to control the spread of this highly contagious variant. This approach involves the use of both mitigation and vaccination measures. The increased transmissibility of B.1.1.7 warrants the implementation of robust public health strategies to minimize its impact and prevent further spread. Data from the Centers for Disease Control and Prevention show that increasing the use of effective mitigation measures, such as vaccinations, is critical to curbing the spread of the disease.