A repeat pattern of founder events for SARS-CoV-2 variants in Alaska (preprint)

Alaska is a unique US state because of its large size, geographically disparate population density, and physical distance from the contiguous United States. Here, we describe a pattern of SARS-CoV-2 variant emergence across Alaska reflective of these differences. Using genomic data, we found that in Alaska the Omicron sublineage BA.2.3 overtook BA.1.1 by the week of 2022-02-27, reaching 48.5% of sequenced cases. On the contrary in the contiguous United States, BA.1.1 dominated cases for longer, eventually being displaced by BA.2 sublineages other than BA.2.3. BA.2.3 only reached a prevalence of 10.9% in the contiguous United States. Using phylogenetics, we found evidence of potential origins of the two major clades of BA.2.3 in Alaska and with logistic regression estimated how it emerged and spread throughout the state. The combined evidence is suggestive of founder events in Alaska and is reflective of how Alaskas unique dynamics influence the emergence of SARS-CoV-2 variants.

Founder effect contributes to the unique pattern of SARS-CoV-2 variant B.1.1.519 emergence in Alaska (preprint)

Alaska is the largest geographic state in the United States with the lowest population density and a mix of urban centers and isolated rural communities. The differences in population dynamics in Alaska from the contiguous United States may have contributed to a unique pattern of emergence and spread of SARS-CoV-2 variants observed in early 2021. Here we examined 2,323 virus genomes from Alaska and 278,635 virus genomes from the contiguous United States collected between the first week of December 2020 through the last week of June 2021. We focused on this timeframe because of the notable emergence and spread of the SARS-CoV-2 lineage B.1.1.519 observed in Alaska. We found that this variant was consistently detected in Alaska from the end of January through June of 2021 with a peak prevalence in April of 77.9% unlike the rest of the United States with a peak prevalence of 4.6%. In Alaska, the earlier emergence of B.1.1.519 coincided with a later peak of Alpha (B.1.1.7) when compared to the rest of the United States. We also observed differences in the composition of lineages and variants over time between the two most populated regions of Alaska. Although there was a modest increase in COVID-19 cases during the peak incidence of B.1.1.519, it is difficult to disentangle how social dynamics conflated changes in COVID-19 during this time. We suggest that the viral characteristics, such as amino acid substitutions in the spike protein, and a founder effect likely contributed to the unique spread of B.1.1.519 in Alaska.

Identification of a Novel SARS-CoV-2 Strain with Truncated Protein in ORF8 Gene by Next Generation Sequencing (preprint)

Using next generation sequencing technology, we identified a truncated protein mutation located in the ORF8 gene which is near the end of the genome from nucleotides 27,878 to 27,958. The mutation in this novel strain created a stop codon and translates to the novel truncated ORF8 protein, creating a much smaller protein than most other strains of SARS-CoV-2. The novel truncated mutation is most closely related to nine SARS-CoV-2 strains found in Washington state. Our results show a novel strain of SARS-CoV-2 with a truncated ORF8 gene. This shortens the translated ORF8 protein. The effects of ORF8 protein and its functions are still uncertain but a truncated ORF8 could affect antibody response, severity of infection and inflammatory response.

Mask Wearing and Control of SARS-CoV-2 Transmission in the United States (preprint)

Introduction: Cloth face coverings and surgical masks have become commonplace across the United States in response to the SARS-CoV-2 epidemic. While evidence suggests masks help curb the spread of respiratory pathogens, research is limited. Face masks have quickly become a topic of public debate as government mandates have started requiring their use. Here we investigate the association between self-reported mask wearing, social distancing and community SARS-CoV-2 transmission in the United States, as well as the effect of statewide mandates on mask uptake. Methods: Serial cross-sectional surveys were administered June 3 through July 31, 2020 via web platform. Surveys queried individuals' likelihood to wear a face mask to the grocery store or with family and friends. Responses (N=378,207) were aggregated by week and state and combined with measures of the instantaneous reproductive number (Rt), social distancing proxies, respondent demographics and other potential sources of confounding. We fit multivariate logistic regression models to estimate the association between mask wearing and community transmission control (Rt <1) for each state and week. Multiple sensitivity analyses were considered to corroborate findings across mask wearing definitions, Rt estimators and data sources. Additionally, mask wearing in 12 states was evaluated two weeks before and after statewide mandates. Results: We find an upward trend in mask usage across the U.S., although uptake varies by geography and demographic groups. A multivariate logistic model controlling for social distancing and other variables found a 10% increase in mask wearing was associated with a 3.53 (95% CI: 2.03, 6.43) odds of transmission control (Rt <1). We also find that communities with high mask wearing and social distancing have the highest predicted probability of a controlled epidemic. These positive associations were maintained across sensitivity analyses. Segmented regression analysis of mask wearing found no statistical change following mandates, however the positive trend of increased mask wearing over time was preserved. Conclusion: Widespread utilization of face masks combined with social distancing increases the odds of SARS-CoV-2 transmission control. Mask wearing rose separately from government mask mandates, suggesting supplemental public health interventions are needed to maximize mask adoption and disrupt the spread of SARS-CoV-2, especially as social distancing measures are relaxed.

The Relationship Between COVID-19 Infection and Risk Perception, Knowledge, Attitude As Well As Four Non-pharmaceutical Interventions (NPIs) During the Late Period Of The COVID-19 Epidemic In China An Online Cross-sectional Survey of 8158 Adults (preprint)

BackgroundSo far, there has been no published population study on the relationship between COVID-19 infection and publics risk perception, information source, knowledge, attitude and four non-pharmaceutical interventions(NPI: hand washing, proper coughing habits, social distancing and mask wearing) during the COVID-19 outbreak in China. MethodsAn online survey of 8158 Chinese adults between 22 February to 5 March 2020 was conducted. Bivariate associations between categorical variables were examined using Fisher exact test. We also explored the determinants of four NPIs as well as their association with COVID-19 infection using logistic regression. ResultsOf 8158 adults included, 57 (0.73%) were infected with COVID-19. The overwhelming majority of respondents showed a positive attitude (99.2%), positive risk perception (99.9%) and high knowledge levels that were among the strongest predictors of four highly adopted NPIs (hand washing:96.8%; proper coughing: 93.1%; social distancing:87.1%; mask wearing:97.9%). There was an increased risk of COVID-19 infection for those who not washing hands (2.28% vs 0.65%; RR=3.53: 95%CI: 1.53-8.15; P<0.009); not practicing proper coughing (1.79% vs 0.73%; RR=2.44: 95%CI: 1.15-5.15;P=0.026); not practicing social distancing (1.52% vs 0.58%; RR=2.63:95%CI:1.48 - 4.67; P=0.002); and not wearing a mask (7.41% vs 0.6%; RR=12.38:95%CI:5.81-26.36; P<0.001). For those who did practice all other three NPIs, wearing mask was associated with significantly reduced risk of infection compared to those who did not wear a mask (0.6% vs 16.7%; p=0.035). Similarly, for those who did not practice all or part of the other three NPIs, wearing mask was also associated with significantly reduced risk of infection. In a penalised logistic regression model including all four NPIs, wearing a mask was the only significant predictor of COVID-19 infection among four NPIs (OR=7.20; 95%CI:2.24-23.11; p<0.001). ConclusionsWe found high levels of risk perception, positive attitude, desirable knowledge as well as a high level of adopting four NPIs. The relevant knowledge, risk perception and attitude were strong predictors of adapting the four NPIs. Mask wearing, among four personal NPIs, was the most effective protective measure against COVID-19 infection with added preventive effect among those who practised all or part of the other three NPIs.