Estimation of secondary household attack rates for emergent spike L452R SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco

Background Sequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. Methods SARS-CoV-2genomicsequencesweregeneratedfrompositivesamplescollected,alongwithepidemiologicalmetadata,atawalk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 1, 2020 and January 10-29, 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants. Results A total of 12,124 tests were performed yielding 1,099 positives. From these, 928 high quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.4% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to the “California” or “West Coast” variants (B.1.427 and B.1.429) were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.36 vs 0.29, RR=1.28; 95% CI:1.00-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.3%). Conclusions The increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants.

Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco

ABSTRACTBackgroundSequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities.MethodsSARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 2, 2020 and January 10-29, 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants.ResultsA total of 12,124 tests were performed yielding 1,099 positives. From these, 811 high quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to “West Coast” variants were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.357 vs 0.294, RR=1.29; 95% CI:1.01-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.1%).ConclusionsThe increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants; however, additional laboratory and epidemiological studies are required to better understand differences between these variants.SummaryWe observed a growing prevalence and elevated attack rate for “West Coast” SARS-CoV-2 variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.

Vulnerable Bodies

This essay examines how the Chicana feminist muralist Juana Alicia fosters environmental justice activism that values vulnerable lives in her two most famous murals, both painted at Twenty-Fourth and York Streets in San Francisco’s Mission District: Las Lechugueras (1983) and La Llorona’s Sacred Waters (2004). It explores how Juana Alicia gives visual form to an environmental ethics that prompts a politics of inclusion, equitable resource distribution, and bodily diversity. Juana Alicia’s murals remind us what antiracist, feminist, disability, environmental, and other social justice movements share: an investment in radical interdependence between different kinds of bodies and beings. They depict disabilities created by environmental hazards (including pollution, pesticide poisoning, and the privatization of water) without reducing disability to tragedy, prompting viewers to envision a world in which working-class communities of color are not forced to bear the brunt of environmental risk.

Let’s get phygital

This paper considers the interplay of physical and digital landscaping in the Mission District (‘the Mission’), a gentrified neighborhood in San Francisco, California. Aligned with recent work on affect and people’s mediations of the linguistic landscape (Wee, 2016; Banda & Jimaima, 2015), I examine how the Mission is filtered – literally and figuratively – in a corpus of 16,756 Instagram posts. Comparing these digital remediated productions of place to the physical landscape, I demonstrate how both are structured semiotically along exclusionary lines. Contrary to the democratic and inclusive mythology of digital / social media, I show how users’ self-positionings and elitist stancetaking (Jaworski & Thurlow, 2009; Mapes, forthcoming) effectively reinscribe privilege and reiterate gentrification of the Mission. As mining of ‘big data’ becomes increasingly valued as empirically ‘objective’ information, my analysis demonstrates geotagged content should not be viewed as a static indicator, but as a subjective, dynamic and – at times – problematic process.

Coda

The coda examines how cultural producers contribute to the Latina/o counter-dictatorial imaginary using non-print-based artistic forms. It focuses in depth on the murals in Balmy Alley in San Francisco’s Mission District, examining how their depiction of authoritarian repression in Central America coexists alongside representations of other forms of oppression in the United States. The murals generate linked histories of violence and are material testaments to interracial solidarity and a collective struggle for social justice. The coda’s analysis of the palimpsests of paint and the visual polyphony across the walls of Balmy Alley adds another texture and layer to the counter-dictatorial imaginary traced in the preceding chapters. It ends by suggesting that other forms of Latina/o cultural production such as music, film, and Day of the Dead altars work together with the murals and the novel to capture the afterlives of the dictatorial past and current dictatorial forms of oppression.