COVID-19 vaccine antibody response is associated with side-effects, chronic health conditions, and vaccine type in a large Northern California cohort (preprint)

As vaccines have become available for COVID-19, it is important to understand factors that may impact response. The objective of this study is to describe vaccine response in a well-characterized Northern California cohort, including differences in side-effects and antibody response by vaccine type, sex, and age, as well as describe responses in subjects with pre-existing health conditions that are known risk factors for more severe COVID-19 infection. From July 2020 to March 2021, ~5,500 adults from the East Bay Area in Northern California were followed as part of a longitudinal cohort study. Comprehensive questionnaire data and biospecimens for COVID-19 antibody testing were collected at multiple time-points. All subjects were at least 18 years of age and members of the East-Bay COVID-19 cohort who answered questionnaires related to vaccination status and side-effects at two time-points. Three vaccines, Moderna (2 doses), Pfizer-BioNTech (2 doses), and Johnson & Johnson (single dose), were examined as exposures. Additionally, pre-existing health conditions were assessed. The main outcomes of interest were anti-SARS-CoV-2 Spike antibody response (measured by S/C ratio in the Ortho VITROS assay) and self-reporting of 11 potential vaccine side effects. When comparing both doses of the Moderna vaccine to respective doses of Pfizer-BioNTech, participants receiving the Moderna vaccine had higher odds of many reported side-effects. The same was true comparing the single-dose Johnson & Johnson vaccine to dose 2 of the Pfizer-BioNTech vaccine. The antibody S/C ratio also increased with each additional side-effect after the second dose. S/C ratios after vaccination were lower in participants aged 65 and older, and higher in females. At all vaccination timepoints, Moderna vaccine recipients had a higher S/C ratio. Individuals who were fully vaccinated with Pfizer-BioNTech had a 72.4% lower S/C ratio compared to those who were fully vaccinated with Moderna. Subjects with asthma, diabetes, and cardiovascular disease all demonstrated more than a 20% decrease in S/C ratio. In support of previous findings, we show that antibody response to the Moderna vaccine is higher than the Pfizer-BioNTech vaccine. We also observed that antibody response was associated with side-effects, and participants with a history of asthma, diabetes, and cardiovascular disease had lower antibody responses. This information is important to consider as further vaccines are recommended.

Burden of SARS-CoV-2 and protection from symptomatic second infection in children (preprint)

Importance The impact of the SARS-CoV-2 pandemic on children remains unclear. Better understanding of the burden of COVID-19 among children and their protection against re-infection is crucial as they will be among the last groups vaccinated. Objective To characterize the burden of COVID-19 and assess how protection from symptomatic re-infection among children may vary by age. Design A prospective, community-based pediatric cohort study conducted from March 1, 2020 through October 15, 2021. Setting The Nicaraguan Pediatric Influenza Cohort is a community-based cohort in District 2 of Managua, Nicaragua. Participants A total of 1964 children aged 0-14 years participated in the cohort. Non-immunocompromised children were enrolled by random selection from a previous pediatric influenza cohort. Additional newborn infants aged [≤] 4 weeks were randomly selected and enrolled monthly, via home visits. Exposures Prior COVID-19 infection as confirmed by positive anti SARS-CoV-2 antibodies (receptor binding domain [RBD] and spike protein) or real time RT-PCR confirmed COVID-19 infection [≥] 60 days prior to current COVID-19. Main Outcomes and Measures Symptomatic COVID-19 cases confirmed by real time RT-PCR and hospitalization within 28 days of symptom onset of confirmed COVID-19 case. Results Overall, 49.8% of children tested were seropositive over the course of the study. There were also 207 PCR-confirmed COVID-19 cases, 12 (6.4%) of which were severe enough to require hospitalization. Incidence of COVID-19 was highest among children aged <2 years -- 16.1 per 100 person-years (95% Confidence Interval [CI]: 12.5, 20.5) -- approximately three times that of children in any other age group assessed. Additionally, 41 (19.8%) symptomatic SARS-CoV-2 episodes were re-infections, with younger children slightly more protected against symptomatic reinfection. Among children aged 6-59 months, protection was 61% (Rate Ratio [RR]:0.39, 95% CI:0.2,0.8), while protection among children aged 5-9 and 10-14 years was 64% (RR:0.36,0.2,0.7), and 49% (RR:0.51,0.3-0.9), respectively.

SARS-CoV-2 Spike triggers barrier dysfunction and vascular leak via integrins and TGF-β signaling (preprint)

Severe COVID-19 is associated with epithelial and endothelial barrier dysfunction within the lung as well as in distal organs. While it is appreciated that an exaggerated inflammatory response is associated with barrier dysfunction, the triggers of this pathology are unclear. Here, we report that cell-intrinsic interactions between the Spike (S) glycoprotein of SARS-CoV-2 and epithelial/endothelial cells are sufficient to trigger barrier dysfunction in vitro and vascular leak in vivo, independently of viral replication and the ACE2 receptor. We identify an S-triggered transcriptional response associated with extracellular matrix reorganization and TGF-{beta} signaling. Using genetic knockouts and specific inhibitors, we demonstrate that glycosaminoglycans, integrins, and the TGF-{beta} signaling axis are required for S-mediated barrier dysfunction. Our findings suggest that S interactions with barrier cells are a contributing factor to COVID-19 disease severity and offer mechanistic insight into SARS-CoV-2 triggered vascular leak, providing a starting point for development of therapies targeting COVID-19 pathogenesis.

Impact of individual-level characteristics and transmission mitigation behaviors on SARS-CoV-2 infection and seroprevalence in a large Northern California Bay Area cohort (preprint)

Comprehensive data on transmission mitigation behaviors and SARS-CoV-2 infection and serostatus are needed from large, community-based cohorts to identify SARS-CoV-2 risk factors and impact of public health measures. From July 2020 to March 2021, {approx}5,500 adults from the East Bay Area, California were followed over three data collection rounds. We estimated the prevalence of antibodies from SARS-CoV-2 infection and COVID-19 vaccination, and self-reported COVID-19 test positivity. Population-adjusted SARS-CoV-2 seroprevalence was low, increasing from 1.03% (95% CI: 0.50-1.96) in Round 1 (July-September 2020), to 1.37% (95% CI: 0.75-2.39) in Round 2 (October-December 2020), to 2.18% (95% CI: 1.48-3.17) in Round 3 (February-March 2021). Population-adjusted seroprevalence of COVID-19 vaccination was 21.64% (95% CI: 19.20-24.34) in Round 3. Despite >99% of participants reporting wearing masks, non-Whites, lower-income, and lower-educated individuals had the highest SARS-CoV-2 seroprevalence and lowest vaccination seroprevalence. Our results demonstrate that more effective policies are needed to address these disparities and inequities.

Development and Implementation of Dried Blood Spot-based COVID-19 Serological Assays for Epidemiologic Studies (preprint)

Serological surveillance studies of infectious diseases provide population-level estimates of infection and antibody prevalence, generating crucial insight into population-level immunity, risk factors leading to infection, and effectiveness of public health measures. These studies traditionally rely on detection of pathogen-specific antibodies in samples derived from venipuncture, an expensive and logistically challenging aspect of serological surveillance. During the COVID-19 pandemic, guidelines implemented to prevent the spread of SARS-CoV-2 infection made collection of venous blood logistically difficult at a time when SARS-CoV-2 serosurveillance was urgently needed. Dried blood spots (DBS) have generated interest as an alternative to venous blood for SARS-CoV-2 serological applications due to their stability, low cost, and ease of collection; DBS samples can be self-generated via fingerprick by community members and mailed at ambient temperatures. Here, we detail the development of four DBS-based SARS-CoV-2 serological methods and demonstrate their implementation in a large serological survey of community members from 12 cities in the East Bay region of the San Francisco metropolitan area using at-home DBS collection. We find that DBS perform similarly to plasma/serum in enzyme-linked immunosorbent assays and commercial SARS-CoV-2 serological assays. In addition, we show that DBS samples can reliably detect antibody responses months post-infection and track antibody kinetics after vaccination. Implementation of DBS enabled collection of valuable serological data from our study population to investigate changes in seroprevalence over an eight-month period. Our work makes a strong argument for the implementation of DBS in serological studies, not just for SARS-CoV-2, but any situation where phlebotomy is inaccessible.

An immune correlate of SARS-CoV-2 infection and severity of reinfections (preprint)

Background. An immune correlate of protection from SARS-CoV-2 infection is urgently needed. Methods. We used an ongoing household cohort with an embedded transmission study that closely monitors participants regardless of symptom status. Real-time reverse-transcription polymerase chain reaction (RT-PCR) and Enzyme-linked immunosorbent assays (ELISAs) were used to measure infections and seropositivity. Sequencing was performed to determine circulating strains of SARS-CoV-2. We investigated the protection associated with seropositivity resulting from prior infection, the anti-spike antibody titers needed for protection, and we compared the severity of first and second infections. Results. In March 2021, 62.3% of the cohort was seropositive. After March 2021, gamma and delta variants predominated. Seropositivity was associated with 69.2% protection from any infection (95% CI: 60.7%-75.9%), with higher protection against moderate or severe infection (79.4%, 95% CI: 64.9%-87.9%). Anti-spike titers of 327 and 2,551 were associated with 50% and 80% protection from any infection; titers of 284 and 656 were sufficient for protection against moderate or severe disease. Second infections were less severe than first infections (Relative Risk (RR) of moderated or severe disease: 0.6, 95% CI: 0.38-0.98; RR of subclinical disease:1.9, 95% CI: 1.33-2.73). Conclusions. Prior infection-induced immunity is protective against infection when predominantly gamma and delta SARS-CoV-2 circulated. The protective antibody titers presented may be useful for vaccine policy and control measures. While second infections were somewhat less severe, they were not as mild as ideal. A strategy involving vaccination will be needed to ease the burden of the SARS-CoV-2 pandemic.

Epidemics of chikungunya, Zika, and COVID-19 reveal bias in case-based mapping (preprint)

ABSTRACT Accurate tracing of epidemic spread over space enables effective control measures. We examined three metrics of infection and disease in a pediatric cohort (N ≈ 3,000) over two chikungunya and one Zika epidemic, and in a household cohort (N=1,793) over one COVID-19 epidemic in Managua, Nicaragua. We compared spatial incidence rates (cases/total population), infection risks (infections/total population), and disease risks (cases/infected population). We used generalized additive and mixed-effects models, Kulldorf’s spatial scan statistic, and intracluster correlation coefficients. Across different analyses and all epidemics, incidence rates considerably underestimated infection and disease risks, producing large and spatially non-uniform biases distinct from biases due to incomplete case ascertainment. Infection and disease risks exhibited distinct spatial patterns, and incidence clusters inconsistently identified areas of either risk. While incidence rates are commonly used to infer infection and disease risk in a population, we find that this can induce substantial biases and adversely impact policies to control epidemics. Article summary line Inferring measures of spatial risk from case-only data can substantially bias estimates, thereby weakening and potentially misdirecting measures needed to control an epidemic.

An intranasal ASO therapeutic targeting SARS-CoV-2 (preprint)

The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity1. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic2. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identified an LNA ASO binding to the 5 leader sequence of SARS-CoV-2 ORF1a/b that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the K18-hACE2 humanized COVID-19 mouse model potently (98-99%) suppressed viral replication in the lungs of infected mice, revealing strong prophylactic and treatment effects. We found that the LNA ASO also represses viral infection in golden Syrian hamsters, and is highly efficacious in countering all SARS-CoV-2 "variants of concern" tested in vitro and in vivo, including B.1.427, B.1.1.7, and B.1.351 variants3. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce transmission of variants partially resistant to vaccines and monoclonal antibodies, and could be deployed intranasally for prophylaxis or via lung delivery by nebulizer to decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences4, and they may have particular impact in areas where vaccine distribution is a challenge, and could be stockpiled for future coronavirus pandemics.

Have news reports on suicide and attempted suicide during the COVID-19 pandemic adhered to guidance on safer reporting? A UK-wide content analysis study (preprint)

Associations between sensational news coverage of suicide and subsequent increases in suicidal behaviour in the general population have been well documented. Amidst growing concern over the impact of the COVID-19 pandemic on suicide rates, it is especially important that news coverage of suicidal behaviour adheres to recommended standards for the responsible reporting of suicide. Using a set of dimensions based on international media guidelines, we analysed the quality and content of all UK news reports of possible COVID-19 related suicides and suicide attempts in the first four months of the pandemic (N=285 reports of 78 individual incidents published in print and online newspapers between 16th March and 12th July 2020). The majority of news reports made an explicit link between suicidal behaviour and the COVID-19 pandemic in the headline (187/285, 65.5%), and portrayed this association as strong and direct (n=196/272, 72.1%), mostly based on statements by family, friends or acquaintances of the deceased (171/285, 60%). The impact of the pandemic on suicidal behaviour was most often attributed to feelings of isolation (78/285, 27.4%), poor mental health (42, 14.7%) and sense of entrapment (41, 14.4%) as a result of government-imposed restrictions. Although rarely of poor overall quality, reporting was biased towards young people, frontline staff and relatively unusual suicides (including those involving a celebrity, murder-suicide and violent methods) Also, to varying degrees, reports failed to meet recommended standards; for example, 41.1% (117/285) did not signpost readers to sources of support, a quarter (69, 24.2%) included examples of sensational language and a third provided over-simplistic explanations for the suicidal behavior (93, 32.6%). While news reporting has improved compared to earlier coverage of suicide in the UK, it is essential that careful attention is paid to the quality and content of reports, especially as longer-term consequences of the COVID-19 pandemic develop.

Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection (preprint)

SARS-CoV-2 can cause a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of the host factors mediating viral infection or restriction is critical to elucidate SARS-CoV-2 host-pathogen interactions and the progression of COVID-19. To this end, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. These screens uncovered proviral and antiviral host factors across highly interconnected host pathways, including components implicated in clathrin transport, inflammatory signaling, cell cycle regulation, and transcriptional and epigenetic regulation. Mucins, a family of high-molecular weight glycoproteins and the main constituent of mucus, are central components of a prominent viral restriction pathway that we identified. We demonstrate that multiple membrane-anchored mucins are critical inhibitors of SARS-CoV-2 entry and are upregulated in response to viral infection. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and suggests interactions between SARS-CoV-2 and airway mucins of COVID-19 patients as a host defense mechanism.

Risk factors for SARS-CoV-2 infection among farmworkers in Monterey County, California (preprint)

Importance: Essential workers in agriculture and food production have been severely affected by the ongoing COVID-19 pandemic. Objective: To identify risk factors associated with SARS-CoV-2 shedding and antibody response in farmworkers in California. Design: This cross-sectional study collected survey data and determined current SARS-CoV-2 shedding and seropositivity among 1,107 farmworkers in California's Salinas Valley from 16 July to 30 November 2020. Setting: Farmworkers receiving transcription-mediated amplification (TMA) tests for SARS-CoV-2 infection at federally qualified community clinics and community sites were invited to participate in our study. Participants: Individuals were eligible if they were not pregnant, were 18 years old or older, had conducted farm work since the pandemic started, and were proficient in English or Spanish. Exposures: Sociodemographic, household, community, and workplace characteristics. Main Outcome(s) and Measure(s): Current (as indicated by TMA positivity) and historical (as indicated by IgG seropositivity) SARS-CoV-2 infection. Results: Most farmworkers enrolled in the study were born in Mexico, had primary school or lower levels of educational attainment, and were overweight or obese. Current SARS-CoV-2 shedding was associated in multivariable analyses with attained only primary or lower educational levels (RR=1.32; 95% CI: 0.99-1.76), speaking an indigenous language at home (RR=1.30; 0.97-1.73), working in the fields (RR=1.60; 1.03-2.50), and exposure to known or suspected COVID-19 case at home (RR=2.98; 2.06-4.32) or in the workplace (RR=1.59; 1.18-2.14). Antibody detection was associated with residential exposures including living in crowded housing (RR=1.23; 0.98-1.53), with children (RR=1.40; 1.1-1.76) or unrelated roommates (RR=1.40; 1.19-1.64), and with a known or suspected COVID-19 case (RR=1.59; 1.13-2.24). Those who were obese (RR=1.65; 1.01-2.70) or diabetic (RR=1.31; 0.98-1.75) were also more likely to be seropositive. Farmworkers who lived in rural areas other than Greenfield (RR=0.58; 0.47-0.71), worked indoors (RR=0.68; 0.61-0.77), or whose employer provided them with information on how to protect themselves at work (RR=0.59; 0.40-0.86) had lower risk of prior infection.

Prevalence and clinical profile of SARS-CoV-2 infection among farmworkers in Monterey County, California: June-November, 2020 (preprint)

As essential personnel, United States farmworkers have continued working in-person throughout the COVID-19 pandemic. We undertook prospective surveillance of SARS-CoV-2 infection and antibody prevalence among farmworkers in Californias Salinas Valley from 15 June to 30 November, 2020. Over this period, we observed 22.1% (1514/6864) positivity for current SARS-CoV-2 by nucleic acid detection among farmworkers tested at federally-qualified migrant and community health clinics, as compared to 17.2% (1255/7305) among other adults from the same communities (risk ratio, 1.29; 95% confidence interval, 1.20-1.37). In a nested study enrolling 1,115 farmworkers, prevalence of current infection was 27.7% among farmworkers reporting [≥]1 potential COVID-19 symptom, and 7.2% among farmworkers without symptoms (adjusted odds ratio 4.17; 2.86-6.09). Prevalence of anti-SARS-CoV-2 IgG antibodies increased from 10.5% (6.0-18.4%) between 16 July-31 August to 21.2% (16.6-27.4%) between 1-30 November. The high observed prevalence of infection among farmworkers underscores the need for vaccination and other preventive interventions.

Rapid detection of SARS-CoV-2 with Cas13 (preprint)

To combat disease outbreaks such as the COVID-19 pandemic, flexible diagnostics for rapid viral detection are greatly needed. We report a nucleic acid test that integrates distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We paired this workflow, termed Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER), with extraction-free sample lysis using shelf-stable reagents that are widely available at low cost. DISCoVER has been validated on saliva samples to incentivize frequent testing for more widespread community surveillance and robustly detected attomolar levels of SARS-CoV-2 within 30 minutes, while avoiding false positives in virus-negative saliva. Furthermore, DISCoVER is compatible with multiplexed CRISPR probes to enable simultaneous detection of a human gene control or alternative pathogens.

Lymphocytopaenia is associated with severe SARS-CoV-2 disease: A Systematic Review and Meta-Analysis of Clinical Data (preprint)

Background: Most patients infected by SARS-CoV-2 have favourable outcomes, however some develop severe disease which may progress to acute respiratory distress syndrome, multi-organ failure, and death. Markers that could predict patients at risk of poor outcomes would be extremely useful clinically. Evidence has emerged that low lymphocyte count is associated with increased disease severity. Methods: We performed a systematic review and meta-analysis to assess the association between lymphocyte count and severity of SARS-CoV-2 associated clinical disease. Results: Seven papers were included in the meta-analysis. These papers included data from 2083 patients, 25% (n=521) with severe SAR-CoV-2 disease and 75% (n=1562) with non-severe SAR-CoV-2 disease. Heterogenicity was seen in the definition of severe disease. Metanalysis produced metamedians of 1x109/L (95% CI 1-1.1) and 0.7x109/L (95% CI 0.63-0.8) lymphocytes for patients with non-severe and severe disease respectively (p-value of p=0.006 Wilcoxon test). Calculation of metamedians from the two papers classifying severe disease according to death alone gave 1.1 1x109/L lymphocytes (95% CI 1.0-1.1) for "survivors" (n=163) and 0.63 1x109/L lymphocytes (95% CI 0.60-0.63) for "non-survivors" (n=253) of SAR-CoV-2 disease. Conclusions: Lower lymphocyte counts are significantly associated with more severe disease in patients with SARS-CoV-2 infection. Lymphocytopenia may therefore be useful laboratory measure to allow prognostication of patients presenting with SARS-CoV-2 infection.