COVID-19 Literature Situation Report Jan 28, 2021

Using publicly available SARS-CoV-2 sequencing data and COVID-19 surveillance data collected from August to December 2020 in the UK, Zhao et al. reconstructed the variant-specific instantaneous reproduction number, Rt, and estimated that the variant containing the N501Y mutation is 52% more transmissible than the wild-type virus.

Zhao et al. (Jan 28, 2021). Quantifying the Transmission Advantage Associated with N501Y Substitution of SARS-CoV-2 in the United Kingdom: An Early Data-Driven Analysis. Journal of Travel Medicine. https://doi.org/10.1093/jtm/taab011

Despite a high SARS-CoV-2 seroprevalence of 76% among blood donors in Manaus, Brazil by October 2020, the area experienced a sudden rise in COVID-19 hospitalizations from 552 in December 2020 to 3,431 in January 2021. The authors suggest possible explanations for the resurgence in this setting where seroprevalence was higher than common estimates of the herd immunity threshold, including overestimating seroprevalence, waning immunity, introduction of new variants capable of escaping prior infection, and circulation of variants with higher inherent transmissibility.

Sabino et al. (Jan 27, 2021). Resurgence of COVID-19 in Manaus, Brazil, despite High Seroprevalence. The Lancet. https://doi.org/10.1016/S0140-6736(21)00183-5 

A systematic review and meta-analysis of studies examining alternative sample types for testing (n=46) found that nasal swab (NS), saliva samples, and oropharyngeal (OP) swabs consistently captured lower percent positives than nasopharyngeal (NP) swabs, though performance of OP and NS combined was similar to NP. The percent agreement between most alternative sample types and NP were low, with OP/NS having the highest agreement. 

Lee et al. (Jan 27, 2021). Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-Analysis. Journal of Clinical Microbiology. https://doi.org/10.1128/JCM.02881-20 

[Press release, not peer-reviewed] Preliminary results for phase 2/3 trials for the recombinant protein-based COVID-19 vaccine NVX-CoV2373 made by Novavax showed up to 89.3% efficacy in the UK cohort (n= >15,000), where 56 participants in the placebo group developed COVID-19 vs 6 in the vaccine group. Of note, the B.1.1.7 variant was observed in 32 of the COVID-19 cases, yielding an estimate of 85.6% efficacy against the variant.

Preliminary results from the South Africa cohort (n= >4,400) showed efficacy of 60% in the HIV-negative study population vs. 49.4% in the overall study population, with 29 COVID-19 cases observed in the placebo group vs. 15 in the vaccine group. Among 27 of the 44 cases with sequence data, mutations consistent with the B.1.351 variant were detected in 25 (93%).

Approximately 1/3 of patients in the South Africa cohort (but not included in the preliminary results) were seropositive at baseline, indicating prior COVID-19 infection. 

Novavax. (Jan 28, 2021). Novavax COVID-19 Vaccine Demonstrates 89.3% Efficacy in UK Phase 3 Trial. Press release downloaded Jan 28 from https://ir.novavax.com/node/15506/pdf

[Pre-print, not peer-reviewed] Sera from recipients who completed the 2-dose regimen of the Pfizer vaccine BNT162b2 (n=20) had similar neutralizing geometric mean titers (GMTs) against SARS-CoV-2 viruses engineered to contain key spike protein mutations from variants emerging from the UK (B.1.1.7) and South Africa (B.1.351) compared to GMTs against the wild-type virus. Compared to the GMTs against the wild-type virus, GMTs against viruses with the N501Y mutation (present in both variants) and the key B.1.1.7 mutations (Δ69/70+N501Y+D614G) were 1.46- and 1.41-fold higher, respectively. In contrast, GMTs against the key B.1.351 mutations (E484K+N501Y+D614G) were 19% lower than wild-type. The authors note that the engineered viruses do not contain the full set of mutations present in variants B.1.1.7 and B.1.351.

Xie et al. (Jan 27, 2021). Neutralization of Spike 6970 Deletion E484K and N501Y SARS-CoV-2 by BNT162b2 Vaccine-Elicited Sera. Pre-print downloaded Jan 28 from https://doi.org/10.1101/2021.01.27.427998 

[Pre-print, not peer-reviewed] A nationally representative online survey of 1,315 US adults conducted in June 2020 found that 45% of respondents supported some form of immunity privileges. Among the forms, private certificates were favored over government-issued immunity passports (48% vs 43%). Respondents were more likely to justify immunity privileges for high-risk jobs or to attend large recreational events than for returning to work. Support did not vary significantly across COVID-19 risk factors such as age, chronic disease, or employment type. Women, Hispanics, and members of non-Black minority groups were less supportive of immunity privileges.

Hall et al. (Jan 27, 2021). U.S. Public Views about COVID-19 “Immunity Passports.” Pre-print downloaded Jan 28 from https://doi.org/10.1101/2021.01.26.21250184 

Among a cohort of 240 pregnant patients with SARS-CoV-2 infection in Washington State, the COVID-19 hospitalization and case fatality rates were 3.5-fold and 13.6-fold higher, respectively, compared to rates among similarly-aged females and males with SARS-CoV-2 infections in Washington State.  One in 11 developed severe or critical disease, 1 in 10 were hospitalized for COVID-19. Patients who were hospitalized were slightly older (median 32 vs. 28 years) and more likely to have at least one comorbidity (45.8% vs 17.6%) than those who were not hospitalized. Three maternal deaths from COVID-19 were reported, corresponding to a maternal mortality rate of 1,250 per 100,000 pregnancies and a 1.2% absolute rate difference compared to similarly-aged adults.

Lokken et al. (Jan 26, 2021). Disease Severity, Pregnancy Outcomes and Maternal Deaths among Pregnant Patients with SARS-CoV-2 Infection in Washington State. American Journal of Obstetrics and Gynecology. https://doi.org/10.1016/j.ajog.2020.12.1221 

Respiratory, physical, and psychological sequelae were common 3-4 months after hospital discharge in an Italian cohort of COVID-19 survivors (n=238, median age = 61 [IQR 50-71]). 113 of 219 patients (52%) had a significant reduction in lung function measured by diffusing lung capacity for carbon monoxide (80% of expected value), and 128 (54%) patients had functional impairment using the Short Physical Performance Battery (SPPB) score. 41 (17%) patients reported posttraumatic stress symptoms.

Bellan et al. (Jan 27, 2021). Respiratory and Psychophysical Sequelae Among Patients With COVID-19 Four Months After Hospital Discharge. JAMA Network Open. https://doi.org/10.1001/jamanetworkopen.2020.36142 

Transgender and gender nonbinary (TGNB) individuals (n=208) from an established longitudinal cohort experienced increased psychological distress due to the COVID-19 pandemic, as expressed by significantly higher raw scores during than pandemic than pre-pandemic on the Global Severity Index (GSI) . Additionally, a significantly higher percentage of respondents met criteria for clinically significant depressive (41% vs 28%) and anxiety (41% vs 31%) symptoms. After controlling for pre-pandemic GSI, reduced LGBTQ/TGNB support was associated with greater GSI, though interruption/delay in gender-affirming healthcare was not associated with greater GSI.

Kidd et al. (Jan 27, 2021). Understanding the Impact of the COVID-19 Pandemic on the Mental Health of Transgender and Gender Nonbinary Individuals Engaged in a Longitudinal Cohort Study. Journal of Homosexuality. https://doi.org/10.1080/00918369.2020.1868185 

A retrospective study of adults hospitalized for COVID-19 in Michigan (n=2038) found that patients from neighborhoods with median income in the lowest vs. highest quartile were more likely to require invasive mechanical ventilation (IMV) (25% vs 16%) and ICU admission (35% vs 20%). The median income of neighborhoods of Black patients was lower than neighborhoods of white patients ($34,758 vs $63,317). After adjusting for age, sex, race, and comorbidities, patients whose neighborhoods had a $10,000 higher median income had 5% and 8% lower odds of requiring IMV or ICU admission.

Quan et al. (Jan 27, 2021). Impact of Race and Socioeconomic Status on Outcomes in Patients Hospitalized with COVID-19. Journal of General Internal Medicine. https://doi.org/10.1007/s11606-020-06527-1