07 March, 2021

SARS-CoV-2 viral RNA is not viral load -

Several recent studies used results of SARS-CoV-2 RT-qPCR, Ct (threshold cycle), as proxies of viral load1. Unfortunately, an important aspect of this virus’ biology is neglected: Coronaviruses being (+)ssRNA viruses the form of RNA they use for replication is identical to the form used for transcription. It is therefore not obvious which process, replication or transcription, is quantified by RT-qPCR. To make matters more complicated, Coronaviruses produce several kinds of mRNA, genomic (= full size) and subgenomic (carrying only some genes), hence modulating their gene expression1. As shown by Finkel et al. the different mRNAs of SARS-CoV-2 occur at different densities in cell cultures. Because of their location on the viral genome the different targets of RT-qPCR are differentially affected, some being carried by more types of mRNA than others. Further, gene expression being affected by environmental and genetic factors, the quantity of RNA revealed by RT-qPCR may consequently vary due to differences in replication rates, in expression rates, or in both. It is thus unclear how good a proxy of viral load Ct values are, or what differences in Ct values may reflect. Even though the process underlying them is poorly characterized, and despite additional known biases in sample quality and RT-PCR protocols, quantitative analyses of Ct may nevertheless be highly informative e.g. in allowing to detect patterns in ‘levels of RNA’ in patients with different properties (gender, age, severe vs. mild disease, stage of infection) or in allowing to relate these patterns to epidemic properties in populations. For example, given that a priori replication levels should be the same for all genes of these monopartite viruses, differences in Ct among markers lying in different viral genes for should reflect different expression profiles. Such observations could thus help reveal interesting, and potentially epidemiologically significant, variations e.g. among SARS-CoV-2 variants.

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Prevalence of vitamin D is not associated with the COVID-19 epidemic in Europe. A judicial update of the existing evidence. -

Background: COVID-19 has emerged as a global pandemic, affecting nearly 104 million people worldwide as of February 4th 2021. In previous published studies, the association between the mean Vit D status of each country and COVID-19 infection rate, and mortality among the adult population in European countries was examined. The aim of this study was to re-examine the relationship between the Vit D status of each country and COVID-19 infection, recovery, and mortality using updated data and a different methodological approach. Methods: Information only form the last decade on Vit D concentration/deficiency for each country was retrieved through literature search on PubMed database. As of February, 4th 2021, COVID-19 infections and mortalities per one million population as well as total recoveries were extracted from the Worldometer website. The association between vitamin D deficiency and COVID-19 infection, recovery, and mortality were explored using correlation coefficients and scatterplots. Results: The prevalence of vitamin D deficiency among European countries ranged from 6.0 (Finland) to 75.5% (Turkey), with several countries facing more than 50% of vitamin D deficiency among their population. Non-significant correlations were observed between the number of COVID-19 infections (r=0.190; p=0.374), recoveries (rs=0.317, p=0.131), and mortalities (r=0.129; p=0.549) per one million population, with the prevalence of vitamin D deficiency. Conclusions: Prevalence of vitamin D deficiency was not significantly associated with either number of infections, recoveries or mortality rate of COVID-19 among European countries. Thus, it is an important parameter to be considered when implementing preventive measures to face COVID-19.

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Rapid increase of SARS-CoV-2 variant B.1.1.7 detected in sewage samples from England between October 2020 and January 2021 -

SARS-CoV-2 variants with multiple amino acid mutations in the spike protein are emerging in different parts of the world raising concerns on their possible impact on human immune response to the virus and vaccine efficacy against them. Recently, a variant named lineage B.1.1.7 was detected and shown to be rapidly spreading across the UK since November 2020. As surveillance for these SARS-CoV-2 variants of concern (VOCs) becomes critical, we have investigated the use of environmental surveillance (ES) for the rapid detection and quantification of B.1.1.7 viruses in sewage as a way of monitoring its expansion that is independent on the investigation of identified clinical cases. B.1.1.7 mutations in viral sequences from sewage were first identified in a sample collected in London on 10th November 2020 and shown to rapidly increase in frequency to >95% in January 2021, in agreement with clinical data over the same period. We show that ES can provide an early warning of VOCs becoming prevalent in the population and that, as well as B.1.1.7, our method can potentially detect VOCs B.1.351 and P.1, first identified in South Africa and Brazil, respectively, and other viruses also carrying critical spike mutation E484K, known to have an effect on virus antigenicity.

🖺 Full Text HTML: Rapid increase of SARS-CoV-2 variant B.1.1.7 detected in sewage samples from England between October 2020 and January 2021

The impact of COVID-19 on air travel demand and CO2 emissions in Brazil -

The drastic reduction in economic activities caused by the COVID-19 pandemic creates a unique and timely opportunity to examine the environmental impacts of human activity. In several countries, the aviation sector was dramatically affected by the travel restrictions, resulting in a change of trip demand and in a drop of fuel consumption. Nonetheless, little attention has been paid to the impact of the pandemic on air travel demand, one of the fastest-growing sources of emissions globally. This paper estimates the impact of the COVID-19 on air travel demand and emissions in Brazil, the largest aviation market in Latin America. Combining detailed flight data with daily number of passengers and fuel consumption and data on combustion emission factors, we estimate CO2 emissions of domestic flights in Brazil. A Bayesian structural time-series model was used to estimate the impact of COVID-19 on daily trends of air travel demand and emissions. We find that the COVID-19 pandemic caused a reduction of 68% on national passengers and 62% in total CO2 emissions compared to what would have occurred if the pandemic had not happened. It avoided a total of approximately 4.6 megatons of CO2 between March and December 2020 in Brazil, the equivalent of one year of domestic flight emissions in France. Despite such a sharp drop in commercial aviation, passenger demand recovered to 64.2% of pre-pandemic levels by the end of 2020. CO2 emissions had a 52.6% reduction in 2020 and the emissions per capita increased after the COVID-19 outbreak. Although the precise impact of the COVID-19 on this figure is not yet fully understood, the fast recovery in domestic flights by December 2020 indicates that the emissions could soon return to pre-pandemic levels, demonstrating the challenges of reducing emissions in the aviation sector in the short term.

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Distinguishing non severe cases of dengue from COVID-19 in the context of co-epidemics: a cohort study in a SARS-CoV-2 testing center on Reunion island -

Background. As coronavirus 2019 (COVID-19) is spreading globally, several countries are handling dengue epidemics. As both infections are deemed to share similarities at presentation, it would be useful to distinguish COVID-19 from dengue in the context of co-epidemics. Hence, we performed a retrospective cohort study to identify predictors of both infections. Methodology/Principal Findings. All the subjects suspected of COVID-19 between March 23 and May 10, 2020, were screened for COVID-19 within the testing center of the University hospital of Saint-Pierre, Reunion island. The screening consisted in a questionnaire surveyed in face-to-face, a nasopharyngeal swab specimen for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) reverse transcription polymerase chain-reaction and a rapid diagnostic orientation test for dengue. Factors independently associated with COVID-19 or with dengue were sought using multinomial logistic regression models, taking other febrile illnesses (OFIs) as controls. Adjusted Odds ratios (OR) and 95% Confidence Intervals (95%CI) were assessed. Over a two-month study period, we diagnosed 80 COVID-19, 60 non-severe dengue and 872 OFIs cases. Among these, we identified delayed presentation (>3 days) since symptom onset (Odds ratio 1.91, 95% confidence interval 1.07-3.39), contact with a COVID-19 positive case (OR 3.81, 95%CI 2.21-6.55) and anosmia (OR 7.80, 95%CI 4.20-14.49) as independent predictors of COVID-19, body ache (OR 6.17, 95%CI 2.69-14.14), headache (OR 5.03, 95%CI 1.88-13.44) and retro-orbital pain (OR 5.55, 95%CI 2.51-12.28) as independent predictors of dengue, while smoking was less likely observed with COVID-19 (OR 0.27, 95%CI 0.09-0.79) and upper respiratory tract infection symptoms were associated with OFIs. Conclusions/Significance. Although prone to potential biases, these data suggest that non-severe dengue may be more symptomatic than COVID-19 in a co-epidemic setting with higher dengue attack rates. At clinical presentation, eight basic clinical and epidemiological indicators may help to distinguish COVID-19 or dengue from each other and other febrile illnesses.

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Long-read sequencing of SARS-CoV-2 reveals novel transcripts and a diverse complex transcriptome landscape. -

Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2 (COVID-19), is a positive single-stranded RNA virus with a 30 kb genome that is responsible for the current pandemic. To date, the genomes of global COVID-19 variants have been primarily characterized via short-read sequencing methods. Here, we devised a long-read RNA (IsoSeq) sequencing approach to characterize the COVID-19 transcript landscape and expression of its ~27 coding regions. Our analysis identified novel COVID-19 transcripts including a) a short ~65-70 nt 5’-UTR fused to various downstream ORFs encoding accessory proteins such as the envelope, ORF 8, and ORF 9 (nucleocapsid) proteins, that are relatively highly expressed, b) novel SNVs that are differentially expressed, whereby a subset are suggestive of partial RNA editing events, and c) SNVs at functional sites, whereby at least one is associated with a differentially expressed spike protein isoform. These previously uncharacterized COVID-19 isoforms, expressed genes, and gene variants were corroborated using ddPCR. Understanding this transcriptional complexity may help provide insight into the biology and pathogenicity of SARS-CoV-2 compared to other coronaviruses.

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SARS-CoV-2 surveillance in Norway rats (Rattus norvergicus) from Antwerp sewer system, Belgium -

Background: SARS-CoV-2 human-to-animal transmission can lead to the establishment of novel reservoirs and the evolution of new variants with the potential to start new outbreaks in humans. Aim: We tested Norway rats inhabiting the sewer system of Antwerp, Belgium, for the presence of SARS-CoV-2 following a local COVID-19 epidemic peak. In addition, we discuss the use and interpretation of SARS-CoV-2 serological tests on non-human samples. Methods: Between November and December 2020, Norway rat oral swabs, feces and tissues from the sewer system of Antwerp were collected to be tested by RT-qPCR for the presence of SARS-CoV-2. Serum samples were screened for the presence of anti-SARS-CoV-2 IgG antibodies using a Luminex microsphere immunoassay (MIA). Samples considered positive were then checked for neutralizing antibodies using a conventional viral neutralization test (cVNT). Results: The serum of 35 rats was tested by MIA showing 3 potentially positive sera that were later shown to be negative by cVNT. All tissue samples of 39 rats analyzed tested negative for SARS-CoV-2 RNA. Conclusion: This is the first study that evaluates SARS-CoV-2 infection in urban rats. We can conclude that the sample of 39 rats had never been infected with SARS-CoV-2. We show that diagnostic serology tests can give misleading results when applied on non-human samples. SARS-CoV-2 monitoring activities should continue due to the emergence of new variants prone to infect Muridae rodents.

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SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies -

Neutralization escape by SARS-CoV-2 variants, as has been observed in the 501Y.V2 (B.1.351) variant, has impacted the efficacy of first generation COVID-19 vaccines. Here, the antibody response to the 501Y.V2 variant was examined in a cohort of patients hospitalized with COVID-19 in early 2021 - when over 90% of infections in South Africa were attributed to 501Y.V2. Robust binding and neutralizing antibody titers to the 501Y.V2 variant were detected and these binding antibodies showed high levels of cross-reactivity for the original variant, from the first wave. In contrast to an earlier study where sera from individuals infected with the original variant showed dramatically reduced potency against 501Y.V2, sera from 501Y.V2-infected patients maintained good cross-reactivity against viruses from the first wave. Furthermore, sera from 501Y.V2-infected patients also neutralized the 501Y.V3 (P.1) variant first described in Brazil, and now circulating globally. Collectively these data suggest that the antibody response in patients infected with 501Y.V2 has a broad specificity and that vaccines designed with the 501Y.V2 sequence may elicit more cross-reactive responses.

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Resolving the Dynamic Motions of SARS-CoV-2 nsp7 and nsp8 Proteins Using Structural Proteomics -

Coronavirus (CoV) non-structural proteins (nsps) assemble to form the replication-transcription complex (RTC) responsible for viral RNA synthesis. nsp7 and nsp8 are important cofactors of the RTC, as they interact and regulate the activity of RNA-dependent RNA polymerase (RdRp) and other nsps. To date, no structure of full-length SARS-CoV-2 nsp7:nsp8 complex has been published. Current understanding of this complex is based on structures from truncated constructs or with missing electron densities and complexes from related CoV species with which SARS-CoV-2 nsp7 and nsp8 share upwards of 90% sequence identity. Despite available structures being solved using crystallography and cryo-EM representing detailed snapshots of the nsp7:nsp8 complex, it is evident that the complex has a high degree of structural plasticity. However, relatively little is known about the conformational dynamics of the complex and how it assembles to interact with other nsps. Here, the solution-based structural proteomic techniques, hydrogen-deuterium exchange mass spectrometry (HDX-MS) and crosslinking mass spectrometry (XL-MS), illuminate the structural dynamics of the SARS-CoV-2 full-length nsp7:nsp8 complex. The results presented from the two techniques are complementary and validate the interaction surfaces identified from the published three-dimensional heterotetrameric crystal structure of SARS-CoV-2 truncated nsp7:nsp8 complex. Furthermore, mapping of XL-MS data onto higher order complexes suggests that SARS-CoV-2 nsp7 and nsp8 do not assemble into a hexadecameric structure as implied by the SARS-CoV full-length nsp7:nsp8 crystal structure. Instead our results suggest that the nsp7:nsp8 heterotetramer can dissociate into a stable dimeric unit that might bind to nsp12 in the RTC without altering nsp7-nsp8 interactions.

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COVID-19 vaccine hesitancy: shortening the last mile -

We offer three recommendations to increase COVID-19 vaccination rates. First, use communication campaigns leveraging evidence-based levers and argumentation tools with experts. Second, use behavioral insights to make vaccination more accessible. Third, help early adopters communicate about their decision to be vaccinated to accelerate the emergence of pro-vaccination norms.

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“Zoom Developmentalists”: Home-Based Videoconferencing Developmental Research during COVID-19 -

As home-based video conferencing has become increasingly popular among developmental researchers during the COVID-19 pandemic, there is a pressing need to discuss its potentials and challenges. We have augmented our own experiences with insights from many “Zoom developmentalists” (see Acknowledgments) to provide recommendations for those who are considering engaging in home-based videoconferencing studies.

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What to target when reopening universities in times of COVID-19? Selecting relevant and changeable determinants and underlying beliefs of university students’ adherence to COVID-19-guidelines -

Objective: When reopening universities in times of COVID-19, students still have to adhere to COVID-19 behavioral guidelines. We explored what behavioral determinants (and underlying beliefs) related to the adherence to guidelines are both relevant and changeable, as input for future interventions. Design: A cross-sectional online survey was conducted (Oct-Nov 2020), identifying behavioral determinants (and underlying beliefs) of university students’ adherence to COVID-19-guidelines, including keeping 1.5m distance, getting tested, and isolating (N = 255). Main Outcomes: Determinants and underlying beliefs of students’ adherence to COVID-19-guidelines. Results: Attitude, perceived norm, self-efficacy, and several beliefs (e.g., risk perception beliefs ‘I am not afraid because I am young’; attitudinal beliefs, e.g., ‘I feel responsible for telling people to adhere to guidelines’; self-efficacy beliefs, e.g., ‘COVID-19-prevention guidelines are difficult to adhere to’) were strongly associated with intention to adhere to guidelines, and for those beliefs there was room for improvement, making them suitable as possible intervention targets. Conclusion: Students mostly adhere to COVID-19 guidelines, but there is room for improvement. Interventions need to enhance students’ adherence behavior by targeting the most relevant determinants as identified in this study. Based on these findings, a small intervention was introduced targeting the determinants of students’ adherence to guidelines.

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The Behavioral Immune System and Vaccination Intentions During the Coronavirus Pandemic -

The behavioral immune system is considered to be a psychological adaptation that decreases the risk of infection. Research suggests that, in the current environment, this system can produce attitudes with negative health consequences, such as increased vaccine hesitancy. In three studies, we investigated whether two facets of the behavioral immune system—contamination aversion (i.e., avoiding potential contamination) and perceived infectability (i.e., perceived susceptibility to disease)—predicted intentions to accept COVID-19, influenza, and measles or general childhood vaccinations. Both contamination aversion and perceived infectability were higher during than before the pandemic. In contrast to previous research, those with higher contamination aversion during the pandemic perceived vaccines to be safer and had higher intentions to accept vaccination. Contamination aversion before the pandemic was not associated with perceived vaccine safety or vaccination intentions during the pandemic. Individuals who perceived themselves as more susceptible to diseases were slightly more willing to accept vaccination. We conjecture that high disease threat reverses the relationship between the behavioral immune system response and vaccination. As the associations were weak, individual differences in contamination aversion and perceived infectability are of little practical relevance for vaccine uptake.

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Society for the Improvement of Psychological Science Global Engagement Task Force Report -

The Society for the Improvement of Psychological Science (SIPS) is an organization whose mission focuses on bringing together scholars who want to improve methods and practices in psychological science. The organization reaffirmed in June 2020 that “[we] cannot do good science without diverse voices,” and acknowledged that “right now the demographics of SIPS are unrepresentative of the field of psychology, which is in turn unrepresentative of the global population. We have work to do when it comes to better supporting Black scholars and other underrepresented minorities.” The purpose of the Global Engagement Task Force, started in January 2020, was to explore suggestions made after the 2019 Annual Conference, held in Rotterdam, the Netherlands, around inclusion and access for scholars from regions outside of the United States, Canada, and Western Europe (described in the report as “geographically diverse” regions), a task complicated by the COVID-19 pandemic and civil unrest in several task force members’ countries of residence. This report outlines several suggestions, specifically around building partnerships with geographically diverse open science organizations; increasing SIPS presence at other, more local events; diversifying remote events; considering geographically diverse annual conference locations; improving membership and financial resources; and surveying open science practitioners from geographically diverse regions.

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Overviews of Reviews of the comorbidities, symptoms and perinatal clinical characteristics of patients with coronavirus 2019 (COVID-19) -

What is the incidence in pregnant women of: preterm labor, C-section operation, pneumonia, cough, fever, radiological alterations in the chest, alterations in the blood count, liver function, C-reactive protein, procalcitonin, high D-dimer, thrombocytopenia, globular sedimentation rate. What is the incidence in the neonate of: low birth weight, fetal well-being commitment, low Apgar score, radiological alterations in chest, alterations in the blood count, liver function, C-reactive protein, procalcitonin, high D-dimer, thrombocytopenia, and what is the globular sedimentation rate, the vertical transmission of COVID-19 symptoms, and what are the clinical characteristics?

🖺 Full Text HTML: Overviews of Reviews of the comorbidities, symptoms and perinatal clinical characteristics of patients with coronavirus 2019 (COVID-19)

Covid-19 Sentry

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