Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction (preprint)

BackgroundThe emergence of SARS-CoV-2 variants is a current public health concern possibly impacting COVID-19 disease diagnosis, transmission patterns and vaccine effectiveness. ObjectivesTo describe the SARS-CoV-2 lineages circulating early pandemic among samples with S gene dropout and characterize a novel mutation in receptor-binding domain (RBD) of viral spike protein. Study designAdults and children older than 2 months with signs and symptoms of COVID-19 were prospectively enrolled from May to October 2020 in Porto Alegre, Brazil. All participants performed RT-PCR assays for diagnosing SARS-CoV-2, samples with S gene dropout and Ct < 30 (cycle threshold) were submitted to whole genome sequencing (WGS), and homology modeling and physicochemical properties analysis were performed. Results484/1,557 participants tested positive for SARS-CoV-2. The S gene dropout was detected in 7.4% (36/484) as early as May, and a peak was observed in early August. WGS was performed in 8 samples. The B.1.1.28, B.1.91 and B.1.1.33 lineages were circulating in early pandemic. The RBD novel mutation (Y380Q) was found in one sample occurring simultaneously with C379W and V395A, and the B.1.91 lineage in the spike protein. ConclusionMutations in the SARS-CoV-2 spike region were detected early in the COVID-19 pandemic in Southern Brazil, regarding the B.1.1.28, B.1.91 and B.1.1.33 lineages identified. The novel mutation (Y380Q) with C379W, modifies important RBD properties, which may interfere with the binding of neutralizing antibodies (CR3022, EY6A, H014, S304). HighlightsO_LICharacterization of novel mutation (Y380Q) in RBD of SARS-CoV-2 spike protein C_LIO_LIThe Y380Q and C379W modify important properties in the SARS-CoV-2 RBD region C_LIO_LIThe RBD mutations may interfere with the binding of neutralizing antibodies C_LIO_LIThe B.1.1.28, B.1.91 and B.1.1.33 lineages were circulating in early pandemic C_LI

Infants have lower RT-PCR cycle threshold for SARS-CoV-2 in comparison with older children and adults (preprint)

BackgroundThe viral dynamics and the role of children in the spread of SARS-CoV-2 are not completely understood. Our aim was to evaluate how RT-PCR Ct values among children with confirmed SARS-CoV-2 compared with that of adult subjects. MethodsPatients (aged from 2 months to [≤]18 years, and adults) with signs and symptoms of acute SARS-CoV-2 infection for less than 7 days, were prospectively enrolled in the study from May to November 2020. All participants performed RT-PCR assay for SARS-CoV-2 detection; Ct values of ORF1ab, N, and S gene-targets, and the average of all the three probes were used as surrogates of viral load. ResultsOf the total of 376 participants with confirmed SARS-CoV-2 infection there were 21 infants, 62 children and 293 adults. The RT-PCR Ct values of children under 18 were not significantly different from that of adults, as observed by the analyzed probes (namely ORF1ab, N, and S), and by the mean of all 3 gene-targets. However, infants had significantly lower Ct values compared to children and adults (P = 0.044). DiscussionCt values for children were not significantly different than that of adults with positive SARS-CoV-2. Interestingly, infants had even lower Ct values when compared to older children and adults. Although viral load is not the only determinant of transmission, infants may play a significant role in the spread of SARS-CoV-2 in the community, especially if or when this population returns to regular daycare activities.

Monitoring Social Distancing and SARS-CoV-2 Transmission in Brazil Using Cell Phone Mobility Data (preprint)

BACKGROUND: In the absence of vaccines and effective pharmacological interventions to reduce with the COVID-19 transmission, social distancing measures have been implemented to mitigate the impact on healthcare systems and secure time to prepare the public health response. METHODS: We assessed the relationship between mobility data collected by mobile phone and time-dependent reproduction number R(t) using severe acute respiratory illness cases reported by 102 Brazilian cities with COVID-19 confirmed cases until April 15, grouped by demographic density (low, intermediate and high). FINDINGS: The mean social distancing index from February 1 to April 15 was 43.6% (27.2% to 63.7%), and no significant difference observed comparing the groups of demographic density (p-value = 0.809). The social distancing index measure obtained from mobility data was able to predict future values of R(t) in all groups of demographic density. Furthermore, using SARI cases, cross-correlation analyses showed that isolation was highly correlated with R(t) (ccfINTERPRETATION: The early implementation of social distancing measures greatly reduced the COVID-19 spread. A major advantage to our approach is that the social distancing index data is available on a daily basis, in contrast with R(t) measurement, which is subject to significant delays. This index metric can be monitored in real time to assess adherence to social distancing measures and help guide, with real time data, the public health policy decision making process.FUNDING: FADQ and JC were granted a fellowship for research productivity from the Brazilian National Council for Scientific and Technological Development – CNPq, process/contract identification: 312656/2019-0 and 310551/2018-8, respectively.DECLARATION OF INTERESTS: Authors declare no competing interests.ETHICS APPROVAL STATEMENT: This study followed Brazilian and International legislation for conducting human research. This research project was approved by the National Research Ethics Committee (Comissão Nacional de Ética em Pesquisa, CONEP) in Brazil, Register number (CAAE): 11946619.5.0000.5421.

Monitoring social distancing and SARS-CoV-2 transmission in Brazil using cell phone mobility data (preprint)

Social distancing measures have emerged as the predominant intervention for containing the spread of COVID-19, but evaluating adherence and effectiveness remains a challenge. We assessed the relationship between aggregated mobility data collected from mobile phone users and the time-dependent reproduction number R(t), using severe acute respiratory illness (SARI) cases reported by Sao Paulo and Rio de Janeiro. We found that the proportion of individuals staying home all day (isolation index) had a strong inverse correlation with R(t) (rho