Prevalence of symptoms, comorbidities, and reinfections in individuals infected with Wild-Type SARS-CoV-2, Delta, or Omicron variants: a comparative study in western Mexico.

Introduction: The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been classified into variants of interest (VOIs) or concern (VOCs) to prioritize global monitoring and research on variants with potential risks to public health. The SARS-CoV-2 high-rate mutation can directly impact the clinical disease progression, epidemiological behavior, immune evasion, vaccine efficacy, and transmission rates. Therefore, epidemiological surveillance is crucial for controlling the COVID-19 pandemic. In the present study, we aimed to describe the prevalence of wild-type (WT) SARS-CoV-2 and Delta and Omicron variants in Jalisco State, Mexico, from 2021 to 2022, and evaluate the possible association of these variants with clinical manifestations of COVID-19. Methods: Four thousand and ninety-eight patients diagnosed with COVID-19 by real-time PCR (COVIFLU, Genes2Life, Mexico) from nasopharyngeal samples from January 2021 to January 2022 were included. Variant identification was performed by the RT-qPCR Master Mut Kit (Genes2Life, Mexico). A study population follow-up was performed to identify patients who had experienced reinfection after being vaccinated. Results and Discussion: Samples were grouped into variants according to the identified mutations: 46.3% were Omicron, 27.9% were Delta, and 25.8% were WT. The proportions of dry cough, fatigue, headache, muscle pain, conjunctivitis, fast breathing, diarrhea, anosmia, and dysgeusia were significantly different among the abovementioned groups (p < 0.001). Anosmia and dysgeusia were mainly found in WT-infected patients, while rhinorrhea and sore throat were more prevalent in patients infected with the Omicron variant. For the reinfection follow-up, 836 patients answered, from which 85 cases of reinfection were identified (9.6%); Omicron was the VOC that caused all reported reinfection cases. In this study, we demonstrate that the Omicron variant caused the biggest outbreak in Jalisco during the pandemic from late December 2021 to mid-February 2022 but with a less severe form than the one demonstrated by Delta and WT. The co-analysis of mutations and clinical outcomes is a public health strategy with the potential to infer mutations or variants that could increase disease severity and even be an indicator of long-term sequelae of COVID-19.

Biosensing strategies for the detection of SARS-CoV-2 nucleic acids

The COVID-19 pandemic had devastating effects throughout the world, producing a severe crisis in the health systems and in the economy of a long list of countries, even developed ones. Therefore, highly sensitive and selective analytical bioplatforms that allow the descentralized and fast detection of the severe acute respiratory síndrome coronavirus 2 (SARS-CoV-2), are extremely necessary. Since 2020, several reviews have been published, most of them focused on the different strategies to detect the SARS-CoV-2, either from RNA, viral proteins or host antibodies produced due to the presence of the virus. In this review, the most relevant biosensors for the detection of SARS-CoV-2 RNA are particularly addressed, with special emphasis on the discussion of the biorecognition layers and the different schemes for transducing the hybridization event. Graphical abstract

Impedimetric and amperometric genosensors for the highly sensitive quantification of SARS-CoV-2 nucleic acid using an avidin-functionalized multi-walled carbon nanotubes biocapture platform.

We report two novel genosensors for the quantification of SARS-CoV-2 nucleic acid using glassy carbon electrodes modified with a biocapture nanoplatform made of multi-walled carbon nanotubes (MWCNTs) non-covalently functionalized with avidin (Av) as a support of the biotinylated-DNA probes. One of the genosensors was based on impedimetric transduction offering a non-labelled and non-amplified detection of SARS-CoV-2 nucleic acid through the increment of [Fe(CN)6]3-/4- charge transfer resistance. This biosensor presented an excellent analytical performance, with a linear range of 1.0 × 10-18 M - 1.0 × 10-11 M, a sensitivity of (5.8 ± 0.6) x 102 Ω M-1 (r2 = 0.994), detection and quantification limits of 0.33 aM and 1.0 aM, respectively; and reproducibilities of 5.4% for 1.0 × 10-15 M target using the same MWCNTs-Av-bDNAp nanoplatform, and 6.9% for 1.0 × 10-15 M target using 3 different nanoplatforms. The other genosensor was based on a sandwich hybridization scheme and amperometric transduction using the streptavidin(Strep)-biotinylated horseradish peroxidase (bHRP)/hydrogen peroxide/hydroquinone (HQ) system. This genosensor allowed an extremely sensitive quantification of the SARS-CoV-2 nucleic acid, with a linear range of 1.0 × 10-20 M - 1.0 × 10-17 M, detection limit at zM level, and a reproducibility of 11% for genosensors prepared with the same MWCNTs-Av-bDNAp1 nanoplatform. As a proof-of-concept, and considering the extremely high sensitivity, the genosensor was challenged with highly diluted samples obtained from SARS-CoV-2 RNA PCR amplification.

Specific T-Cell Immune Response to SARS-CoV-2 Spike Protein over Time in Naïve and SARS-CoV-2 Previously Infected Subjects Vaccinated with BTN162b2.

Due to the COVID-19 pandemic, the rapid development of vaccines against SARS-CoV-2 has been promoted. BNT162b2 is a lipid-nanoparticle mRNA vaccine with 95% efficacy and is the most administered vaccine globally. Nevertheless, little is known about the cellular immune response triggered by vaccination and the immune behavior over time. Therefore, we evaluated the T-cell immune response against the SARS-CoV-2 spike protein and neutralization antibodies (nAbs) in naïve and SARS-CoV-2 previously infected subjects vaccinated with BTN162b2. METHODS: Forty-six BTN162b2 vaccinated subjects were included (twenty-six naïve and twenty SARS-CoV-2 previously infected subjects vaccinated with BTN162b2). Blood samples were obtained at basal (before vaccination), 15 days after the first dose, and 15 days after the second dose, to evaluate cellular immune response upon PBMC's stimulation and cytokine levels. The nAbs were determined one and six months after the second dose. RESULTS: SARS-CoV-2 previously infected subjects vaccinated with BTN162b2 showed the highest proportion of nAbs compared to naïve individuals one month after the second dose. However, women were more prone to lose nAbs percentages over time significantly. Furthermore, a diminished CD154+ IFN-γ+ CD4+ T-cell response was observed after the second BTN162b2 dose in those with previous SARS-CoV-2 infection. In contrast, naïve participants showed an overall increased CD8+ IFN-γ+ TNF-α+ T-cell response to the peptide stimulus. Moreover, a significant reduction in IP-10, IFN-λI, and IL-10 cytokine levels was found in both studied groups. Additionally, the median fluorescence intensity (MFI) levels of IL-6, IFNλ-2/3, IFN-𝛽, and GM-CSF (p < 0.05) were significantly reduced over time in the naïve participants. CONCLUSION: We demonstrate that a previous SARS-CoV-2 infection can also impact cellular T-cell response, nAbs production, and serum cytokine concentration. Therefore, the study of T-cell immune response is essential for vaccination scheme recommendations; future vaccine boost should be carefully addressed as continued stimulation by vaccination might impact the T-cell response.

COVID-19 Preventive Measures in Northern California Jails: Perceived Deficiencies, Barriers, and Unintended Harms.

Background: Carceral facilities are high-risk settings for COVID-19 transmission. Little is known about the hidden burden of infection or practical barriers to infection control in these settings, especially in jails. There is also limited research on the mental health impacts of the pandemic among people living and working in carceral facilities. Methods: Between July 8, 2020 and April 30, 2021, we performed SARS-CoV-2 rapid antibody testing and administered a questionnaire among residents and staff of four Northern California jails. We utilized multivariable logistic regression, adjusting for demographic and carceral characteristics, to analyze factors associated with prior infection, including perceived likelihood of prior infection and access to new masks. We additionally assessed the implementation of, perceptions toward, and impacts of COVID-19 policies in practice. We engaged stakeholder representatives, including incarcerated individuals, to guide study design, procedures, and results interpretation. Results: We enrolled 788 jail residents and 380 jail staff. Nearly half of residents and two-thirds of staff who were antibody-positive had not previously tested positive for COVID-19. Among residents without a prior COVID-19 diagnosis, antibody positivity was significantly associated with perceived likelihood of prior infection (adjusted OR = 8.9; 95% CI, 3.6-22.0). Residents who had flu-like illness in jail cited inadequate responses to reported illness and deterrents to symptom reporting, including fears of medical isolation and perceptions of medical neglect. Residents also disclosed deficient access to face masks, which was associated with antibody positivity (adjusted OR = 13.8, 95% CI, 1.8-107.0). Worsened mental health was pervasive among residents, attributed not only to fear of COVID-19 and unsanitary jail conditions but also to intensified isolation and deprivation due to pandemic restrictions on in-person visitation, programs, and recreation time. Conclusion: Carceral settings present significant challenges to maintaining infection control and human rights. Custody officials should work diligently to transform the conditions of medical isolation, which could mitigate deterrents to symptom reporting. Furthermore, they should minimize use of restrictive measures like lockdowns and suspension of visitation that exacerbate the mental health harms of incarceration. Instead, custody officials should ensure comprehensive implementation of other preventive strategies like masking, testing, and vaccination, in conjunction with multisector efforts to advance decarceration.

An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection.

SARS-CoV-2 variants surveillance is a worldwide task that has been approached with techniques such as Next Generation Sequencing (NGS); however, this technology is not widely available in developing countries because of the lack of equipment and limited funding in science. An option is to deploy a RT-qPCR screening test which aids in the analysis of a higher number of samples, in a shorter time and at a lower cost. In this study, variants present in samples positive for SARS-CoV-2 were identified with a RT-qPCR mutation screening kit and were later confirmed by NGS. A sample with an abnormal result was found with the screening test, suggesting the simultaneous presence of two viral populations with different mutations. The DRAGEN Lineage analysis identified the Delta variant, but there was no information about the other three mutations previously detected. When the sequenced data was deeply analyzed, there were reads with differential mutation patterns, that could be identified and classified in terms of relative abundance, whereas only the dominant population was reported by DRAGEN software. Since most of the software developed to analyze SARS-CoV-2 sequences was aimed at obtaining the consensus sequence quickly, the information about viral populations within a sample is scarce. Here, we present a faster and deeper SARS-CoV-2 surveillance method, from RT-qPCR screening to NGS analysis.

Factors associated with COVID-19 vaccine acceptance and hesitancy among residents of Northern California jails.

Carceral facilities are high-risk settings for COVID-19 transmission. Factors associated with COVID-19 vaccine acceptance and hesitancy among incarcerated individuals are poorly understood, especially among jail residents. Here, we conducted a retrospective review of electronic health record (EHR) data on COVID-19 vaccine uptake in custody and additionally administered a survey to assess reasons for vaccine hesitancy, sources of COVID-19 information, and medical mistrust among residents of four Northern California jails. We performed multivariate logistic regression to determine associations with vaccine acceptance. Of 2,564 jail residents offered a COVID-19 vaccine between March 19, 2021 and June 30, 2021, 1,441 (56.2%) accepted at least one dose. Among vaccinated residents, 497 (34.5%) had initially refused. Vaccine uptake was higher among older individuals, women, those with recent flu vaccination, and those living in shared housing. Among 509 survey respondents, leading reasons for vaccine hesitancy were concerns around side effects and suboptimal efficacy, with cost and the need for an annual booster being other hypothetical deterrents to vaccination. Vaccine hesitancy was also associated with mistrust of medical personnel in and out of jail, although this association varied by race/ethnicity. Television and friends/family were the most common and most trusted sources of COVID-19 information, respectively. Overall, vaccine acceptance was much lower among jail residents than the local and national general population. Interventions to increase vaccination rates in this setting should utilize accessible and trusted sources of information to address concerns about side effects and efficacy, while working to mitigate medical and institutional mistrust among residents.

An Evaluation of Reinforcer Magnitude and Echoic Prompts on Vocal Requesting of Individuals with Autism Spectrum Disorder.

Individuals with autism spectrum disorder (ASD) often have communication support needs and many rely on augmentative and alternative communication (AAC) systems to communicate. Previous research suggests that AAC use does not preclude the acquisition of spoken language and, in some cases, may facilitate improvements in spoken communication in children with ASD. This study systematically applied echoic prompting and manipulated reinforcer magnitude in an effort to increase the spoken requests of 3 children with ASD, ages 10-12 years, who used iPad-based speech generating devices (SGDs). The spoken language (vocal requests) of all 3 participants increased in frequency and 1 participant began using spoken language exclusively, even when the SGD was an option. Implications for practitioners and directions for future research in this area are discussed.

Acute meningoencephalitis associated with SARS-CoV-2 infection in Colombia.

We present the case of a patient in the third decade of life, with asthma as comorbidity, who presented to the emergency department due to odynophagia, dyspnea, and cough of 2 days of evolution, later developing acute ventilatory failure requiring orotracheal intubation. The high-resolution chest tomography study showed consolidation due to a pneumonic process towards the posterior segment of the right lower lobe with areas of ground-glass infiltrates with a peripheral distribution. During the clinical course, the patient presented multiple seizure episodes that met the criteria for status epilepticus with MRI compatible with changes due to leptomeningitis. Given symptoms and thorax imaging, tests for SARS-CoV-2 ensued, with both positive RT-PCR in bronchoalveolar lavage and cerebrospinal fluid for the virus also positive. RT-PCR multiplex panel of meningitis/encephalitis results negative for 14 common organisms. A diagnosis of acute meningoencephalitis associated with COVID-19 was considered, with an adequate response to corticosteroid management; to our knowledge, this is the first adult patient with CNS involvement and CSF positive test in Latin America.

A Comprehensive Descriptive Epidemiological and Clinical Analysis of SARS-CoV-2 in West-Mexico during COVID-19 Pandemic 2020.

This study aimed to summarize the epidemiological and clinical characteristics of COVID-19 from Western Mexico people during 2020. A retrospective analysis from an electronic database of people visiting a sentinel center for molecular SARS-CoV-2 confirmatory diagnosis by RT-PCR from April to December 2020 was carried out for epidemiological and clinical description of COVID-19. Out of 23,211 patients evaluated, 6918 (29.8%) were confirmed for SARS-CoV-2 infection (mean age 38.5 ± 13.99), mostly females (53.8%). Comorbidities, such as diabetes (34.7%), obesity (31.15%), and hypertension (31.8%), presented an increased odds OR = 1.27, CI = 1.14-1.41; OR = 1.08, CI = 1.01-1.16; and OR = 1.09, CI = 0.99-1.19, respectively, for viral-infection. Moreover, fever, headache, and dry cough were the most frequent symptoms. No infection difference among sex was found. Those patients >60 years old were prone to COVID-19 severity (OR = 3.59, CI = 2.10-6.14), evaluated by the number of manifested symptoms, increasing with age. In conclusion, a high SARS-CoV-2 prevalence was found in Western Mexico. Comorbidities were frequent in infected people; nevertheless, no association with disease outcomes was observed, in contrast with the highest disease severity risk found in older patients; however, continuous monitoring should be carried since comorbidities have been reported as aggravating factors. This study can help the health officials for the elaboration of planning efforts of the disease management and others in the future.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact.

Background: Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population. Methods: Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico. Results: In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico. Conclusion: This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

Performance evaluation of a lateral flow assay for nasopharyngeal antigen detection for SARS-CoV-2 diagnosis.

BACKGROUND: SARS-CoV-2 has become a global pandemic due to its capacity for rapid transmission. In this context, an early and rapid diagnosis of infected patients that do not require expensive equipment or highly trained personnel is crucial in order to reduce the contagious rate. The aim of this study was to evaluate a chromatographic immunoassay's performance for the rapid diagnosis of SARS-CoV-antigen. METHODS: A cross-sectional study included 369 adults from Western México with diagnosis or suspicion of SARS-CoV-2 infection. Two samples were collected; a naso-oropharyngeal was used for a molecular determination of SARS-CoV-2 RNA. The molecular analysis was carried out using DeCoV19 Kit Triplex (Genes2life S.A.P.I.) based on the CDC diagnostic panel for N1, N2, and N3 regions. The second sample was retrieved from a nasopharyngeal rub and used for the rapid diagnosis of SARS-CoV-2 antigen employing the commercial STANDARD™ Q COVID-19 Ag Test (SD BIOSENSOR). RESULTS: Overall, in 28.2% of the patients was detected the SARS-CoV-2 RNA, and 21.4% were positive for antigen detection. The rapid antigen test showed a sensitivity and specificity of 75.9% and 100%, respectively, with a positive predictive and negative values of 100% and 91%. Symptoms as anosmia presented a high OR for the positive diagnosis for both test, reverse transcription-polymerase chain reaction (RT-PCR), and the rapid antigen test of 8.86 (CI = 4.91-16) and 6.09 (CI = 3.42-10.85), respectively. CONCLUSION: SD BIOSENSOR is a useful assay, but some caveats must be considered before the general implementation.