Bayesian Molecular Dating Analyses Combined with Mutational Profiling Suggest an Independent Origin and Evolution of SARS-CoV-2 Omicron BA.1 and BA.2 Sub-Lineages

The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus’s genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, the most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be that of 18 September 2021 (95% highest posterior density (HPD), 4 August–22 October 2021) and 1.435 × 10⁻³ (95% HPD  =  1.021 × 10⁻³ − 1.869 × 10⁻³) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September–28 November 2021) and 1.074 × 10⁻³ (95% HPD  =  6.444 × 10⁻⁴ − 1.586 × 10⁻³) substitution/site/year were estimated for the BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in the spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study sheds light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics of the virus and, as a result, mitigate the impact of emerging variants on public health.     

Wooden foreign body impalement through the right shoulder region – an unusual penetrating injury: A case report

BACKGROUNDImpalement of the body is a rare injury and comes with varied presentation. There is no set classification or defined protocols for managing this injury. This case report aims to create awareness among trauma surgeons about unusual presentation and management of such case. CASE SUMMARYA 45-year-old man presented to the emergency department with a sharp penetrating wooden plank at right clavicular region between the neck and shoulder following a road traffic accident. The vehicle had crashed into a roadside wooden hut, thus causing an impalement injury. He was meticulously worked up and taken to emergency theatre. The wooden plank was removed and the wound healed uneventfully. Postoperatively, he had fairly good shoulder function and was able to return back to work successfully.CONCLUSIONEach impalement injury brings in challenges in management as no two cases are the same. The varied presentation and risks involved should be known to medical professionals handling the emergency. Coordinated multidisciplinary team approach is needed for successful outcome.     

Immunotherapy-induced neutralizing antibodies disrupt allergen binding and sustain allergen tolerance in peanut allergy

In IgE-mediated food allergies, exposure to the allergen activates systemic allergic responses. Oral immunotherapy (OIT) treats food allergies through incremental increases in oral allergen exposure. However, OIT only induces sustained clinical tolerance and decreased basophil sensitivity in a subset of individuals despite increases in circulating allergen-specific IgG in all treated individuals. Therefore, we examined the allergen-specific antibodies from 2 OIT cohorts of patients with sustained and transient responses. Here, we compared antibodies from individuals with sustained or transient responses and discovered specific tolerance-associated conformational epitopes of the immunodominant allergen Ara h 2 recognized by neutralizing antibodies. First, we identified what we believe to be previously unknown conformational, intrahelical epitopes using x-ray crystallography with recombinant antibodies. We then identified epitopes only recognized in sustained tolerance. Finally, antibodies recognizing tolerance-associated epitopes effectively neutralized allergen to suppress IgE-mediated effector cell activation. Our results demonstrate the molecular basis of antibody-mediated protection in IgE-mediated food allergy, by defining how these antibodies disrupt IgE-allergen interactions to prevent allergic reactions. Our approach to studying the structural and functional basis for neutralizing antibodies demonstrates the clinical relevance of specific antibody clones in antibody-mediated tolerance. We anticipate that our findings will form the foundation for treatments of peanut allergy using neutralizing antibodies and hypoallergens.     

Severe wasting among Indian infants <6 months: Findings from the National Family Health Survey 4

Burden and risk factors for wasting in the first 6 months of life among Indian children are not well documented. We used data from India's National Family Health Survey 4 to estimate the prevalence of severe wasting (weight for length < ‐3 SD) among 18,898 infants under 6 months of age. We also examined the association of severe wasting with household, maternal, and child‐related factors using multivariable logistic regression analysis. Prevalence of severe wasting among infants less than 6 months of age was 14.8%, ranging from 3.5 to 21% across states. Low birth weight (<2,500 g; adjusted odds ratio [AOR] 1.40, 95% CI [1.19, 1.65]), nonutilization of supplementary nutrition by mother during lactation (AOR 1.23, 95% CI [1.05, 1.43]), and anthropometric assessment during summer (AOR 1.37, 95% CI [1.13, 1.65]) and monsoon months (AOR 1.53, 95% CI [1.20, 1.95]) were associated with higher odds of severe wasting. Infants aged 2 to 3 months (AOR 0.78, 95% CI [0.66, 0.93]) and 4 to 5 months (AOR 0.65, 95% CI [0.55, 0.73]) had lower odds of severe wasting as compared with the 0‐ to 1‐month category. This analysis reveals a high burden of severe wasting in infants less than 6 months in India. Preventive interventions must be targeted at reducing low birth weight due to fatal growth restriction and prematurity. Appropriate care practices at facilities and postdischarge with extra attention to those born small and sick can prevent further deterioration in nutritional status.     

Extended Kalman smoother with differential evolution technique for denoising of ECG signal

Electrocardiogram (ECG) signal gives a lot of information on the physiology of heart. In reality, noise from various sources interfere with the ECG signal. To get the correct information on physiology of the heart, noise cancellation of the ECG signal is required. In this paper, the effectiveness of extended Kalman smoother (EKS) with the differential evolution (DE) technique for noise cancellation of the ECG signal is investigated. DE is used as an automatic parameter selection method for the selection of ten optimized components of the ECG signal, and those are used to create the ECG signal according to the real ECG signal. These parameters are used by the EKS for the development of the state equation and also for initialization of the parameters of EKS. EKS framework is used for denoising the ECG signal from the single channel. The effectiveness of proposed noise cancellation technique has been evaluated by adding white, colored Gaussian noise and real muscle artifact noise at different SNR to some visually clean ECG signals from the MIT-BIH arrhythmia database. The proposed noise cancellation technique of ECG signal shows better signal to noise ratio (SNR) improvement, lesser mean square error (MSE) and percent of distortion (PRD) compared to other well-known methods.     

Cocaine-induced methemoglobinemia

Dear editor,We congratulate Chowdhury et al[1] for their excellentreport and successful management of a young ladysuffering from cocaine-induced methemoglobinemia.Through this letter, we aim to address some additionalconcerns, which would certainly be helpful for acomplete understanding of this topic.