Genomic surveillance of SARS-CoV-2 by sequencing the RBD region using Sanger sequencing from North Kerala.

Next Generation Sequencing (NGS) is the gold standard for the detection of new variants of SARS-CoV-2 including those which have immune escape properties, high infectivity, and variable severity. This test is helpful in genomic surveillance, for planning appropriate and timely public health interventions. But labs with NGS facilities are not available in small or medium research settings due to the high cost of setting up such a facility. Transportation of samples from many places to few centers for NGS testing also produces delays due to transportation and sample overload leading in turn to delays in patient management and community interventions. This becomes more important for patients traveling from hotspot regions or those suspected of harboring a new variant. Another major issue is the high cost of NGS-based tests. Thus, it may not be a good option for an economically viable surveillance program requiring immediate result generation and patient follow-up. The current study used a cost-effective facility which can be set up in a common research lab and which is replicable in similar centers with expertise in Sanger nucleotide sequencing. More samples can be processed at a time and can generate the results in a maximum of 2 days (1 day for a 24 h working lab). We analyzed the nucleotide sequence of the Receptor Binding Domain (RBD) region of SARS-CoV-2 by the Sanger sequencing using in-house developed methods. The SARS-CoV-2 variant surveillance was done during the period of March 2021 to May 2022 in the Northern region of Kerala, a state in India with a population of 36.4 million, for implementing appropriate timely interventions. Our findings broadly agree with those from elsewhere in India and other countries during the period.

Correlation of periodontal inflamed surface area with glycemic status in controlled and uncontrolled type 2 diabetes mellitus.

BACKGROUND: The bidirectional link between periodontitis and diabetes mellitus (DM) has been established. Periodontitis causes systemic inflammatory burden through inflammatory mediators. The currently utilized tools [clinical attachment loss (CAL) and probing pocket depth (PPD)] are linear measurements, that do not exactly quantify the inflammatory burden of periodontitis. Periodontal inflamed surface area (PISA) quantifies the surface area of bleeding pocket epithelium and estimates the inflammatory burden. Studies relating to the periodontal status of diabetic patients with and without microvascular complications are scarce. This study assessed the proportion of periodontitis and correlation of PISA with glycemic status in controlled, uncontrolled type 2 DM (T2DM) with and without microvascular complications. AIM: To assess the proportion of periodontitis and correlation of PISA with glycemic status in controlled, and uncontrolled T2DM with and without microvascular complications. METHODS: This study comprised 180 T2DM patients. Based on glycated hemoglobin (HbA1c) levels, they were grouped into: (1) Controlled T2DMgroup: (HbA1c ≤ 7%); (2) Uncontrolled T2DM group: (HbA1c > 7%) without microvascular complications; and (3) Uncontrolled T2DM group: (HbA1c > 7%) with microvascular complications. Each group comprised 60 patients. All patients were assessed for periodontal parameters (Bleeding on Probing, PPD, CAL, Oral hygiene index simplified and PISA), and systemic parameters (HbA1c, fasting plasma glucose and post prandial plasma glucose). RESULTS: The proportion of periodontitis among controlled T2DM group, uncontrolled T2DM group without microvascular complications, uncontrolled T2DM group with microvascular complications was 75%, 93.4% and 96.6% respectively. Extent and severity of periodontitis were high in the uncontrolled T2DM group. A significant positive correlation was found between PISA and HbA1c among all patients (r = 0.393, P < 0.001). The dose-response relationship between PISA and HbA1c was observed. An increase of PISA with 168 mm2 was associated with a 1.0% increase of HbA1c. CONCLUSION: High proportion and severity of periodontitis, and increased inflamed surface area in uncontrolled T2DM may have contributed to the poor glycemic control and microvascular complications.

Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions.

Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new variants in the Indian isolated SARS-CoV-2. Phylogenetic and haplotype analysis revealed that the virus was dominated by three distinct introductions followed by local spread suggesting recent outbreaks and that it belongs to the A2a clade. Further analysis of the functional variants revealed that two variants in the S gene associated with increased infectivity and five variants mapped in primer binding sites affect the efficacy of RT-PCR. To the best of our knowledge, this is the first and most comprehensive report of SARS-CoV-2 genetic epidemiology from Kerala.