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.

COVID-19 infection among health care workers in a tertiary care teaching hospital in Kerala - India.

Health care workers are at the frontline for management and containment of COVID-19 infection which has put them at additional risk of the disease. Infection and subsequent quarantine of contacts among HCW may produce considerable strain on the health care system. It is essential that we study the modes by which HCW may get infected in the work environment. Methods: All HCW testing positive for SARS COV 2 from 1st March 2020 to 31st Jan 2021 were included in the study. Data regarding possible source of infection, details of symptoms along with demographic details were collected. Results: A total of 390 health-care workers tested positive for SARS CoV-2 in the institution. The mean age of affected health-care workers was 32.82 (±10.6) years (range 20-65 years), and 61.3% were female 33% of the positive HCW were doctors and 19.5% nurses. 29% of the infections occurred during patient care of which majority were from the non-COVID areas of the hospital. Interactions with infected colleagues constituted 27.4% of the infections. Symptomatics constituted 67% and the predominant symptoms included Fever, myalgia and severe headache. 57.2% of those followed up reported persistence of symptoms, commonly fatigue (53%), dyspnea on exertion (48%) and myalgia (18%). Conclusion and Recommendation: Infection control practices in non-COVID areas of the hospital needs to be stepped up. Adherence to masking and personal protection during clinical interactions and with colleagues needs to be maintained. Physical distancing at workplace and during mealtimes needs to be ensured by the system.