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BackgroundOmicron a new variant of SARS COV2 was first detected in November 2021. This was believed to be highly transmissible and evade immunity as a result urgent need was felt to screen all positive, identify Omicron cases and isolate them to prevent spread of infection and study their clinico-epidemiological profile. MethodologyAll positive cases detected in state of Rajasthan during November to January beginning were selected for next generation sequencing. Processing was done as per protocol on Ion Torrent S5 system for 1210 samples and bioinformatics analysis was done. ResultsAmong the 1210 samples tested 762(62.9%) were Delta/Delta like and other lineages, 291(24%) were Omicron and 157(12.9%) were invalid or repeat samples. Within a month the proportion of Delta and other variants was reversed, from zero omicron became 81% and delta and other variants 19%, initially all omicron cases were international travelers and their contacts but soon community transmission was seen. Majority of omicron patients were asymptomatic (56.7%) or had mild disease (33%), 9.2% had moderate symptoms and 2(0.7%) had severe disease requiring hospitalization, of which one (0.3%) died and rest (99.7%) recovered. History of vaccination was seen in 81.1%, of previous infection in 43.2%. Among the Omicron cases BA.1 (62.8%) was the predominant lineage followed by BA.2(23.7%) and B.1.529 (13.4%), however rising trends were seen initially for BA.1 and later for BA.2 also. ConclusionIn very short time Omicron has spread in community and has taken over the preexisting Delta/Delta like and other lineages, it evades immunity, but the good part is most of the cases were asymptomatic or had mild disease and mortality rate was very low.
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HighlightsWith the emergence of the Variant of Concern, omicron (B.1.1.529), India has enhanced genomic surveillance in international travellers. The omicron variant was detected in 59 cases from different States; 40 from Maharashtra, 17 from Rajasthan and one each from Gujrat and Tamil Nadu. The positive cases and their contacts were asymptomatic and genomic surveillance could identify two clusters, one from Maharashtra and another from Rajasthan.
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Emergence of Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) Variants of Concern (VOC) possessing improved virulence, transmissibility and/or immune-escape capabilities has raised significant public health concerns. In order to identify VOCs, WHO recommends Whole-Genome Sequencing approach, which is costly and involves longer completion time. Hence, potential role of commercial multiplex RT-PCR kit to screen variants rapidly is being attempted in this study. A total of 1200 suspected COVID samples from different districts of Tamil Nadu State (India) were screened with Thermo TaqPath RT-PCR kit and Altonas Realstar RT-PCR Assay kit. Among 1200 screened, S-gene target failure (SGTF) phenomenon were identified in 112 samples while testing with TaqPath RT-PCR Kit. 100% concordant results were observed between SGTF phenomenon and whole-genome sequencing (WGS) results in detecting SARS-CoV-2 VOC B.1.1.7. TaqPath RT-PCR assay testing can be utilized by laboratories to screen rapidly the VOC B.1.1.7 variants, thus enabling early detection of B.1.1.7 variant infection and transmission in population. This in turn will pave way to implement suitable preventive measures by appropriate authorities to control the transmission of the viral variant.
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Background: Recent studies on antiviral susceptibiliy from South-East Asia,Europe and the United States have shown sporadic neuraminidase inhibitor (NAI)resistance in A(H1N1)pdm09 viruses. We undertook a study to evaluate NAIresistance in these viruses isolated in India.Methods: Pandemic influenza viruses, isolated from 2009 to 2013, along withclincal samples were genetically analysed for known resistance markers in theneuraminidase (NA) gene. Clinical samples (n=1524) were tested for H275Y (N1numbering; H274Y in N2 numbering) mutation by real time reverse transcriptasePCR (rRT-PCR). One hundred and ten randomly selected resistant and sensitiveviruses were analysed by phenotypic assay.Results: All but one of the 2013 A(H1N1)pdm09 isolates were sensitive tooseltamivir. Genetic analysis of this isolate as well as the original clinical materialshowed that the presence of H275Y mutation was responsible for reducedsusceptibility to oseltamivir in the patient. This was confirmed by phenotypic assay.Conclusion: The emergence of a pandemic influenza strain resistant to oseltamiviremphasizes the need for monitoring antiviral resistance as part of the NationalInfluenza Programme in India
