key: cord-0803777-nn3mz7sf authors: Dhar, M. S.; Marwal, R.; VS, R.; Ponnusamy, K.; Jolly, B.; Bhoyar, R. C.; Fatihi, S.; Datta, M.; Singh, P.; Sharma, U.; Ujjainia, R.; Naushin, S.; Batheja, N.; Divakar, M. K.; Sardana, V.; Singh, M. K.; Imran, M.; Senthivel, V.; Maurya, R.; Jha, N.; Mehta, P.; Rophina, M.; VR, A.; Choudhary, U.; Thukral, L.; Pandey, R.; Dash, D.; Faruq, M.; Lall, H.; Gogia, H.; Madan, P.; Kulkarni, S.; Chauhan, H.; Sengupta, S.; Kabra, S.; The Indian SARS-CoV-2 Genomics Consortium,; Singh, S. K.; Agrawal, A.; Rakshit, P. title: Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India date: 2021-06-03 journal: nan DOI: 10.1101/2021.06.02.21258076 sha: d1342edbc3861cdcd92eff975a2abbada66b6435 doc_id: 803777 cord_uid: nn3mz7sf In April 2021, after successfully enduring three waves of the SARS-CoV2 pandemic in 2020, and having reached population seropositivity of about 50%, Delhi, the national capital of India was overwhelmed by the fourth wave. Here, we trace viral, host, and social factors contributing to the scale and exponent of the fourth wave, when compared to preceding waves, in an epidemiological context. Genomic surveillance data from Delhi and surrounding states shows an early phase of the upsurge driven by the entry of the more transmissible B.1.1.7 variant of concern (VOC) into the region in January, with at least one B.1.1.7 super spreader event in February 2021, relatable to known mass gatherings over this period. This was followed by seeding of the B.1.617 VOC, which too is highly transmissible, with rapid expansion of B.1.617.2 sub-lineage outpacing all other lineages. This unprecedented growth of cases occurred in the background of high seropositivity, but with low median neutralizing antibody levels, in a serially sampled cohort. Vaccination breakthrough cases over this period were noted, disproportionately related to VOC in sequenced cases, but usually mild. We find that this surge of SARS-CoV2 infections in Delhi is best explained by the introduction of a new highly transmissible VOC, B.1.617.2, with likely immune-evasion properties; insufficient neutralizing immunity, despite high seropositivity; and social behavior that promoted transmission. After escaping relatively unscathed during the first wave of the COVID-19 pandemic, and after a brief respite from November 2020 until Feb 2021, India witnessed a ferocious second Covid- 19 wave, accounting for about half the cases worldwide in the first week of May 2021. SARS-CoV-2 had spread widely throughout India in the first wave, with initial results from the Indian We have previously shown in a cohort-based serosurvey that high seropositivity was associated with declining test positivity rate across India in September, but there is a 20-30% decline in neutralizing activity over a 6 month period (Naushin et al., 2021) . A follow-up study of the same cohort was conducted in January and February 2021, with semi-quantitative antinucleocapsid, quantitative anti-spike, and a neutralization surrogate assay being measured. 473 of 1115 employees were seropositive across ten Delhi sites where we have serial data. When compared to the prior serosurvey in August/September 2020, that seropositivity had increased across these sites in Delhi ( Figure 2 ). The seropositivity was unevenly distributed, with samples collected from laboratories and public-office employees having much higher seropositivity Tests conducted Confirmed cases Positivity rate All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2021. ; than samples collected from family members living at residential complexes. The median level of anti-spike antibodies in this sample from Delhi was well below 132 U/ml, the cutoff for convalescent plasma titres, suggesting that the protection against infection may be limited to a subset of the sero-positive fraction ( Figure 2B ) (USFDA, 2021). Further, in 35 sero-positive cases from 2020 under follow-up, retested in April 2021 and with three or more time-points since 2020, three showed a greater than 100 U and more than 50% increase in antibody levels after a decline, suggestive of possible reinfections and limited immunity. Red dash dot line denotes convalescent plasma titres considered to be sufficient for immunity: 132 U/ml C) Log Antibody Levels (x-axis) against surrogate Neutralizing Antibody Percentage (y-axis) in Delhi from Phase 2 data of CSIR-Cohort (Pearson's r -0.74). Blue dash dot line along xaxis denotes 30% neutralization (cut-off) and along y-axis denotes plasma titres considered to be sufficient for immunity: 132 U/ml To determine whether SARS-CoV2 variants may be responsible for the April 2021 outbreak in Delhi, we sequenced and analyzed the community samples from Delhi from the previous outbreak in November 2020 until May 2021 and related it to effective reproductive number (Rt). It can be seen in Fig 3A that detection Fig. 2A ). This may be due to the sudden decrease of All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. was rising again towards the end of the period. Since CFR may be due to an amalgamation of multiple factors, including the short-term collapse of the healthcare system, there is currently no clear evidence linking B.1.617.2 to change in CFR. This will be reexamined once final information is available on all deaths and COVID-related deaths over this period. All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2021. ; All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2021. ; https://doi.org/10.1101/2021.06.02.21258076 doi: medRxiv preprint The All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (Figure 5a) . It is noted that when compared to population prevalence ( Figure 3A) (Fig 5b) . (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2021. ; To understand the molecular interactions, we generated a structural model representing B.1.617.2 spike protein, as shown in Figure 7 . The resulting map provides insights into the plausible mechanisms of regulation of virus entry and binding. It contains seven mutations in the spike protein, excluding the predominant D614G substitution. Three of these mutations, two substitutions (T19R and R158G) and one deletion (ΔE156-F157), were found in NTD region. The six nucleotides spanning the entire stretch of deletion (ΔE156-F157) was juxtaposed with R158G mutation, with one nucleotide of glycine contributed from E156 and the rest two nucleotides contributed by R158, resulting in GGA codon for glycine. The mutations within NTD occur on N1 and N3 loops that composes the prominent mABs recognition sites Chi et al, 2020; Naveenchandra, et al.,2021) . In our mutated model, R19 and All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2021. ; https://doi.org/10.1101/2021.06.02.21258076 doi: medRxiv preprint G158 residues are surface accessible while in wild-type the T19, E156-F157 were relatively buried. We also found a unique RBD mutation T478K, in addition to previously reported L452R in All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2021. ; Figure 7: Mutant spike protein of B.1.617.2 lineage. The structural model of spike protein with seven mutations was generated and side-chains are highlighted in blue and red color to illustrate amino-acid substitutions. On the right panel, we show a zoomed snapshot of three critical regions namely, NTD, RBD, and furin cleavage sites. The location of mutated residues is marked in red and, and critical regions such as RBM and S1/S2 site is highlighted for clarity. Northern India underwent seeding with B.1.1.7 in February 2021 followed by regional outbreaks that stretched the healthcare system but remained within its capacity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted June 3, 2021. ; https://doi.org/10.1101/2021.06.02.21258076 doi: medRxiv preprint rising outbreaks with vaccination breakthroughs. We would re-emphasize that prior infections, high seropositivity and partial vaccination are insufficient impediments to its spread, as seen in Delhi, and strong public health response will be needed globally for its containment. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is a qualitative kit which was used for screening and a Cut-off index COI >1 was considered seropositive. Positive samples were further tested for quantitative antibody titers using the same manufacture's kit directed against the spike protein (S-antigen). An antibody levels >0.8 U/ml was considered sero-positive as per manufacturer's protocol. The detection range of this kit is from 0.4 U/ml to 250 U/ml. For samples, where values of >250 U/ml were obtained; appropriate dilutions were made. Neutralizing antibody (NAB) response directed against the spike protein (RBD site) was assessed using GENScript cPass kit which is a surrogate virus neutralization test (sVNT). A value of 30% or above was considered to have neutralizing ability. In total of 8,477 SARS-CoV-2 genomes were annotated for amino-acid substitutions by SnpEff All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 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The copyright holder for this preprint this version posted Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2 A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England The establishment of reference sequence for SARS-CoV-2 and variation analysis Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation Acknowledgments -Support from Ministry of Health and Family Welfare, Council of Scientific and Industrial Research, and Department of Biotechnology, India, is acknowledged.