Dear Editor,
In the present study, we report the early evidence of community transmission of SARS-CoV-2 variant, Omicron (B.1.1.529) in the Delhi population. To the best of our knowledge, this is the first study from India highlighting the epidemiological and clinical presentation of the Omicron infections in the National capital. This study holds importance due to the unique position of Delhi in, 1) experiencing a high caseload during previous waves, 2) having seropositivity of 89.5% and 3) having a record of excellent vaccination coverage [[1], [2], [3]].
The respiratory specimens from all RT-PCR positive cases between November 25th-December 23rd 2021 from five districts of Delhi (South, South-East, South-West, East, and West) were subjected to sequencing at the Institute of Liver and Biliary Sciences, Delhi. The details of submitted sequences on GISAID are provided in Supplementary Table S1.
Among the 332 samples sequenced, 264 were quality passed and were included in analysis. Omicron was identified in 82 (31.06%) cases with BA.1 in 73.1% and BA.2 in 26.9% while Delta and its sub-lineages in 182 cases (68.9%). A total of 39.1% of Omicron cases had either travel or contact, compared to only 3.3% of Delta cases. A higher proportion of Omicron was reported among vaccinated groups. The majority of Omicron cases (61%) were asymptomatic. Re-infection was documented in 17.1% of Omicron cases, as compared to 8.2% in Delta. Overall, 15 cases (9.6%) required hospitalization, the majority of them with underlying co-morbidities. Mortality was noted in 1.2% cases (n = 2), both infected with Delta variant (Table 1 ). Among Omicron cases, 32 cases were having international travel and/or their contacts history, and the rest 50 were of community transmission. Asymptomatic cases were proportionately higher among travelers/contacts compared to the community (Table 1).
Table 1.
Clinical and demographic characteristics of the studied population (November 25th-December 23rd 2021).
| Clinical and demographic characteristics of SARS-CoV-2 infected cases | ||||
|---|---|---|---|---|
| Characteristics | Category | Total cases (N = 264) | Delta cases (N = 182) | Omicron cases (N = 82) |
| Age, Median (IQR), years | 40(28–56) | 42 (22–62) | 35(24–53) | |
| <18 years, n(%) | 27(10.2) | 15(8.2) | 12 (14.6) | |
| 18–60 years, n(%) | 182(68.9) | 132(72.5) | 56 (68.3) | |
| >60 years, n(%) | 55(20.9) | 35(19.2) | 14 (17.1) | |
| Sex | Male, n(%) | 150 (56.8) | 103(56.5) | 47 (57.3) |
| Female, n(%) | 114 (43.2) | 79(43.4) | 35 (42.7) | |
| Vaccination statusa | Vaccinated, n(%) | 213(80.6) | 141(77.5) | 72 (87.8) |
| Unvaccinated, n(%) | 19 (7.1) | 9(4.9) | 10 (12.2) | |
| Unknown, n(%) | 32 (12.1) | 32(17.6) | 0(0) | |
| Travellers/Contacts | Yes, n(%) | 38 (14.4) | 6(3.3) | 32 (39.1) |
| No, n(%) | 226 (85.6) | 176(96.7) | 50 (60.9) | |
| Previous SARS-CoV-2 infection confirmed by RT-PCRbc (n = 155) | Yes, n(%) | 20(12.9) | 6 (8.2) | 14 (17.1) |
| No, n(%) | 135(87) | 67 (91.8) | 68 (83.9) | |
| Clinical featuresc (n = 155) | Asymptomatic | 64(41.2) | 14(19.2) | 50 (61.0) |
| Symptomatic | 91(58.7) | 59(80.8) | 32 (39.0) | |
| Comorbidityc (n = 155) | Diabetes Mellitus | 39 (25.1) | 29 (39.7) | 10(12.2) |
| Hypertension | 27 (17.4) | 20(27.4) | 07 (8.5) | |
| Chronic lung disease | 05 (3.2) | 0(−) | 05 (6.1) | |
| Chronic kidney disease | 02 (1.2) | 0(−) | 02(2.4) | |
| Hospitalizationc (n = 155) | Yes | 15 (9.6) | 12(16.4) | 03(3.6) |
| Intensive care treatmentc (n = 155) | Yes | 05 (3.2) | 05(6.8) | 0(0) |
| Mortality |
02 (1.2) |
02(2.7) |
0(0) |
|
| Comparison between Omicron cases with travel/contact history and community origin | ||||
| Characteristic |
Community (N = 50) |
Travellers/Contacts (N = 32) |
p-value |
|
| Asymptomatic, n (%) | 27 (54) | 23 (71.8) | 0.1 | |
| Symptomatic, n (%) | 23 (46) | 09 (28.1) | ||
| Previous SARS-CoV-2 infection confirmed by RT-PCRb, n (%) | 9 (18) | 5 (15.6) | 0.78 | |
| Co-morbidities, n (%) | 9 (18) | 6 (18.7) | 0.93 | |
Vaccinated with two doses of any one of these: ChAdOx1 nCoV-19(Covishield, Serum Institute of India, Pune), BBV152 (Covaxin; Bharat Biotech International, Hyderabad), Pfizer-BioNTech (BNT162b2) vaccine, Moderna(mRNA-1273), Sputnik V (Gam-COVID-Vac) andAd26.COV2.S(Johnson & Johnson–Janssen)vaccine at least 30 days before positive test.
Previous infection is defined as having a positive PCR test more than 90 days from the current sample.
The data was available for 155 cases, among which Delta cases were 73 and Omicron were 82.
Overall, the majority of SARS-CoV-2 cases were reported from South (45%) district (Fig. 1 A), whereas the Omicron cases were identified from the West (49%), followed by South-West (40%) district (Fig. 1B). The first two cases of Omicron were detected during the first week of December, both with travel history from South Africa following which an exponential rise in Omicron cases was observed leading to its community spread (1.8%–54%) (Fig. 1C). When Omicron cases (n = 82) were geotagged, we found the formation of six local clusters (three each from West and South-East) (Fig. 1D). Among these, 46.3% (n = 38) belonged to 14 families. Out of these 14 family clusters, only four (5 individuals) had international travel history, while three of them contracted Omicron infection following contact with a non-family member having international travel history. The remaining seven families contracted Omicron due to possible community transmission (Fig. 1E).
Fig. 1.
Lineage and timeline profile of SARS-CoV-2 in Delhi (November 25th- December 23rd, 2021) with formation of local clusters and eventual community transmission of Omicron. A) The district-wise distribution of cases (n = 264). B) Variant distribution across five districts of Delhi. The Omicron BA.1 is shown in red and BA.2 in orange colour. The Delta parent lineage (B.1.617.2) is shown in blue and rest Delta sub-lineages in grey colour. C) Daily progression of SARS-CoV-2 lineages with respect to travel history and community transmission. T/C- History of Travel or Contact; NoT- No history of travel or contact. D) Geo-tagging of Omicron cases (n = 82) from five districts of Delhi. Black dotted circles represent local cluster with three or more cases in close vicinity. Red solid circles denote multiple cases from same families. Cases are labeled based on confirmed travel history (Green), Contacts of cases with travel history (Red) and cases with no travel history (Blue). E) Location of family clusters in Delhi. A total of 14 families with 38 Omicron cases were identified. Plotted here are families colored by their respective travel history, possible community acquired infection and both. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Our study documented a definite shift from Delta to Omicron predominance along with its community spread. We observed significantly increased breakthrough infections, decreased hospitalization, and lower rates of symptomatic infections among individuals from the highly seropositive Delhi population. Our data point towards several reasons of concern, (i) a rapid community spread shortly after the introduction of the first Omicron case in Delhi and (ii) a high proportion of Omicron infections among fully vaccinated individuals.
Author contributions
Conceptualization:E.G, A.A, S.K.S.; Data curation: R.A, R.G., P.G, V.S., A.B.; Formal Analysis:P.G.,R.G.;Fundingacquisition:E.G.,C.B.,A.A,S.K.S.Experiments:V.S.,U.S.K,S.D.;Project administration:E.G.,C.B., S.K.S.;Resources:E.G., C.B., A.A, S.K.S.; Supervision: E.G., C.B., A.A,S.K.S.; Visualization: P.G.; Writing – original draft: R.G.,P.G.,Writing – review & editing: E.G, R.G., P.G., R.A., S.K.S, A.A.
All authors have read and agreed to the published version of the manuscript.
Data availability statement
All the sequences have been submitted to the GISAID database (Supplementary Table S1).
Declaration of competing interest
The authors declare no conflict of interest.
Acknowledgments
We acknowledge the Government of NCT, Delhi for facilitating the Whole Genome Sequencing Laboratory for COVID-19 at our institute. We also extend our gratitude to National Liver Disease Biobank, ILBS, New Delhi for providing Next Generation Sequencing platforms.
Footnotes
Supplementary data to this article can be found online at https://doi.org/10.1016/j.tmaid.2022.102276.
Appendix A. Supplementary data
The following is the Supplementary data to this article:
References
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Data Availability Statement
All the sequences have been submitted to the GISAID database (Supplementary Table S1).