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Year : 2020  |  Volume : 152  |  Issue : 1  |  Page : 111-115

Identification of SARS-CoV-2 clusters from symptomatic cases in India

1 Department of Microbiology, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
2 Maximum Containment Laboratory, ICMR-National Institute of Virology, Pune 411 021, Maharashtra, India
3 Department of Medicine, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India
4 Department of Microbiology, S.N. Medical College, Agra 282 002, Uttar Pradesh, India
5 Department of Radiotherapy, King George's Medical University, Lucknow 226 003, Uttar Pradesh, India

Date of Submission06-Jun-2020
Date of Web Publication17-Sep-2020

Correspondence Address:
Amita Jain
Department of Microbiology, King George's Medical University, Lucknow 226 003, Uttar Pradesh
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ijmr.IJMR_2411_20

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How to cite this article:
Jain P, Prakash O, Nyayanit DA, Verma AK, Yadav PD, Khan DN, Prakash S, Mishra H, Reddy H, Agarwal A, Bhatt MB, Jain A. Identification of SARS-CoV-2 clusters from symptomatic cases in India. Indian J Med Res 2020;152:111-5

How to cite this URL:
Jain P, Prakash O, Nyayanit DA, Verma AK, Yadav PD, Khan DN, Prakash S, Mishra H, Reddy H, Agarwal A, Bhatt MB, Jain A. Identification of SARS-CoV-2 clusters from symptomatic cases in India. Indian J Med Res [serial online] 2020 [cited 2021 Apr 17];152:111-5. Available from:


In December 2019, cases of pneumonia-like illness due to an unknown aetiological agent were reported in Wuhan city, Hubei province of China[1]. The aetiological agent was identified as a member of the Coronaviridae family and was termed the 2019 novel Coronavirus. Due to its genetic similarity with the severe acute respiratory syndrome (SARS) of 2003, the International Committee on Taxonomy of Viruses renamed it as SARS coronavirus 2 (SARS-CoV-2)[2]. The first case of SARS-CoV-2 was reported from Kerala, India, on January 30, 2020[3] and since then, the numbers are increasing continuously. The present study is a retrospective analysis of two clusters of laboratory-confirmed coronavirus disease 2019 (COVID-19) patients from India and highlights their series of events, clinical features and sequence analysis. The present study is a retrospective analysis of two clusters of laboratory-confirmed coronavirus disease 2019 (COVID-19) patients from India and highlights their series of events, clinical features and sequence analysis.

This study was conducted in the departments of Microbiology and Medicine, King George's Medical University (KGMU), Lucknow, Uttar Pradesh (UP), India. The study protocol was approved by the Institutional Ethics Committee (251/Ethics/2020).

People in close contact with a laboratory-confirmed case and persons who had undertaken international travel within the last 14 days and had developed symptoms, were taken as SARS-CoV-2 suspects as per the prevailing recommendations of the Ministry of Health and Family Welfare, Government of India[4]. These cases were either admitted in the medical wards of KGMU or other district hospitals or were traced by the team of UP Integrated Disease Surveillance Programme (UP-IDSP) during March 2020. Nasal and throat swabs were collected from these individuals and transported to the virology laboratory at the department of Microbiology, KGMU, in a virus transport medium maintaining a cold chain. RNA was extracted using the commercial kits as per the manufacturer's instructions (Thermo Fisher Scientific, USA) and screened for the SARS-CoV-2 specific E gene using real-time reverse transcription-polymerase chain reaction (RT-PCR)[5]. The E gene-positive samples were confirmed by real-time RT-PCR assay targeting the HKU-ORF1b and RdRp genes[5]. Clinical, demographic, contact and international travel details of the individuals were recorded from the clinical record forms.

Statistical analysis was done using GraphPad Prism v5.0 (GraphPad Software Inc., San Diego, CA, USA).

Inter-group comparisons of continuous variables were done using Chi-square test.

Extensive contact tracing was done by employing personal and family interviews of the SARS-CoV-2-positive patients along with a check on their travel history. All the known contacts were quarantined and monitored for the development of disease symptoms, and their samples were also subjected to real-time RT-PCR testing.

A total of 1,473 patients were referred from various districts of Uttar Pradesh to the department of Microbiology, KGMU, where they were tested for SARS-CoV-2, of whom 29 (1.96%) patients tested positive from March 3 to 31, 2020. The hierarchy of contact tracing for the two clusters of cases, one from Agra and the other from Lucknow, was observed from the positive cases detected, which is depicted in [Figure 1].
Figure 1: Depiction of the two different clusters studied. The first cluster had travel history to Budapest, Hungary; Amsterdam (Holland), Iceland. The second cluster had travel history to Canada and the UK along with their contact cases. TCO and TCP numbers represent patient ID; FM, family member; HCW, healthcare worker.

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The two index cases of the first cluster from Agra (TCO461, -462) had sore throat and travel history to Milan, Italy; Budapest, Hungary; Amsterdam (Holland) and Iceland. Three of the 10 samples (TCO464, -465, -467) from the family members of these patients tested positive for SARS-CoV-2. A total of 233 contacts of these five positive cases were also tested, of whom two five were found to be positive within 14 days of coming in contact with the index cases. Of these, one (TCO788) was symptomatic and the other was asymptomatic (TCO869). No further cases could be linked to this cluster. The index case of the second cluster (TCP057) was a symptomatic traveller from Canada. The healthcare worker (TCP504) who attended the index case without appropriate personal protective equipment developed symptoms on day 5 of attending the index case and tested positive. Later, three family members of TCP504 (TCP745, -746,

-747) also tested positive [Figure 1], but no other contact was found to be positive. All the positive cases were hospitalized, and their contacts were home quarantined for 14 days.

The age, sex, history of travel or contact and their symptoms are mentioned in the [Table 1]. The median age of the infected patients was 37 yr (age range: 15-72). The majority of the patients (7, 58.3%) were found to be asymptomatic (did not develop any symptom over a 10 day follow up period); four (33.3%) had mild symptoms such as sore throat, body ache or fever and only one (8.3%) had breathlessness. The cyclic threshold values (Ct values) for the E gene of SARS-CoV-2 are shown in the Table. No significant difference was observed among the Ct values of the symptomatic (range: 18.89 to 26.93) and asymptomatic (range: 15.23 to 35.39) patients. The symptomatic cases could be linked to new cases. However, none of the asymptomatic patients could be linked to a new case. Recent studies have observed that the percentage of asymptomatic and symptomatic cases infecting others varied from 0 to 2.2 per cent and 0.8 to 15.4 per cent, respectively[6],[7].
Table 1: Demographic and clinical details of the index cases and their contacts demonstrating two clusters and details of whole genome (WG) sequencing

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Clinical samples that formed two different clusters were sequenced using next-generation sequencing at the ICMR-National Institute of Virology, Pune[8],[9]. The complete genome sequences retrieved from this study were aligned with the SARS-CoV-2 sequences downloaded from the Global Initiative on Sharing All Influenza Data (GISAID) database[10]. The alignment was done in the CLC Genomics Workbench (Qiagen Aarhus, v11.0, Aarhus C, Denmark), and the tree was generated [Figure 2] using the MEGA software v7.0[11] and visualized in the Figtree v1.4.2 (
Figure 2: Phylogenetic tree for the SARS-CoV-2 sequences from India: A phylogenetic tree based on the Kimura-2-parameter model is generated using the MEGA software. A bootstrap replication of 1000 cycles was performed to assess the statistical robustness of the tree generated. The figure is displayed using Figtree v1.4.2. Different clades are marked using colours on branches and taxa. Branch colours: light red colour → A2a clade, pink colour → B4, violet → A1a, green colour → A3. Taxa colour: brown colour → B clade and blue colour → B1 clade,

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The Ct values for the E gene of the seven genomes using real-time RT-PCR ranged from 15.23 to 26.93. The details of Ct values, along with the percentage of relevant reads mapped and genome size recovered, are given in the Table. The phylogenetic analysis of the retrieved sequences demonstrated that the sequences formed two different groups that matched sequences from Italy and Canada. Despite segregating into different groups, the sequences studied clustered in genotype A2a, as observed in the Nextstrain site (, analyzed for the other Indian SARS-CoV-2 sequences. Further comparison of the amino acid variation between the sequences retrieved in this study demonstrated a single change at N gene. The hCoV-19/TCP-057/India/2020 and hCoV-19/TCP-504/India/2020 had histidine at amino acid position 343, whereas the other sequences had aspartic acid.

In conclusion, the present pilot study showed that the majority of the SARS-CoV-2-positive patients were asymptomatic. Chances of asymptomatic cases infecting others were less likely as compared to that of symptomatic cases. The analysis of a larger sample of patients needs to be conducted to confirm this interpretation.

Acknowledgment: Authors acknowledge the Indian Council of Medical Research and Department of Health Research, Ministry of Health and Family Welfare, New Delhi, for providing the testing reagents for real-time RT-PCR. We also acknowledge UP-IDSP Team for performing the contact tracing.

Financial support & sponsorship: None.

Conflicts of Interest: None.

   References Top

Chan JF, Kok KH, Zhu Z, Chu H, To KK, Yuan S, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg MicrobesInfect 2020; 9 : 221-36.  Back to cited text no. 1
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species severe acute respiratory syndrome-related coronavirus: Classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5 : 536-44.  Back to cited text no. 2
Andrews MA, Areekal B, Rajesh KR, Krishnan J, Suryakala R, Krishnan B, et al. First confirmed case of COVID-19 infection in India: A case report. Indian J Med Res 2020; 151 : 490-2.  Back to cited text no. 3
Ministry of Health and Family Welfare, Government of India. COVID 19 India. Available from:, accessed on March 3, 2020.  Back to cited text no. 4
Choudhary ML, Vipat V, Jadhav S, Basu A, Cherian S, Abraham P, et al. Development of in vitro transcribed RNA as positive control for laboratory diagnosis of SARS-CoV-2 in India. Indian J Med Res 2020; 151 : 251-4.  Back to cited text no. 5
Luo L, Liu D, Liao X, Wu X, Jing Q, Zheng J, et al. Modes of contact and risk of transmission in COVID-19 among close contacts. medRxiv 2020. doi: 10.1101/2020.03.24.20042606.  Back to cited text no. 6
Cheng HY, Jian SW, Liu DP, Ng TC, Huang WT, Lin HH, et al. Contact tracing assessment of COVID-19 transmission dynamics in Taiwan and risk at different exposure periods before and after symptom onset. JAMA Intern Med 2020; e202020.   Back to cited text no. 7
Yadav PD, Albariño CG, Nyayanit DA, Guerrero L, Jenks MH, Sarkale P, et al. Equine Encephalosis virus in India, 2008. Emerg Infect Dis 2018; 24 : 898-901.  Back to cited text no. 8
Yadav PD, Nyayanit DA, Shete AM, Jain S, Majumdar TP, Chaubal GY, et al. Complete genome sequencing of Kaisodi virus isolated from ticks in India belonging to Phlebovirus genus, family Phenuiviridae. Ticks Tick Borne Dis 2019; 10 : 23-33.  Back to cited text no. 9
Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data - From vision to reality. Euro Surveill 2017; 22 : 30494.  Back to cited text no. 10
Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33 : 1870-4.  Back to cited text no. 11


  [Figure 1], [Figure 2]

  [Table 1]

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