Fig 1.
District wise distribution of SARS-CoV-2 positive cases in Karnataka sampled between March 5, 2020 to May 21, 2020.
Left—Map of India highlighting the state of Karnataka. Right—Heat map shows the distribution of cases across 30 districts in Karnataka with high burden districts in deep purple. Size of the circle is proportional to the number of cases tested at our centre (green) and the number of cases sequenced (lime). The density of cases are represented by the heat map (horizontal bar) and concentric circles.
Table 1.
Characteristics of positive cases.
Fig 2.
Seven lineages of SARS-CoV-2 circulating in Karnataka.
(A) Pie chart shows the proportion of different lineages of 91 SARS-CoV-2 sequences from this study. (B) Maximum likelihood tree was constructed from 91 complete genomes with the reference (NC_045512) and hCoV19/Wuhan/WH04/2020 as the outgroup. Bootstrap support values over 80 are shown. (C) Time scaled maximum likelihood tree of genomes from this study providing a chronology to introduction/importation events and propagation of the lineages post introduction into the state. Sequences are coloured by lineage, grey lines indicate sequences that were reassigned to parent or sister clades. Grey circles indicate sequences from symptomatic individuals. (D) Figure shows SNP frequency for different lineages. The x-axis shows the genome position of the SNP and the y-axes represent the frequency (number of sequences from the lineage that have the SNP/total number of sequences in the lineage). Rows 1–7 represent the seven lineages from Karnataka. Gene boundaries are shaded in blue. Lineage defining SNPs are marked with *. Details of SNPs are provided in S2 Table.
Fig 3.
Contact graphs showing lineages, clinical state, and geographical location of clusters.
The graphs were made from analysis of contacts from the state line-list of cases and 91 sequences clustered into 17/104 clusters and 24 singletons (individuals with no known contact). These 17 clusters (C1-C17) and 24 singletons (n = 333 individuals) are shown in all the panels (A-C). (A) Contact graph with individuals from whom genomes were obtained are coloured by lineage. Note: Lineages were assigned to all 24 singletons. (B) Contact graph of sequenced clusters and singletons are coloured by clinical status—symptomatic or asymptomatic. Orange depicts symptomatic individuals and black represents the asymptomatic individuals. (C) Graph representing geographic distribution of contact cluster by place of residence. Note: Most of the clusters are restricted to a district. A minority of cases (blue) are from districts other than those listed.
Table 2.
Lineage assignments of positive cases with no known contacts.
Fig 4.
Time course of positive cases in Karnataka by cluster and lineage.
The x-axis represents time (March 5-May21, 2020). The y-axis represents number of cases. Note, the first row shows the epi curve, with each bar representing the number of cases recorded on a day while rows 2–11 show the cumulative fraction of cases for the top ten clusters. In rows 2–11, each coloured dot within a vertical bar represents a sequenced sample collected on that date. The dots are coloured by lineage as show in column 2 in the figure. Date of interventions are demarcated by vertical lines and described on top -(a) International travel ban (passenger aircrafts) (b) Closure of domestic travel routes including railways and airways (c) Nationwide lockdown 1.0 (d) Quarantine of migrant workers to restrict movement (e) Nationwide lockdown 2.0 (f) Zone wise easing of movement restrictions.