A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India

BACKGROUND

Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data.

METHODS

A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a "band of five" outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3-4), and geospatial mapping (Band 5).

RESULTS

The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM.

CONCLUSIONS

The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implications for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.

Case Report: A Fatal Case of Babesiosis in a Splenectomized Male Patient from Western India

Human babesiosis is a rare disease, caused by Babesia species and commonly transmitted by tick bite. Although human babesiosis is known to be asymptomatic in immunocompetent hosts, clinical cases of severe babesiosis have been reported from splenectomized or immunocompromised individuals. To our knowledge, only one case of human babesiosis in India has been previously reported. Here, we report a case of severe babesiosis with high parasitemia (∼70%) in a 30-year-old asplenic farmer. The patient presented with fever, yellowish discoloration of skin, oliguria, and anemia; he eventually developed multiorgan failure syndrome and died. Peripheral blood films were prepared and used to confirm the presence of piroplasms by microscopy. Total DNA isolated from blood was used for 18S ribosomal RNA gene fragment amplification by polymerase chain reaction, which was subject to Sanger sequencing. Although 18S sequence indicated that the Babesia species infecting the patient was similar to that of other Babesia species originating from wild mammals, species identification could not be done. Phylogenetic analysis revealed that the patient-derived pathogen is distinct because it forms a separate clade in the cladogram.

Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2

To understand the spread of SARS-CoV2, in August and September 2020, the Council of Scientific and Industrial Research (India) conducted a serosurvey across its constituent laboratories and centers across India. Of 10,427 volunteers, 1058 (10.14%) tested positive for SARS-CoV2 anti-nucleocapsid (anti-NC) antibodies, 95% of which had surrogate neutralization activity. Three-fourth of these recalled no symptoms. Repeat serology tests at 3 (n = 607) and 6 (n = 175) months showed stable anti-NC antibodies but declining neutralization activity. Local seropositivity was higher in densely populated cities and was inversely correlated with a 30-day change in regional test positivity rates (TPRs). Regional seropositivity above 10% was associated with declining TPR. Personal factors associated with higher odds of seropositivity were high-exposure work (odds ratio, 95% confidence interval, p value: 2.23, 1.92-2.59, <0.0001), use of public transport (1.79, 1.43-2.24, <0.0001), not smoking (1.52, 1.16-1.99, 0.0257), non-vegetarian diet (1.67, 1.41-1.99, <0.0001), and B blood group (1.36, 1.15-1.61, 0.001).