Data from: Impact of the COVID-19 pandemic and TCV introduction on typhoid fever in Nepal

Tamrakar, Dipesh1 2; Naga, Shivram2; Jung, Esther 3 ; Shrestha, Basuda4; Roka, Pratibha5; Pokharel, Rabin6; Shah, Sabin2; Bajracharya, Aarjya2; Mahadup, Surendra1; Katuwal, Nishan2; Doyle, Kate7; Seidman, Jessica7; Carter, Alice7; Luby, Stephen3; Bogoch, Isaac8; Aiemjoy, Kristen9 10; Garrett, Denise7; Shrestha, Rajeev2 1; Andrews, Jason3

Published Jan 13, 2026; Updated Feb 20, 2026 on Dryad. https://doi.org/10.5061/dryad.kprr4xhhj

Data files

Jan 13, 2026 version files 12.13 KB

AggregateCountsbyTime.csv

9 KB
README.md

3.14 KB

Feb 20, 2026 version files 4.06 MB

AggregateCountsbyTime.csv

9 KB
Deidentified_Individual_Data.csv

4.05 MB
README.md

3.67 KB

Abstract

While typhoid conjugate vaccines (TCV) offer promise for reducing risk in endemic settings, their population-level impact remains unclear. In 2022, Nepal introduced TCV nationally on the heels of the COVID-19 pandemic, which disrupted healthcare services, surveillance, and potentially typhoid transmission dynamics, complicating vaccine impact evaluation. We investigated the impact of TCV introduction amid shifting typhoid burden during the pandemic by analyzing blood culture data from four Kathmandu Valley health facilities, comparing culture positivity for Salmonella Typhi across three periods: pre-pandemic (January 2018-March 2020); pandemic, pre-vaccine introduction (April 2020-April 2022); post-vaccine introduction (May 2022-April 2024). S. Typhi blood culture positivity declined sharply during the pandemic before TCV introduction. The subsequent rollout of TCV substantially reduced typhoid burden in vaccine-eligible children; however, rising cases among older, vaccine-ineligible populations following the relaxation of pandemic measures highlight the need for additional control measures, such as improved water and sanitation infrastructure and broader age eligibility for typhoid vaccination.

Dataset DOI: 10.5061/dryad.kprr4xhhj

Description of the data and file structure

Blood culture data were collected from four Kathmandu Valley health facilities, which were used to compare culture positivity for Salmonella Typhi across three periods: pre-pandemic (January 2018-March 2020); pandemic, pre-vaccine introduction (April 2020-March 2022); post-vaccine introduction (April 2022-April 2024).

Files and variables

File directory

"AggregateCountsbyTime.csv": Aggregate counts of total blood cultures (TBC) and total Salmonella Typhi and Paratyphi positive results per site by month and year

"Deidentified_Individual_Data.csv": Individual de-identified data of culture findings

"owid-covid-data.xlsx": National COVID-19 case data sourced from Our World in Data (https://ourworldindata.org/covid-cases)

File content

The "AggregateCountsbyTime.csv" dataset includes 360 rows of 8 columns.

The included surveillance sites ("SITE") in which blood culture data was collected are abbreviated as the following:

Dhulikhel Hospital: "DH"
Bir Hospital: "BIR"
Helping Hands Hospital: "HH"
Kathmandu Model Hospital: "KMH"

The time period identifier ("Period") refers to the three analyzed periods:

Pre-pandemic (January 2018-March 2020) = 1
Pandemic, pre-vaccine introduction (April 2020-March 2022) = 2
Post-vaccine introduction (April 2022-April 2024) = 3

The remaining columns are in numeric format and refer to the following:

("YEAR") = Year of observation
("MONTH") = Month of observation (1-12)
("TBC") = Total blood culture count
("Typhi") = Count of cultures positivie for Salmonella Typhi
("Paratyphi") = Count of cultures positive for Salmonella Paratyphi
("OTHERS") = Count of other bacteria

The dataset contains 12 empty cells in the ("OTHERS") column that represent missing data where the count of other bacteria was not recorded or available. These have been left as empty cells to preserve the numeric data type for analysis scripts.

The "Deidentified_Individual_Data.csv" dataset includes 69,973 rows of 5 columns.

("Site") = Letter representing site (de-identified in accordance with HIPAA guidelines for individual data regarding geographic subdivisions smaller than a state as protected health information)
("YEAR") = Year of observation
("AGE") = Age in years
("SEX") = Sex assigned at birth
("FINDING") = Result of individual blood culture

Other publicly accessible locations of the data:

Our World in Data: https://docs.owid.io/projects/covid/en/latest/dataset.html

Data was derived from the following sources:

Hasell, J., Mathieu, E., Beltekian, D. et al. A cross-country database of COVID-19 testing. Sci Data 7, 345 (2020). https://doi.org/10.1038/s41597-020-00688-8
Edouard Mathieu, Hannah Ritchie, Lucas Rodés-Guirao, Cameron Appel, Daniel Gavrilov, Charlie Giattino, Joe Hasell, Bobbie Macdonald, Saloni Dattani, Diana Beltekian, Esteban Ortiz-Ospina, and Max Roser (2020) - “Coronavirus (COVID-19) Cases” Published online at OurWorldinData.org. Retrieved from: 'https://archive.ourworldindata.org/20260113-064045/covid-cases.html' [Online Resource] (archived on January 13, 2026).