Infectious diseases carry large global burdens and have implications for society at large. Therefore, reproducible, transparent research is extremely important.
We evaluated transparency indicators (code and data sharing, registration, conflict and funding disclosures) in the 5340 PubMed Central Open Access articles published in 2019 or 2021 in the 9 most-cited specialty journals in infectious disease using the text-mining R package, rtransparent.
5340 articles were evaluated (1860 published in 2019 and 3480 in 2021 (of which 1828 on COVID-19)). Text-mining identified code sharing in 98 (2%) articles, data sharing in 498 (9%), registration in 446 (8%), conflict of interest disclosures in 4209 (79%) and funding disclosures in 4866 (91%). There were substantial differences across the 9 journals: 1-9% for code sharing, 5-25% for data sharing, 1-31% for registration, 7-100% for conflicts of interest, and 65-100% for funding disclosures. Validation-corrected imputed estimates were 3%, 11%, 8%, 79% and 92%, respectively. There were no major differences between articles published in 2019 and non-COVID-19 articles in 2021. In 2021, non-COVID-19 articles had more data sharing (12%) than COVID-19 articles (4%).
Data sharing, code sharing, and registration are very uncommon in infectious disease specialty journals. Increased transparency is required.

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