Introduction: Infectious diseases carry a large global burden and have implications for society at large. Therefore, reproducible, transparent research is extremely important. To assess the current state of transparency in this field, we investigated code sharing, data sharing, protocol registration, conflict of interest and funding disclosures in articles published in the most influential infectious disease journals. Methods: We evaluated transparency indicators in the 5340 PubMed Central Open Access (PMC OA) articles published in 2019 or 2021 in the 9 most-cited specialty journals in infectious disease. We used a previously validated text-mining R package, rtransparent. The approach was manually validated for a random sample of 200 articles for which study characteristics were also extracted in detail. Main comparisons assessed 2019 versus 2021 articles, 2019 versus 2021 non-COVID-19 articles, and 2021 non-COVID-19 articles versus 2021 COVID-19 articles. Results: A total of 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 in the proportion of articles fulfilling each transparency indicator: 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. 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%). Validation-corrected imputed estimates were 3% for code sharing, 11% for data sharing, 8% for registrations, 79% for conflict of interest disclosures and 92% for funding disclosures. Conclusion: Data sharing, code sharing, and registration are very uncommon in infectious disease specialty journals. Increased transparency is required.
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