Dataset of RT-PCR detection of SARS-CoV-2 and Influenza viruses in suspected respiratory infection cases from Oaxaca, Mexico (2023)

This dataset contains clinical and molecular diagnostic data from patients with suspected respiratory viral infection evaluated in the state of Oaxaca, Mexico, during January–June 2023. The dataset includes information from 1076 suspected COVID-19 cases analyzed at the State Public Health Laboratory of Oaxaca (LESPO) using multiplex real-time RT-PCR for simultaneous detection of: SARS-CoV-2 Influenza A virus Influenza B virus Samples were obtained from all six sanitary jurisdictions of Oaxaca: Valles Centrales Istmo Tuxtepec Costa Mixteca Sierra The study included patients of any age and sex who met the epidemiological criteria for: Influenza-like illness (ILI) Severe Acute Respiratory Infection (SARI) Nasopharyngeal and pharyngeal swabs were processed for nucleic acid extraction using the QIAamp Viral RNA Mini Kit. Molecular detection was performed using real-time RT-PCR on the Applied Biosystems 7500 FAST platform. The dataset includes demographic variables, epidemiological information, RT-PCR Ct values, and diagnostic results for SARS-CoV-2 and influenza viruses. This dataset was generated as part of a graduate research thesis focused on the molecular diagnosis and epidemiological characterization of respiratory viral infections in Oaxaca, Mexico. The dataset may be useful for: respiratory virus epidemiology influenza surveillance COVID-19 surveillance diagnostic test evaluation co-infection analysis public health studies One Health research 3. Methods This observational laboratory-based study included 1076 suspected COVID-19 cases submitted to the State Public Health Laboratory of Oaxaca (LESPO) between January and June 2023. Samples were collected from patients meeting the national operational definition for Influenza-like Illness (ILI) and/or Severe Acute Respiratory Infection (SARI). Sample collection Nasopharyngeal and pharyngeal swabs were obtained by trained healthcare personnel from public healthcare centers across the six sanitary jurisdictions of Oaxaca. RNA extraction Total nucleic acids were extracted using the QIAamp Viral RNA Mini Kit according to manufacturer instructions. RT-PCR detection Multiplex real-time RT-PCR was performed using the FLU-COVID MMix kit. Amplification was carried out using the Applied Biosystems 7500 FAST thermocycler under the following conditions: Reverse transcription: 55°C for 15 min 45 amplification cycles: 95°C for 15 sec 56°C for 40 sec 72°C for 15 sec Fluorescence channels: FAM: SARS-CoV-2 ROX: Influenza A HEX/JOE/VIC: Influenza B Cy5: Internal control Samples with Ct ≤ 38 were considered positive. 4. Dataset structure Dataset structure The dataset is provided as an Excel spreadsheet (.xlsx). Each row represents an individual patient sample analyzed by RT-PCR. Variables may include: Demographic variables Patient ID Age Sex Jurisdiction of origin Clinical variables Influenza-like illness (ILI) Severe acute respiratory infection (SARI) Molecular diagnostic variables SARS-CoV-2 RT-PCR result Influenza A RT-PCR result Influenza B RT-PCR result Ct values for each target Laboratory variables Internal control result Sample type Processing date