## 1 Introduction  
Coronavirus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2, formerly known as 2019-nCoV) was first reported in Chinaand has been spread worldwide. On 11 March 2020, the World Health Organization (WHO) announced COVID-19 as a public health emergency of international interest. According to the last report of January 2024, over 700 million confirmed cases and almost 7 million deaths have been recorded worldwide [1]. The rapidly contagious nature of SARS-CoV-2 makes it urgent to multiply testing for COVID-19 diagnostics, to identify the active viral shedding cases (current infection, carriage state or residual viral RNA) and decrease the risk of transmission to other patients and healthcare professionals, including transmission from asymptomatic people [2; 3]. Currently, the gold standard method for the identification of SARS-CoV-2 is quantitative reverse transcription polymerase chain reaction (RT-qPCR) of upper respiratory tract samples collected with naso- and/or oropharyngeal swabs (NPSs and OPSs) [4; 5; 6]. Although the NPS is the most common specimen type used for COVID-19 diagnosis, it requires the skills of a trained health professional to perform sample collection [7]. Furthermore, there is concern regarding the exposure of healthcare staff, procedure complexity, and patient discomfort during collection [8]. Viral transmission can occur through dispersal in the air of droplets from the respiratory tract generated when the patient talks, coughs, or sneezes, even in asymptomatic individuals. As saliva is one of the secreted fluids [9] that can be self-collected without supervision by the drooeling technique, the use of this specimen as an alternative to NPSs and OPS has been suggested [7; 10]. Viral RNA can also be found in blood [11], detecting SARS-CoV-2 RNA in plasma or serum could be an alternative diagnostic approach [12]. Additionally, this type of sample is convenient in some occasions, such as when the patient is in a coma or unresponsive [12]. Bronchoalveolar lavage fluid (BLA) samples can also be an option because it is a very good specimen with a high viral detection rate. However, the collection procedure is extremely invasive and requires the use of specific medical material, and it is typically collected from patients with severe illness or those undergoing mechanical ventilation [13]. Moreover, although previous studies have reported that most symptomatic COVID-19 patients have low sputum production levels [14], which makes specimen collection difficult in many clinical settings [8], this biological fluid can also be considered a viable option since it is a non-invasive method [14]. With the available information regarding this disease, it is clear that the most common symptoms are related to the respiratory tract system; however, gastrointestinal symptoms such as nausea and diarrhoea have also been observed [15]. Therefore, transmission through stool shedding or the oral-f faecal route is possible, making faeces specimens another target for SARS-CoV-2 identification methods [16]. In addition to gastrointestinal symptoms, several cases of acute kidney injury have also been noticed and, for that reason, urine specimens are being considered as another option for COVID-19 diagnosis and an alternative specimen for the use of swabs [17]. This comprehensive scientific analysis aims to provide updated information about the most suitable, cost-efficient and safe biological sample to identify SARS-CoV-2 using the qRT-PCR methodology, considering the risk assessment, specialization required for sampling, test cost and complexity of the collection and sample treatment associated with the different types of specimens: urine, sputum, nasopharyngeal, oropharyngeal, bronchoalveolar, saliva and faeces. For this purpose, an indexed score was developed based on seven categories, namely: Materials and Equipment; Infection Risk for the Health Professional; Infection Risk for the Patient; Collection; Cost; Specialized Human Resources; RNA Extraction Type.