Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the cause of Coronavirus Disease 2019 (COVID-19). Although Real Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) of respiratory specimens is the gold standard test for detection of SARS-CoV-2 infection, collecting nasopharyngeal swabs causes discomfort to patients and may represent considerable risk for healthcare workers. The use of saliva as a diagnostic sample has several advantages. The aim of this study was to validate the use of saliva as a biological sample for diagnosis of COVID-19. This study was conducted at Infectious Diseases Research Laboratory (LAPI), in Salvador, Brazil. Participants presenting with signs/symptoms suggesting SARS-CoV-2 infection underwent a nasopharyngeal swab (NPS) and/or oropharyngeal swab (OPS), and saliva collection. Saliva samples were diluted in PBS, followed by RNA isolation and RT-Real Time PCR for SARS-CoV-2. Results of conventional vs saliva samples testing were compared. Statistical analyses were performed using Statistical Package for the Social Sciences software (SPSS) version 18.0. One hundred fifty-five participants were recruited and samples pairs of NPS/OPS and saliva were collected. The sensitivity and specificity of RT-PCR using saliva samples were 94.4% (95% CI 86.4–97.8) and 97.62% (95% CI 91.7–99.3), respectively. There was an overall high agreement (96.1%) between the two tests. Use of self-collected saliva samples is an easy, convenient, and low-cost alternative to conventional NP swab-based molecular tests. These results may allow a broader use of molecular tests for management of COVID19 pandemic, especially in resources-limited settings.

Objectives: This study aimed to evaluate the effect of 0.12% chlorhexidine gluconate on the salivary load of SARS‐CoV‐2.Materials and Methods: A randomized, double‐blind, placebo‐controlled trial was performed on 100 participants positive for SARS‐CoV‐2. In the test group (n = 50), volunteers gargled with a mouthwash containing 15 ml of 0.12% chlorhexidine gluconate for 1 min, while the control group (n = 50) used a placebo. Saliva samples were obtained before (baseline) and 5 and 60 min after using the solutions. Real‐time reverse transcription polymerase chain reaction assays (qRT‐PCR) were carried out and the cycle threshold (Ct) was computed. The chi‐square test and t‐test were used for group comparison (p ≤ 0.05).Results: The differences in Ct values between the 5‐min evaluation and baseline (test group: 2.19 ± 4.30; control: −0.40 ± 3.87, p = 0.002) and between 60 min and baseline (test group: 2.45 ± 3.88; control: 0.76 ± 4.41, p = 0.05) were significantly greater in the test group, revealing a reduction of viral load. Furthermore, there was a reduction in the load of SARS‐CoV‐2 in 72% of the volunteers using chlorhexidine versus 30% in the control group (p = 0.001).Conclusions: Chlorhexidine gluconate (0.12%) was effective in reducing salivary SARS‐CoV‐2 load for at least 60 min.

In the pandemic, rapid and accurate detection of SARS-CoV-2 is crucial in controlling the outbreak. Recent studies have shown a high detection rate using saliva/oral fluids as specimens for laboratory detection of the virus. We intended to evaluate the test performance of the Xpert Xpress SARS-CoV-2 cartridge assay in comparison to a conventional qRT-PCR testing, using saliva as biological specimen. Forty saliva samples from symptomatic participants were collected. Conventional qRT-PCR was performed for amplification of E and RdRp genes and the Xpert Xpress SARS-CoV-2 assay amplified E and N2 genes. In the conventional assay, the median cycle threshold value of the E gene was 34.9, and of the RdRp gene was 38.3. In the Xpert Xpress assay, the median cycle threshold value of the E gene was 29.7, and of the N2 gene was 31.6. These results can allow a broaden use of molecular tests for management of COVID-19 pandemic, especially in resources-limited settings.

Molecular surveillance of the new coronavirus through new genomic sequencing technologies revealed the circulation of important variants of SARS-CoV-2. Sanger sequencing has been useful in identifying important variants of SARS-CoV-2 without the need for whole-genome sequencing. A sequencing protocol was constructed to cover a region of 1000 base pairs, from a 1120 bp product generated after a two-step RT-PCR assay in samples positive for SARS-CoV-2. Consensus sequence construction and mutation identification were performed. Of all 103 samples sequenced, 69 contained relevant variants represented by 20 BA.1, 13 delta, 22 gamma, and 14 zeta, identified between June 2020 and February 2022. All sequences found were aligned with representative sequences of the variants. Using the Sanger sequencing methodology, we were able to develop a more accessible protocol to assist viral surveillance with a more accessible platform.

RT-PCR testing data provides opportunities to explore regional and individual determinants of test positivity and surveillance infrastructure. Using Generalized Additive Models, we explored 222,515 tests of a random sample of individuals with COVID-19 compatible symptoms in the Brazilian state of Bahia during 2020. We found that age and male gender were the most significant determinants of test positivity. There was evidence of an unequal impact among socio-demographic strata, with higher positivity among those living in areas with low education levels during the first epidemic wave, followed by those living in areas with higher education levels in the second wave. Our estimated probability of testing positive after symptom onset corroborates previous reports that the probability decreases with time, more than halving by about two weeks and converging to zero by three weeks. Test positivity rates generally followed state-level reported cases, and while a single laboratory performed ~90% of tests covering ~99% of the state’s area, test turn-around time generally remained below four days. This testing effort is a testimony to the Bahian surveillance capacity during public health emergencies, as previously witnessed during the recent Zika and Yellow Fever outbreaks.

COVID-19 can trigger different clinical presentations in distinct population groups, some of which are considered at higher risk of SARS-CoV-2 infection. Little is known about the susceptibility of certain populations to the infection. We aimed to determine the prevalence of COVID-19 among People Living With HIV/AIDS (PLWH) attending a tertiary public hospital in Salvador, Brazil, patients with active pulmonary tuberculosis and Hospital's Healthcare Workers (HCW), and to compare their SARS-CoV-2 antibody levels. In this observational study we included 2294 participants from June 9, 2020 to August 10, 2021. IgG SARS-CoV-2 antibodies from all participants (275 PLWH, 42 with active tuberculosis and 1977 healthcare workers) were measured. Prevalence of COVID-19 and antibodies indexes were compared across groups. We detected a higher prevalence of COVID-19 in patients with active tuberculosis (42.9%) than in PLWH (22.5%) or HCW (11.7%). Previously vaccinated participants with a COVID-19 history had median higher IgG antibody indexes (8.2; IQR: 5.5‒10) than those vaccinated who did not have COVID-19 until the time of this study (4.1; IQR: 1.6‒6.2, p < 0.001). Prevalence of previous SARS-CoV-2 infection was higher among tuberculosis patients than that found in HCW and PLWH, but antibodies levels were similar across groups.