Testing for SARS-CoV-2 in resource-limited settings: A cost analysis study of diagnostic tests using different Ag-RDTs and RT-PCR technologies in Mozambique

Early diagnosis of SARS-CoV-2 is fundamental to reduce the risk of community transmission and mortality, as well as public sector expenditures. Three years after the onset of the SARS-CoV-2 pandemic, there are still gaps on what is known regarding costs and cost drivers for the major diagnostic testing strategies in low- middle-income countries (LMICs). This study aimed to estimate the cost of SARS-CoV-2 diagnosis of symptomatic suspected patients by reverse transcription polymerase chain reaction (RT-PCR) and antigen rapid diagnostic tests (Ag-RDT) in Mozambique. We conducted a retrospective cost analysis from the provider's perspective using a bottom-up, micro-costing approach, and compared the direct costs of two nasopharyngeal Ag-RDTs (Panbio and Standard Q) against the costs of three nasal Ag-RDTs (Panbio, COVIOS and LumiraDx), and RT-PCR. The study was undertaken from November 2020 to December 2021 in the country's capital city Maputo, in four healthcare facilities at primary, secondary and tertiary levels of care, and at one reference laboratory. All the resources necessary for RT-PCR and Ag-RDT tests were identified, quantified, valued, and the unit costs per test and per facility were estimated. Our findings show that the mean unit cost of SARS-CoV-2 diagnosis by nasopharyngeal Ag-RDTs was MZN 728.00 (USD 11.90, at 2020 exchange rates) for Panbio and MZN 728.00 (USD 11.90) for Standard Q. For diagnosis by nasal Ag-RDTs, Panbio was MZN 547.00 (USD 8.90), COVIOS was MZN 768.00 (USD 12.50), and LumiraDx was MZN 798.00 (USD 13.00). Medical supplies expenditures represented the main driver of the final cost (>50%), followed by personnel and overhead costs (mean 15% for each). The mean unit cost regardless of the type of Ag-RDT was MZN 714.00 (USD 11.60). Diagnosis by RT-PCR cost MZN 2,414 (USD 39.00) per test. Our sensitivity analysis suggests that focussing on reducing medical supplies costs would be the most cost-saving strategy for governments in LMICs, particularly as international prices decrease. The cost of SARS-CoV-2 diagnosis using Ag-RDTs was three times lower than RT-PCR testing. Governments in LMICs can include cost-efficient Ag-RDTs in their screening strategies, or RT-PCR if international costs of such supplies decrease further in the future. Additional analyses are recommended as the costs of testing can be influenced by the sample referral system.

Clinical Performance of Self-Collected Nasal Swabs and Antigen Rapid Tests for SARS-CoV-2 Detection in Resource-Poor Settings

Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3−85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3−85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2−63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5−82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings.

Molecular characterization of diarrheagenic Escherichia coli isolates from children with diarrhea: A cross-sectional study in four provinces of Mozambique: Diarrheagenic Escherichia coli in Mozambique

OBJECTIVES

Analyze the frequency of diarrheagenic Escherichia coli (DEC) pathotypes and their antimicrobial resistance profiles among children aged <15 years with diarrhea in four Mozambican provinces.

METHODS

A cross-sectional hospital-based surveillance program of diarrhea was implemented in Maputo, Sofala, Zambézia, and Nampula. A single stool sample was collected from each child from May 2014 to May 2017. Culture methods and biochemical characterization were performed to detect E. coli strains. DEC pathotypes were determined by conventional polymerase chain reaction targeting specific virulence genes. Antimicrobial susceptibility was assessed by the Kirby-Bauer method.

RESULTS

From 723 specimens analyzed by culture, 262 were positive for E. coli. A total of 208 samples were tested by polymerase chain reaction for DEC identification, of which 101 (48.6%) were positive for a DEC pathotype. The predominant pathotypes were enteroaggregative (66.3%, 67/101), enteropathogenic (15.8%, 16/101), enterotoxigenic (13.9%, 14/101), and enteroinvasive E. coli (4.0%, 4/101). No Shiga toxin-producing E. coli was identified. Regardless of the province, the most frequent pathotype was enteroaggregative E. coli. Isolated DEC presented high frequency of resistance to ampicillin (97.8%), tetracycline (68.3%), chloramphenicol (28.4%), nalidixic acid (19.5%), and gentamicin (14.4%).

CONCLUSION

Children with diarrhea in Mozambique had DEC and higher resistance to ampicillin and tetracycline.

High Frequency of Cryptosporidium hominis Infecting Infants Points to A Potential Anthroponotic Transmission in Maputo, Mozambique

Cryptosporidium is one of the most important causes of diarrhea in children less than 2 years of age. In this study, we report the frequency, risk factors and species of Cryptosporidium detected by molecular diagnostic methods in children admitted to two public hospitals in Maputo City, Mozambique. We studied 319 patients under the age of five years who were admitted due to diarrhea between April 2015 and February 2016. Single stool samples were examined for the presence of Cryptosporidium spp. oocysts, microscopically by using a Modified Ziehl-Neelsen (mZN) staining method and by using Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) technique using 18S ribosomal RNA gene as a target. Overall, 57.7% (184/319) were males, the median age (Interquartile range, IQR) was 11.0 (7-15) months. Cryptosporidium spp. oocysts were detected in 11.0% (35/319) by microscopy and in 35.4% (68/192) using PCR-RFLP. The most affected age group were children older than two years, [adjusted odds ratio (aOR): 5.861; 95% confidence interval (CI): 1.532-22.417; p-value < 0.05]. Children with illiterate caregivers had higher risk of infection (aOR: 1.688; 95% CI: 1.001-2.845; p-value < 0.05). An anthroponotic species C. hominis was found in 93.0% (27/29) of samples. Our findings demonstrated that cryptosporidiosis in children with diarrhea might be caused by anthroponomic transmission.

Prevalence and genome characterization of porcine rotavirus A in southern Mozambique

Rotavirus A (RVA) is an important pathogen causing gastroenteritis in many species, including humans and pigs. The objective of this study was to determine the prevalence of RVA in pigs from smallholdings and commercial farms in southern Mozambique and characterize the complete genomes of selected strains. RVA was detected at a rate of 11.8% (n = 288), of which 7.6% was detected at commercial farms and 4.2% at smallholdings. The whole genomes of eight rotavirus strains were determined using an Illumina MiSeq platform. Seven displayed a G9P[13] and one a G4P[6] genotype combination, all with a typical porcine backbone (I1/5-R1-C1-M1-A1/8-N1-T1/7-E1-H1). Phylogenetic analysis indicated that the seven G9P[13] strains were in fact one strain that circulated on a commercial pig farm. The genome segments of this strain clustered with diverse segments of human and porcine RVA strains from various Asian countries. Analysis of the G4P[6] strain revealed four distinct genome segments (VP2, VP4, VP6 and VP7) and five genome segments closely related to South African porcine rotavirus strains (NSP1, NSP3, NSP4, NSP5 and VP1). These results suggest that both the G4P[6] and the G9P[13] strains possibly emerged through multiple reassortment events. The presence of these strains on the commercial farms and smallholdings calls for a more in-depth surveillance of rotavirus in Mozambique.