Effectivity Analysis of SARS-CoV-2 Nasopharyngeal Swab Rapid Testing Kits in Pakistan: A Scenario of Inadequate COVID-19 Diagnosis

Abstract COVID-19 pandemic has urged the need of rapid detection of SARS-CoV-2 in limited time frame. To cope with current, COVID-19 expanding scenario, accurate diagnosis of SARS-CoV-2 should be ensured by both national and international health organizations. Sporadic marketing of SARS-CoV-2 rapid detection kits raises questions regarding quality control and assurance. To aim of this study was to examine the effectiveness of SARS-CoV-2 nasopharyngeal swab based rapid detection kits, in comparison to gold standard USFDA approved triple target real-time polymerase chain reaction. A cross-sectional study of 1500 suspected COVID-19 patients was conducted. 100 RT-PCR confirmed patients nasopharyngeal swabs were evaluated for RDT. The COVID-19/SARS-CoV-2 NSP based RDT analysis showed 78% reactivity. Among RT-PCR confirmed negative subjects, 49.3% showed false positivity. The positive predictive analysis revealed 67.82% values, while the negative predictive vales of were 64.40%. The NSP RDTs showed limited sensitivities and specificities compared to gold standard RT-PCR. Accurate surveillance of COVID-19 is dependent upon authentic and validated SARS-CoV-2 detection nation-wide, which needs to be monitored by higher authorities. This study is critical for designing adequate measures by several COVID-19 strategic organizations to prevent future viral epidemics.

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Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy

Virology Journal ◽

10.1186/s12985-021-01505-3 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Umar Saeed ◽

Sara Rizwan Uppal ◽

Zahra Zahid Piracha ◽

Azhar Rasheed ◽

Zubair Aftab ◽

...

Keyword(s):

Gold Standard ◽

Injection Drug Users ◽

Drug Users ◽

Diagnostic Testing ◽

False Negative ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

Negative Results

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

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Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy.

10.21203/rs.3.rs-113852/v2 ◽

2021 ◽

Author(s):

Umar Saeed ◽

Sara Rizwan Uppal ◽

Zahra Zahid Piracha ◽

Azhar Rasheed ◽

Zubair Aftab ◽

...

Keyword(s):

Gold Standard ◽

Injection Drug Users ◽

Drug Users ◽

Diagnostic Testing ◽

False Negative ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

Negative Results

Abstract Rapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

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Prevalence of Cryptosporidiosis in Crossbred Calves in Two Selected Areas of Bangladesh

Bangladesh Journal of Veterinary Medicine ◽

10.3329/bjvm.v12i2.21288 ◽

2014 ◽

Vol 12 (2) ◽

pp. 185-190

Author(s):

A Khair ◽

MM Alam ◽

AKMA Rahman ◽

M Shahiduzzaman ◽

MS Parvez ◽

...

Keyword(s):

Rapid Detection ◽

Clinical Status ◽

Cross Sectional Study ◽

Positive Control ◽

Age Group ◽

Sectional Study ◽

Chain Reaction ◽

Cross Sectional ◽

Fecal Samples ◽

Polymerase Chain

A cross-sectional study was conducted to determine the prevalence of bovine cryptosporidiosis using 110 fecal samples of crossbred diarrhoeic calves from two different areas (Muktagacha, Mymensingh and Shajadpur, Sirajgonj) in Bangladesh during April 2012 to September 2014. The fecal samples were screened by rapid detection kit and confirmed by Modified Ziehl- Neelsen staining, and polymerase chain reaction (PCR). The positive samples along with standard positive control yielded 1325bp band on PCR. The overall prevalence of cryptosporidiosis in crossbred calves was 28.18% (31/110) by rapid detection kit. The higher prevalence of cryptosporidiosis was found in the calves from Shajadpur (29.76%) than the calves from Muktagacha (23.08%).The prevalence of cryptosporidiosis was significantly (p<0.001) higher in calves between 1-2 months (70%) age group than less than one month age group (24.49%). Cryptosporidiosis was not observed in calves over two months age. The prevalence of cryptosporidiosis was higher in males (34.75%) than females (24.64%) although not significant statistically. It is evident that the prevalence of cryptosporidiosis in bovine in these areas is under diagnosed and the clinical status of infection is potentially high.DOI: http://dx.doi.org/10.3329/bjvm.v12i2.21288 Bangl. J. Vet. Med. (2014). 12 (2): 185-190

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Performance of qualitative and quantitative antigen tests for SARS-CoV-2 in early symptomatic patients using saliva

10.1101/2020.11.06.20227363 ◽

2020 ◽

Author(s):

Isao Yokota ◽

Takayo Sakurazawa ◽

Junichi Sugita ◽

Sumio Iwasaki ◽

Keiko Yasuda ◽

...

Keyword(s):

Symptom Onset ◽

Gold Standard ◽

Rapid Detection ◽

Disease Outbreaks ◽

Nasopharyngeal Swab ◽

Chain Reaction ◽

Qualitative And Quantitative ◽

Polymerase Chain ◽

Antigen Tests ◽

Chemiluminescent Enzyme Immunoassay

AbstractBackgroundThe rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an urgent need for the prevention and containment of disease outbreaks in communities. Although the gold standard is polymerase chain reaction (PCR), antigen tests such as immunochromatographic assay (ICA) and chemiluminescent enzyme immunoassay (CLEIA) that can yield results within 30 minutes.MethodsWe evaluated performance of ICA and CLEIA using 34 frozen PCR-positive specimens (17 saliva and 17 nasopharyngeal swab) and 307 PCR-negative samples.ResultsICA detected SARS-CoV-2 in only 14 (41%) samples, with positivity of 24% in saliva and 59% in NPS. Notably, ICA detected SARS-CoV-2 in 5 (83%) of 6 samples collected within 4 days after symptom onset. CLEIA detected SARS-CoV-2 in 31 (91%) samples, with positivity of 82% in saliva and 100% in NPS. CLEIA was negative in 3 samples with low viral load by PCR.ConclusionsThese results suggest that use of ICA should be limited to earlier time after symptom onset and CLEIA is more sensitive and can be used in situations where quick results are required.

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Association of Myeloid Aberrant Antigens and the Presence of BCR-ABL Gene Re-arrangements in ALL Patients

Haematology Journal of Bangladesh ◽

10.37545/haematoljbd202060 ◽

2020 ◽

Vol 4 (1) ◽

pp. 13-15

Author(s):

Md. Shafiul Azam ◽

Khaza Amirul Islam ◽

Sharmin Mafruha ◽

Mirza Golam Sarwar ◽

Md. Salahuddin Shah ◽

...

Keyword(s):

Acute Lymphoblastic Leukaemia ◽

Lymphoblastic Leukaemia ◽

Selection Criteria ◽

Cross Sectional Study ◽

Rt Pcr ◽

Genetic Abnormality ◽

Chain Reaction ◽

Cross Sectional ◽

Polymerase Chain ◽

Made In

Background: BCR-ABL translocation is the most common genetic abnormality associated with adult Acute Lymphoblastic Leukaemia (ALL) with poor outcome. Objective: The aim of the study was to determine the association of myeloid aberrant antigens and the presence of BCR-ABL gene rearrangements in acute lymphoblastic leukaemia (ALL) patients in our context. Method: A total of 38 ALL patients were included in this cross-sectional study from August 2018 to July 2019 according to selection criteria. BCR-ABL was detected by Real Time-Polymerase Chain Reaction (RT-PCR). Results: The median age at diagnosis was 27.5 years with male (76.3%) predominance. Aberrant myeloid markers, e.g.CD13 was present in 9(64.3%) patients who were BCR-ABL positive which was statistically significant (p:<0.05). Conclusion: Early suspicion about BCR-ABL positivity can be made in ALL patients who show aberrant myeloid expression.

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SARS-CoV-2 infection among patients with multiple sclerosis; A cross-sectional study

10.1101/2020.10.17.20214429 ◽

2020 ◽

Author(s):

Mahnaz Bayat ◽

Alireza Fayyazpoor ◽

Afshin Borhani Haghighi ◽

Daniyal Salehi ◽

Hossein Molavi Vardanjan ◽

...

Keyword(s):

Multiple Sclerosis ◽

Demographic Data ◽

Cross Sectional Study ◽

Fars Province ◽

Rt Pcr ◽

Positive Real ◽

Cross Sectional ◽

Polymerase Chain ◽

Group 5 ◽

Disability Level

AbstractBackgroundNeurological disability associated with multiple sclerosis and immunosuppressive or immunomodulatory therapy which is administered for it may increases the risk of SARS-CoV-2 infection and its morbidity/mortality.ObjectiveIn this study, we evaluated the infection rate and the severity of SARS-CoV-2 infection in patients with multiple sclerosis (MS)MethodsOne thousand and three hundred and sixty one MS patients from Fars province, south of Iran, were interviewed by phone from April 3 to June 20, 2020. Basic demographic data, information about MS disease and any symptoms or laboratory results relevant to COVID-19 were gathered and reviewed by treating neurologist and MS nurses. SPSS version 22 was used for data analysis.Results68 (5%) of MS patients were suspected cases and 8 (0.58%) of all patients with positive real-time reverse transcription polymerase chain reaction (RT-PCR) or chest CT were in the confirmed group. 5 cases of the confirmed group needed hospitalization. Two patients died while both of them had PPMS and were taking rituximab. The frequency rate of suspected cases with RRMS was 57 (87.7%), followed by PPMS 5 (7.7%) and CIS 2(3.1%). In the confirmed group 37.5% had RRMS, 50% had PPMS, 25% use corticosteroid drug, and 50% were on rituximab. 62.5% of confirmed cases had high disability level and need assistance to walk. 36.8% of suspected and 25% of the confirmed cases were on IFN-β1; eventually all of them recovered well from COVID-19 infection.ConclusionThe present study showed that rate of developing COVID-19 in MS patients are similar to the general population and the frequency of PPMS phenotype, rituximab therapy and corticosteroid therapy were higher in the confirmed group.

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Detection of blaVIM and blaIMP Carbapenemase-Producing Pseudomonas aeruginosa from Clinical Samples in Iran

International Journal of Medical Laboratory ◽

10.18502/ijml.v8i3.7324 ◽

2021 ◽

Author(s):

Mohammad Reza Zolfaghari

Keyword(s):

Pseudomonas Aeruginosa ◽

Cross Sectional Study ◽

Clinical Samples ◽

Sectional Study ◽

Rt Pcr ◽

Chain Reaction ◽

Cross Sectional ◽

High Prevalence ◽

Polymerase Chain ◽

High Level

Background and Aims: The prevalence of carbapenemase-producing Pseudomonas aeruginosa (P. aeruginosa) strains has been recently reported worldwide. Therefore, accurate and rapid detection of carbapenemase-producing isolates is essential. So, this study aimed to detect blaVIM and blaIMP carbapenemase-producing strains using the modified Hodge test (MHT) and reverse transcription-polymerase chain reaction (RT-PCR). Materials and Methods: In this cross-sectional study, P. aeruginosa strains were collected from clinical samples (blood, urine, wound, and other liquids body) in Firoozgar and Shahid Motahari Hospitals in Tehran and Velayat Hospital in Rasht Province, from May to December 2018. After identifying the isolates using the standard microbial tests, carbapenemase-producing strains were isolated by the modified hodge test. After that, the detection of blaVIM and blaIMP genes was performed by RT-PCR technique. Results: One hundred P. aeruginosa were isolated from different clinical samples. Among these, 74 (74%) isolates were considered as carbapenemase positive using MHT. The frequencies of blaVIM and blaIMP genes were obtained as 83% and 11%, respectively. Conclusions: The results of this study indicate a high level of resistance to most of the antibiotics tested and a high prevalence of blaVIM gene in P. aeruginosa strains.

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Headache associated with COVID-19: Frequency, characteristics and association with anosmia and ageusia

Cephalalgia ◽

10.1177/0333102420966770 ◽

2020 ◽

Vol 40 (13) ◽

pp. 1443-1451 ◽

Cited By ~ 2

Author(s):

Pedro Augusto Sampaio Rocha-Filho ◽

João Eudes Magalhães

Keyword(s):

Polymerase Chain Reaction ◽

Cross Sectional Study ◽

Sectional Study ◽

Rt Pcr ◽

Chain Reaction ◽

Chi Square ◽

Cross Sectional ◽

Severe Intensity ◽

Chi Square Test ◽

Polymerase Chain

Objectives To assess the frequency and characteristics of headache in patients with COVID-19 and whether there is an association between headache and anosmia and ageusia. Methods This was a cross-sectional study. Consecutive patients admitted to hospital with COVID-19, confirmed by reverse transcription polymerase chain reaction (RT-PCR) technique, were assessed by neurologists. Results Seventy-three patients were included in the study, 63% were male; the median age was 58 years (IQR: 47–66). Forty-seven patients (64.4%) reported headaches, which had most frequently begun on the first day of symptoms, were bilateral (94%), presenting severe intensity (53%) and a migraine phenotype (51%). Twelve patients (16.4%) presented with headache triggered by coughing. Eleven (15%) patients reported a continuous headache. Twenty-eight patients (38.4%) presented with anosmia and 29 (39.7%) with ageusia. Patients who reported hyposmia/anosmia and/or hypogeusia/ageusia experienced headache more frequently than those without these symptoms (OR: 5.39; 95% CI:1.66–17.45; logistic regression). Patients with anosmia and ageusia presented headache associated with phonophobia more often compared to those with headache without these complaints (Chi-square test; p < 0.05). Headache associated with COVID-19 presented a migraine phenotype more frequently in those experiencing previous migraine ( p < 0.05). Conclusion Headaches associated with COVID-19 are frequent, are generally severe, diffuse, present a migraine phenotype and are associated with anosmia and ageusia.

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Underestimation of COVID-19 cases in Japan: an analysis of RT-PCR testing for COVID-19 among 47 prefectures in Japan

QJM ◽

10.1093/qjmed/hcaa209 ◽

2020 ◽

Vol 113 (8) ◽

pp. 551-555 ◽

Cited By ~ 2

Author(s):

T Sawano ◽

Y Kotera ◽

A Ozaki ◽

A Murayama ◽

T Tanimoto ◽

...

Keyword(s):

Correlation Analysis ◽

Multiple Regression ◽

Cross Sectional Study ◽

Regression Analyses ◽

Rt Pcr ◽

Geographical Differences ◽

Cross Sectional ◽

Bidirectional Association ◽

Polymerase Chain ◽

Increasing Demand

Summary Background Under the unique Japanese policy to restrict reverse transcriptase–polymerase chain reaction (RT-PCR) testing against severe acute respiratory syndrome coronavirus 2, a nationwide number of its confirmed cases and mortality remains to be low. Yet the information is lacking on geographical differences of these measures and their associated factors. Aim Evaluation of prefecture-based geographical differences and associated predictors for the incidence and number of RT-PCR tests for coronavirus disease 2019 (COVID-19). Design Cross-sectional study using regression and correlation analysis. Methods We retrieved domestic laboratory-confirmed cases, deaths and the number of RT-PCR testing for COVID-19 from 15 January to 6 April 2020 in 47 prefectures in Japan, using publicly available data by the Ministry of Health, Labour and Welfare. We did descriptive analyses of these three measures and identified significant predictors for the incidence and RT-PCR testing through multiple regression analyses and correlates with the number of deaths through correlation analysis. Results The median prefectural-level incidence and number of RT-PCR testing per 100 000 population were 1.14 and 38.6, respectively. Multiple regression analyses revealed that significant predictors for the incidence were prefectural-level population (P < 0.001) and the number of RT-PCR testing (P = 0.03); and those for RT-PCR testing were the incidence (P = 0.025), available beds (P = 0.045) and cluster infections (P = 0.034). Conclusion Considering bidirectional association between the incidence and RT-PCR testing, there may have been an underdiagnosed population for the infection. The restraint policy for RT-PCR testing should be revisited to meet the increasing demand under the COVID-19 epidemic.

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Loss of Sense of Smell and Taste among Reverse Transcriptase Polymerase Chain Reaction Positive COVID-19 Patients of a Tertiary Care Hospital: A Descriptive Cross-sectional Study

Birat Journal of Health Sciences ◽

10.3126/bjhs.v6i2.40359 ◽

2021 ◽

Vol 6 (2) ◽

pp. 1561-1564

Author(s):

Rajeev Shah ◽

Bipin Koirala ◽

Sangya Gyawali

Keyword(s):

Tertiary Care Hospital ◽

Strong Association ◽

Tertiary Care ◽

Cross Sectional Study ◽

Care Hospital ◽

Rt Pcr ◽

Chain Reaction ◽

Cross Sectional ◽

Polymerase Chain ◽

Taste And Smell

Results: A total of 166 patients were included in the study. The age of the patients ranged from 10 to 84 years with a mean age of 44.34 ± 23.059 years. Out of the 166 RT-PCR positive patients 103 (62%) had a loss of taste while 114 (68.7%) had a loss of smell. Nearly half of the subjects about 99 (51.6%) had dysfunction in both taste and smell. Conclusions: The present study shows the strong association between the olfactory and gustatory dysfunction with that of COVID infection. Patients with loss of taste and smell should be evaluated properly at the time of COVID pandemic. Olfactory and Gustatory dysfunction can be the early and only manifestation of COVID infection. The prevalence of loss of smell and taste was similar to other studies done in similar settings.

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