A novel RdRp-based colorimetric RT-LAMP assay for rapid and sensitive detection of SARS-CoV-2 in clinical and sewage samples from Pakistan

Novel corona virus SARS-CoV-2, causing coronavirus disease 2019 (COVID-19), has become a global health challenge particularly for developing countries like Pakistan where overcrowded cities, inadequate sanitation, little health awareness and poor socioeconomic conditions exist. The SARS-CoV-2 has been known to spread primarily through direct contact and respiratory droplets. However, detection of SARS-CoV-2 in stool and sewage have raised the possibility of fecal-oral mode of transmission. Currently, quantitative reverse-transcriptase PCR (qRT-PCR) is the only method being used for SARS-CoV-2 detection, which requires expensive instrumentation, dedicated laboratory setup, highly skilled staff, and several hours to report results. Considering the high transmissibility and rapid spread, a robust, sensitive, specific and cheaper assay for rapid SARS-CoV-2 detection is highly needed. Herein, we report a novel colorimetric RT-LAMP assay for naked-eye detection of SARS-COV-2 in clinical as well as sewage samples. Our SARS-CoV-2 RdRp-based LAMP assay could successfully detect the virus RNA in 26/28 (93%) of RT-PCR positive COVID-19 clinical samples with 100% specificity (n = 7) within 20 min. We also tested the effect of various additives on the performance of LAMP assay and found that addition of 1 mg/ml bovine serum albumin (BSA) could increase the sensitivity of assay up to 10¹ copies of target sequence. Moreover, we also successfully applied this assay to detect SARS-CoV-2 in sewage waters collected from those areas of Lahore, a city of Punjab province of Pakistan, declared as virus hotspots by local government. Our optimized LAMP assay could provide a sensitive first tier strategy for SARS-CoV-2 screening and can potentially help diagnostic laboratories in better handling of high sample turnout during pandemic situation. By providing rapid naked-eye SARS-CoV-2 detection in sewage samples, this assay may support pandemic readiness and emergency response to any possible virus outbreaks in future.

Gender disparities in National Institute of Health funding for hematologic malignancies, hematopoietic stem cell transplantation, and cellular therapeutics

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Background: Gender inequality in research funding has been studied extensively; however, the literature lacks evidence in Hematology. We investigated trends in National Institutes of Health (NIH) funding for hematologic malignancies (HM), hematopoietic stem cell transplantation (HSCT), and cellular therapeutics (CT). Methods: The data on Hematology funding was retrieved from NIH Research Portfolio Online Reporting Tools (RePORT) Categorical Spending for fiscal years 2018 and 2019. A total of 6351 entries were reported. Only grants (n=1834) that were related to HM, HSCT, and CT were included. After excluding non-relevant, 975 principal investigators (PIs) were included in the analysis. Additional data regarding PIs was ascertained from the Scopus database, LinkedIn, Doximity, and departmental websites, including the number of publications, number of years of active research, H-index, highest degree, gender, and institution. Data were analyzed using SPSS version 21. Bivariate analyses, using chi-square and t-test, and linear regression analyses were performed. Results: In 2018 and 2019, 1834 grants totaling $799.4 million were awarded by the NIH for malignant hematology research (men 1301, 71% vs women 533, 29%). Of 975 PIs, 680 (70%) were men and 295 (30%) were women. Table highlights gender disparities in NIH funding and associated factors. Most of the grant recipients were Ph.D. or M.D./Ph.D. About 70% of total funding was awarded to male PIs. There were no gender differences in the mean number of grants and mean grant amount. Women had significantly lower years of active research and academic productivity. Conclusions: Although the gender gap in academic hematology has decreased in recent years, the latest trend suggests significant gender inequality in NIH funding for malignant hematology, transplantation, and cellular therapy.[Table: see text]

High frequency and molecular epidemiology of metallo-β-lactamase-producing gram-negative bacilli in a tertiary care hospital in Lahore, Pakistan

Background

Metallo-β-lactamase (MBL)-producing isolates have a strong impact on diagnostic and therapeutic decisions. A high frequency of MBL-producing gram-negative bacilli has been reported worldwide. The current study was based on determining the incidence of MBL-producing imipenem-resistant clinical isolates and investigating the β-lactamase gene variants in strains conferring resistance to a carbapenem drug (imipenem).

Methods

A total of 924 gram negative isolates were recovered from a tertiary care hospital in Lahore, Pakistan, during a two-year period (July 2015 to February 2017). The initial selection of bacterial isolates was based on antibiotic susceptibility testing. Strains resistant to imipenem were processed for the molecular screening of β-lactamase genes. Statistical analysis for risk factor determination was based on age, gender, clinical specimen and type of infection.

Results

The rate of imipenem resistance was calculated to be 56.51%. Among the 142 strains processed, the phenotypic tests revealed that the incidence of MBLs was 63.38% and 86.61% based on the combination disc test and the modified Hodge test, respectively. The frequencies of bla_TEM, bla_SHV,bla_OXA,bla_IMP-1, and bla_VIM genes were calculated to be 46%, 34%, 24%, 12.5% and 7%, respectively. The co-expression of bla_MBL (bla_IMP and bla_VIM) and bla_ESBL (bla_TEM, bla_SHV,bla_OXA) was also detected through multiplex and singleplex PCR. bla_OXA, bla_TEM and bla_SHV coexisted in 82% of the isolates. Co-expression of ESBL and MBL genes was found in 7% of the isolates.

Conclusion

To our knowledge, this is the first report from Pakistan presenting the concomitant expression of bla_OXA, bla_TEM and bla_SHV with bla_IMP-1 and bla_VIM in MBL-producing gram-negative bacilli.

Extensive perinephric abscess complicated by herpes simplex virus 1 reactivation

A 43-year-old man, admitted with a swollen right thigh, was diagnosed with a deep vein thrombosis. On day 6 he became septic. A CT scan demonstrated a right-sided hydronephrosis and a large retroperitoneal collection. Blood cultures and perinephric pus grew Escherichia coli resistant to amoxicillin only. On day 12 a vesicular rash appeared on the neck and herpes simplex virus 1 (HSV-1) grew on culture. On day 15 an upper leg collection was seen on CT scan. Thigh tissue specimens grew extended-spectrum beta-lactamase (ESBL) producing E coli and HSV-1 was also detected by polymerase chain reaction in the tissue. On day 18 the patient died. This case illustrates an unusual presentation and complication of a perinephric abscess. In critically ill patients herpes simplex reactivation and emergence of multiresistant organisms may occur resulting in treatment failure.

Can urine dipstick testing for urinary tract infection at point of care reduce laboratory workload?

AIM

The University Hospitals of Leicester NHS Trust microbiology laboratory receives 150 000 urine samples each year, approximately 80% of which prove to be culture negative. The aim of this study was to reduce the proportion of culture negative urines arriving in the laboratory, by producing local evidence based guidelines for the use of urine dipstick testing at point of care within the trust's three acute hospitals.

METHODS

One thousand and seventy six unborated urine samples were dipstick tested at the point of care using an automatic strip reader. Quantitative results for the four infection associated markers-leucocyte esterase, nitrite, blood, and protein-were compared with the results of conventional laboratory microscopy and culture.

RESULTS

The performance of different marker combinations was calculated against the routine laboratory methods. One hundred and seventy five (16.3%) samples were negative for all four markers. Of these dipstick negative samples, only three (1.7% of all true positives) were positive by culture. The absence of all four infection associated markers was found to have a greater than 98% negative predictive value and a sensitivity and specificity of 98.3% and 19.2%, respectively.

CONCLUSIONS

A urinary dipstick testing algorithm for infection associated markers was derived for use in hospital patients to screen out negative urines. Two years after distributing the algorithm and promoting access to reagent strips and strip readers, a reduction in the urine workload has been seen against an otherwise increasing laboratory specimen load.

Endemic cross-infection in an acute medical ward

Urine samples from patients on an acute medical ward were examined each week over a three-month period in order to detect endemic cross colonization or infection. The bed positions for each patient in the ward were recorded continuously and the patients cared for by each different nurse team noted. We found an outbreak of urinary colonization/infection with a strain of Klebsiella K8 in nine patients. Two groups of two patients probably suffered cross colonization/infection with different strains of Escherichia coli. These episodes were not detected by our routine laboratory ward liaison surveillance, but by the weekly samples and molecular typing methods applied to these relatively common strains. This survey demonstrates that cross colonization/infection may occur more widely than is normally detected. The implications of these findings to surveillance audit programmes are discussed.

Contamination of surgeons' glove fingertips during surgical operations

The external surfaces of surgeons' gloves were examined for contamination by bacteria during the course of surgical operations. Of 31 operations studied the surgeons' glove surfaces yielded bacteria at the end of the operation in 16 cases. Bacterial contamination increased during the course of the operation. The surgeons' fingertip skin and nail beds were cultured after surgical hand scrub and drying, but before donning gloves; bacteria were recovered from these sites in 10 of 21 and 13 of 21 cases, respectively.

Hepadnaviruses, their infections and hepatocellular carcinoma

Ten years ago hepatitis B virus (HBV) was thought to be a unique virus, not included in any known family of viruses. Following the discovery of a number of HBV-like viruses that infect birds and mammals, the existence of a new family known as hepadnaviridae has been confirmed. Hepadnaviruses are small hepatotropic viruses that have a characteristic partially double stranded genome, exhibit a narrow host range and replicate by reverse transcription. The family currently comprises six viruses of which human hepatitis B virus is the prototype member. Other members include woodchuck hepatitis virus (WHV), ground squirrel hepatitis virus (GSHV), tree squirrel hepatitis virus (TSHV). Peking duck hepatitis B virus (DHBV) and heron hepatitis B virus (HHBV). Candidate members of the family include kangaroo hepatitis virus (KHV) and stink snake hepatitis virus (SSHV). In humans, infection with HBV is associated with a wide spectrum of clinical conditions including acute and chronic hepatitis, cirrhosis and hepatocellular carcinoma (HCC). Infection with HBV is endemic throughout much of the world and the virus is maintained by the enormous reservoir of over 300 million chronic carriers. For almost 20 years experimental work on hepadnaviruses has been carried out using either natural hosts or cultured cells that were capable to support synthesis of a few viral gene products but unable to execute a complete cycle of virus replication. In this article, we have attempted to summarize the efforts made towards understanding the biology of hepadnaviruses, the nature of their infections and their association with primary liver cancer.