The Effect of Cushioned Centrifugation, with and without Enzymatic Reduction of Viscosity, on the Motility Pattern and Kinematic Parameters of Dromedary Camel Bull Spermatozoa.

In order to contribute to the development of semen processing procedures in camelids, the aims of the present study were to evaluate (i) the effect of 35% seminal plasma incubation on dromedary camel epididymal sperm motility and kinematic parameters, (ii) the effects of centrifugation, with cushion fluid and enzymatic reduction of viscosity (Papain + E64) during ejaculate processing, on the motility and kinematic parameters of dromedary camel ejaculates. The incubation with seminal plasma significantly reduced the percentage of progressively motile spermatozoa as well as the proportion of medium progressive spermatozoa whilst increasing the percentage of non-progressive spermatozoa. The centrifugation procedure improved the sperms' kinematic parameters, and the highest values were observed for samples centrifugated with cushion fluid. The samples treated with Papain + E64 showed a significant increase in both total and medium progressive spermatozoa, along with a reduction of non-progressive spermatozoa (p < 0.05). The results of this investigation show that a simple, cheap, and effective procedure, such as cushioned centrifugation, could improve the motility patterns of dromedary camel spermatozoa; in combination with enzymatic reduction of viscosity, this method leads to the best results in terms of recovery rates and sperms' kinematic parameters.

A Step towards Personalised Cancer Treatment in Lower Middle-income Countries (LMICS): Molecular Tumour Boards.

Tumour boards are meetings where physicians from various disciplines treating cancer patients meet to recommend evidence-based or the best possible treatment plan. These meetings have evolved with time and now, in every part of the world; site-specific multi-disciplinary tumour boards are established. These meetings are considered pivotal for improving patient outcomes. The advances in molecular and genetic knowledge and technique and their integration in treatment options have paved the way for multiple therapeutic options. However, the adoption of personalised treatment choices is associated with a huge financial burden, especially in low and middle-income countries (LMICs). A molecular tumour board can help to identify and suggest the most appropriate plan of management. Key Words: Molecular, Genetics, Personalised, Challenges.

Outcomes of Patients with FLT3 Positive Acute Myeloid Leukaemia; an Experience from a Tertiary Care Hospital in Karachi, Pakistan.

Introduction: Molecular genetic abnormalities in acute myeloid leukaemia (AML) are essential for disease diagnosis and determining prognosis and clinical course. Mutations in FLT3 and nucleophosmin (NPM) genes are the most frequent genetic abnormalities, which are also known to impact disease outcomes. FLT3 mutations have been identified in approximately 30% of de novo AML patients and are associated with poor prognoses. This study aimed to determine the response to induction chemotherapy, overall survival (OS) and relapse rate (RR) in patients with FLT3-positive AML. Materials and Methods: In this study, a retrospective analysis was performed of 75 newly diagnosed patients with AML registered between January 2015 and July 2022. Patient demographics and clinical-haematological parameters were noted and molecular analysis for FLT3 ITD/TKD and NPM mutations was performed. All the patients received standard induction chemotherapy and their response to treatment, OS and RR were assessed. Results: A total of 75 cases of AML were analysed. The mean age of the sample was 34.9 years, of which 65.3% were males and 34.7% were females. The patients were stratified into two groups: Those who were positive for FLT3 while negative for NPM (FLT3+/NPM-), representing 17.3% and those who were negative for both FLT3 and NPM (FLT3-/NPM-), representing 82.7% of cases. On day 28 post-induction, the complete remission rate was 69.2% in the FLT3 positive group and 77.4% in the FLT3 negative group. In the FLT3+/NPM- group, 55.6% of cases who were in remission at day 28 subsequently relapsed, compared to 50.0% of FLT3-/NPM- cases. The overall median survival time for the cohort and FLT3+ group was 1467 days, while that of the FLT3-group could not be estimated due to the very high survival rate. Conclusion: No significant differences in outcomes were observed in patients who were FLT3 positive compared to those who were FLT3 negative.

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings.

COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.

Experience in prenatal genetic testing and reproductive decision-making for monogenic disorders from a single tertiary care genetics clinic in a low-middle income country.

OBJECTIVES: Explore health-care seeking behaviour among couples with pregnancies at-risk of monogenic disorders and compare time duration for obtaining Prenatal Genetic Test (PGT) results based on (i) amniocentesis and Chorionic Villus Sampling (CVS) (ii) in-house testing and out-sourced testing. Report the spectrum of monogenic disorders in our cohort. METHODS: Medical records of women consulting prenatal genetic counselling clinic at Aga Khan University Hospital, Karachi from December-2015 to March-2021 with history of miscarriage or a monogenic disorder in previous children were reviewed. RESULTS: Forty-three pregnancies in 40 couples were evaluated, 37(93%) were consanguineous. Twenty-five (63%) couples consulted before and 15(37%) after conception. Thirty-one (71%) pregnancies underwent CVS at the mean gestational age of 13-weeks and 6-days ± 1-week and 3-days and amniocentesis at 16-weeks and 2-days ± 1-week and 4-days. PGT for 30 (70%) pregnancies was outsourced. The mean number of days for in-house PGT was 16.92 ± 7.80 days whereas for outsourced was 25.45 ± 7.7 days. Mean duration from procedure to PGT result was 20.55 days after CVS compared to 28.75 days after amniocentesis. Eight (18%) fetuses were homozygous for disease-causing variant for whom couples opted for termination of pregnancy (TOP). Twenty-six monogenetic disorders were identified in 40 families. CONCLUSION: Proactive health-care seeking behaviour and TOP acceptance is present amongst couples who have experienced a genetic disorder.

Anaplastic Large-cell Lymphoma Involving Gastrointestinal Tract: A Clinicopathologic Study of 25 Cases of a Rare Tumor at a Rare Site.

Background. Anaplastic large-cell lymphoma (ALCL) is an uncommon lymphoma divided into anaplastic lymphoma kinase (ALK) positive, ALK negative, and breast implant-associated (BIA) ALCL. Gastrointestinal tract involvement is very rare and may be difficult to diagnose. Its recognition is crucial as prognostic ramifications are different. Objectives. To describe clinicopathological features of ALCL involving the gastrointestinal tract. Materials and Methods. Slides were reviewed. Diagnosis was confirmed. Histological and immunohistochemical features were described. Results.Twenty-five tumors were diagnosed during the study period. Ages ranged from 14 to 65 years (mean 41 years). Mean age for ALK-negative and ALK-positive patients were 49 and 17 years, respectively. Twenty-one were males and 4 were females. Eighteen involved small intestine. Mean tumor size was 4.2 cm. All showed diffuse sheets of large anaplastic cells with pleomorphic nuclei, abundant pink cytoplasm, and strong positivity for CD30. Epithelial membrane antigen was positive in 17 tumors and keratin was negative in all. Eighteen tumors were ALK negative. Out of 14 patients with follow-up, 12 died within a few months of diagnosis. Seven had stage IE, 5 had stage IIE, and 2 had stage IV disease. Two patients were alive at 35 and 60 months. Twelve received chemotherapy. Conclusion. A marked male predominance was noted. Small intestine was the commonest site of involvement. Majority were ALK negative. ALK-negative tumors occurred in older patients and ALK positive in younger patients. Prognosis was poor. ALCL should be included in the differential diagnosis of anaplastic epithelioid cell neoplasms in the gastrointestinal tract.

Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge, and their identification is important for the public health response to coronavirus disease 2019 (COVID-19). Genomic sequencing provides robust information but may not always be accessible, and therefore, mutation-based polymerase chain reaction (PCR) approaches can be used for rapid identification of known variants. International travelers arriving in Karachi between December 2020 and February 2021 were tested for SARS-CoV-2 by PCR. A subset of positive samples was tested for S-gene target failure (SGTF) on TaqPathTM COVID-19 (Thermo Fisher Scientific) and for mutations using the GSD NovaType SARS-CoV-2 (Eurofins Technologies) assays. Sequencing was conducted on the MinION platform (Oxford Nanopore Technologies). Bayesian phylogeographic inference was performed integrating the patients' travel history information. Of the thirty-five COVID-19 cases screened, thirteen had isolates with SGTF. The travelers transmitted infection to sixty-eight contact cases. The B.1.1.7 lineage was confirmed through sequencing and PCR. The phylogenetic analysis of sequence data available for six cases included four B.1.1.7 strains and one B.1.36 and B.1.1.212 lineage isolate. Phylogeographic modeling estimated at least three independent B.1.1.7 introductions into Karachi, Pakistan, originating from the UK. B.1.1.212 and B.1.36 were inferred to be introduced either from the UK or the travelers' layover location. We report the introduction of SARS-CoV-2 B.1.1.7 and other lineages in Pakistan by international travelers arriving via different flight routes. This highlights SARS-CoV-2 transmission through travel, importance of testing, and quarantine post-travel to prevent transmission of new strains, as well as recording detailed patients' metadata. Such results help inform policies on restricting travel from destinations where new highly transmissible variants have emerged.

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan.

BACKGROUND: We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan. MATERIALS AND METHODS: We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020. RESULTS: In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10-4. The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site. CONCLUSIONS: The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.

Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays.

OBJECTIVE: We investigated the discrepancy between clinical and PCR-based diagnosis of COVID-19. We compared results of ten patients with mild to severe COVID-19. Respiratory samples from all cases were tested on the Roche SARS-CoV-2 (Cobas) assay, Filmarray RP2.1 (bioMereiux) and TaqPath™ COVID19 (Thermofisher) PCR assays. RESULTS: Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested as negative on the SARS-CoV-2 Roche® assay. Further investigation using the BIOFIRE® Filmarray RP2.1 assay identified SARS-CoV-2 as the pathogen in all ten cases. To investigate possible discrepancies between PCR assays, additional testing was conducted using the TaqPath™ COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, variation at primer binding sites. Strains with SGTF indicate the presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.

The association of chest radiographic findings and severity scoring with clinical outcomes in patients with COVID-19 presenting to the emergency department of a tertiary care hospital in Pakistan.

INTRODUCTION: While chest x-rays (CXRs) represent a cost-effective imaging modality for developing countries like Pakistan, their utility for the prognostication of COVID-19 has been minimally explored. Thus, we describe the frequency and distribution of CXR findings, and their association with clinical outcomes of patients with COVID-19. METHODS: All adult (≥ 18 years) patients presenting between 28th February-31st May to the emergency department of a tertiary care hospital in Pakistan, who were COVID-19 positive on RT-PCR with CXR done on presentation, were included. A CXR Severity Score (CXR-SS) of 0-8 was used to quantify the extent of pulmonary infection on CXR, with a score of 0 being negative and 1-8 being positive. The patients' initial CXR-SS and their highest CXR-SS over the hospital course were used for analysis, with cut-offs of 0-4 and 5-8 being used to assess association with clinical outcomes. RESULTS: A total of 150 patients, with 76.7% males and mean age 56.1 years, were included in this study. Initial CXR was positive in 80% of patients, and 30.7% of patients had an initial CXR-SS between 5-8. The mortality rate was 16.7% and 30.6% patients underwent ICU admission with intubation (ICU-Int). On multivariable analysis, initial CXR-SS (1.355 [1.136-1.616]) and highest CXR-SS (1.390 [1.143-1.690]) were predictors of ICU-Int, and ICU-Int was independently associated with both initial CXR-SS 5-8 (2.532 [1.109-5.782]) and highest CXR-SS 5-8 (3.386 [1.405-8.159]). Lastly, age (1.060 [1.009-1.113]), initial CXR-SS (1.278 [1.010-1.617]) and ICU-Int (5.047 [1.731-14.710]), were found to be independent predictors of mortality in our patients. CONCLUSION: In a resource-constrained country like Pakistan, CXRs may have valuable prognostic utility in predicting ICU admission and mortality. Additional research with larger patient samples is needed to further explore the association of CXR findings with clinical outcomes.

MLPA Analyses Reveal a Spectrum of Dystrophin Gene Deletions/Duplications in Pakistani Patients Suspected of Having Duchenne/Becker Muscular Dystrophy: A Retrospective Study.

Introduction: Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are inherited X-linked recessive genetic disorders caused by defects in the dystrophin gene. Abnormality in the dystrophin protein causes progressive muscle damage and weakness leading to long-term disability. Objective: To investigate the spectrum of dystrophin gene variants (deletions and duplications) in Pakistani patients suspected of having DMD/BMD or of being DMD/BMD carriers. Methods: A single center (Aga Khan University Hospital, Karachi, Pakistan) retrospective review of 46 cases was conducted to characterize dystrophin gene variants (deletion/duplication) in DMB/BMD patients using the multiplex ligation-dependent probe amplification-based method to provide coverage for all 79 exons. Results: Dystrophin gene deletions were identified in 40 of 46 cases, whereas duplications were present in 6 of 46 cases. The majority of the deletions were present between exons 45 and 52 followed by the region between exons 8 and 18. The most frequently deleted was exon 46 (8%) followed by exon 49 (7%). Dystrophin gene duplications were clustered between exons 3 and 7. The average deletion or duplication size was five exons for both kinds of variants. Conclusions: The applicability of exon skipping drugs depends on the specific mutational frequencies within populations. Our data suggest that for the Pakistani patients, multiple exon skipping between exons 46 and 49 could potentially be a target for exon skipping therapy. However, a larger nationwide study is required to further identify the predominant deletion/duplication dystrophin gene variants present in the population.

Case Series of Naegleria fowleri Primary Ameobic Meningoencephalitis from Karachi, Pakistan.

Naegleria fowleri causes primary amoebic meningoencephalitis (PAM) which is almost always fatal. Naegleria fowleri is waterborne, and its infections are usually associated with aquatic activities but it can also be transmitted via the domestic water supply. An increasing number of N. fowleri cases have been reported from Pakistan. Improved methods for diagnosis are required. We report the utility of polymerase chain reaction (PCR) for the diagnosis of N. fowleri in patients suspected of PAM. One hundred and sixteen cases suspected of having PAM were examined. Cerebrospinal fluid (CSF) specimens were tested at the Aga Khan University Hospital, Karachi. Nineteen CSF specimens were positive for N. fowleri using PCR. Naegleria fowleri positive patients had a median age of 28 years and were 84% male and 16% female. Overall, CSF wet preparation microscopy was performed in 85 (73%) cases and identified that seven specimens were positive for motile trophozoites. The CSF wet preparation results were available for 15 of the 19 N. fowleri PCR positive CSF samples; seven (40%) wet preparations were positive. Our data highlight the threat of N. fowleri infection as a cause of PAM. It also emphasizes the utility of the PCR-based diagnosis of the amoeba for early diagnosis and management of the disease.