Secondary attack rates and determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) household transmission in Pakistan: A case-ascertained prospective, longitudinal study.

BACKGROUND: Households are considered ideal settings for studying the transmission dynamics of an infectious disease. METHODS: A prospective study was conducted, based on the World Health Organization FFX protocol from October 2020 to January,2021. Household contacts of laboratory-confirmed index cases were followed up for their symptomatic history, nasal swabs for RT-PCR,and blood samples for anti-SARS CoV-2 antibodies were collected at enrollment and days 7, 14 and 28. We estimated secondary attack rate (SAR), effective household case cluster size and determinants of secondary infection among susceptible household contacts using multivariable logistic regression. RESULTS: We enrolled 77 index cases and their 543 contacts. Out of these, 252 contacts were susceptible at the time of enrollment. There were 77 household clusters, out of which, transmission took place in 20 (25.9%) giving rise to 34 cases. The acquired secondary attack rate (SAR) was 14.0% (95% CI 9.0-18.0). The effective household case cluster size was 0.46 (95%CI 0.33,0.56). Reported symptoms of nausea and vomiting (aOR, 7.9; 95% CI, 1.4-45.5) and fatigue (aOR, 9.3; 95% CI, 3.8-22.7) were associated with SARS-CoV-2 transmission. CONCLUSIONS: We observed a low SARS-CoV-2 secondary attack rate in the backdrop of high seroprevalence and asymptomatic transmission among households in Karachi, Pakistan.

Anti-oxidant and Anticancerous Effect of Fomitopsis officinalis (Vill. ex Fr. Bond. et Sing) Mushroom on Hepatocellular Carcinoma Cells In Vitro through NF-kB Pathway.

BACKGROUND: Fomitopsis officinalis (Vill. ex Fr. Bond. et Sing) is a medicinal mushroom, commonly called 'Agarikon'; it has traditionally been used to treat cough and asthma in the Mongolian population. OBJECTIVE: The objective of the study was to examine the significance of biological activity of F. officinalis and evaluation of the antioxidant activity and anticancer activity of six fractions of F. officinalis residues (Fo1-powder form dissolved in ethanol, Fo2-petroleum ether residue, Fo3-chloroformic, Fo4-ethylacetate, Fo5-buthanolic, and Fo6-waterethanolic) against hepatocellular carcinoma cells. METHODS: We performed in vitro studies of cell proliferation and viability assay, annexin V-FITC/Propidium Iodide assay, and NF-kB signaling pathway by immunoblot analysis. RESULTS: Our findings revealed that all six fractions/extracts have antioxidant activity, and somehow, they exert anticancerous effects against cancer cells. In cancerous cell lines (HepG2 and LO2), Fo3 chloroformic extract promoted the cancer cell apoptosis and cell viability, activated G2/M-phase cell cycle, and selectively induced NF-kB proteins, revealing as a novel antitumor extract. CONCLUSION: This study reports that Fo3-chloroformic extract is rich in antitumor activity, which was previously not investigated in cancer. To develop the impact of F. officinalis among natural products to treat/prevent oxidative stress disorders or cancers, further examinations of F. officinalis are needed to develop new natural drugs to treat cancer. However, this study assessed only one extract, Fo3-chloroformic, which has a significant impact against cancer cell lines.

Serial population-based serosurveys for COVID-19 in two neighbourhoods of Karachi, Pakistan.

OBJECTIVE: To determine population-based estimates of coronavirus disease 2019 (COVID-19) in a densely populated urban community of Karachi, Pakistan. METHODS: Three cross-sectional surveys were conducted in April, June and August 2020 in low- and high-transmission neighbourhoods. Participants were selected at random to provide blood for Elecsys immunoassay for detection of anti-severe acute respiratory syndrome coronavirus-2 antibodies. A Bayesian regression model was used to estimate seroprevalence after adjusting for the demographic characteristics of each district. RESULTS: In total, 3005 participants from 623 households were enrolled in this study. In Phase 2, adjusted seroprevalence was estimated as 8.7% [95% confidence interval (CI) 5.1-13.1] and 15.1% (95% CI 9.4-21.7) in low- and high-transmission areas, respectively, compared with 0.2% (95% CI 0-0.7) and 0.4% (95% CI 0-1.3) in Phase 1. In Phase 3, it was 12.8% (95% CI 8.3-17.7) and 21.5% (95% CI 15.6-28) in low- and high-transmission areas, respectively. The conditional risk of infection was 0.31 (95% CI 0.16-0.47) and 0.41 (95% CI 0.28-0.52) in low- and high-transmission neighbourhoods, respectively, in Phase 2. Similar trends were observed in Phase 3. Only 5.4% of participants who tested positive for COVID-19 were symptomatic. The infection fatality rate was 1.66%, 0.37% and 0.26% in Phases 1, 2 and 3, respectively. CONCLUSION: Continuing rounds of seroprevalence studies will help to improve understanding of secular trends and the extent of infection during the course of the pandemic.

A splice-site variant (c.3289-1G>T) in OTOF underlies profound hearing loss in a Pakistani kindred.

BACKGROUND: Hearing loss/deafness is a common otological disorder found in the Pakistani population due to the high prevalence of consanguineous unions, but the full range of genetic causes is still unknown. METHODS: A large consanguineous Pakistani kindred with hearing loss was studied. Whole-exome sequencing and Sanger sequencing were performed to search for the candidate gene underlying the disease phenotype. A minigene assay and reverse transcription polymerase chain reaction was used to assess the effect of splicing variants. RESULTS: The splicing variants of OTOF (NM_194248, c.3289-1G>T) cosegregated with the disease phenotype in this Pakistani family. The substitution of a single base pair causes the deletion of 10 bp (splicing variant 1) or 13 bp (splicing variant 2) from exon 27, which results in truncated proteins of 1141 and 1140 amino acids, respectively. CONCLUSION: Our findings reveal an OTOF splice-site variant as pathogenic for profound hearing loss in this family.

Biallelic loss-of-function variants in NEMF cause central nervous system impairment and axonal polyneuropathy.

We aimed to detect the causative gene in five unrelated families with recessive inheritance pattern neurological disorders involving the central nervous system, and the potential function of the NEMF gene in the central nervous system. Exome sequencing (ES) was applied to all families and linkage analysis was performed on family 1. A minigene assay was used to validate the splicing effect of the relevant discovered variants. Immunofluorescence (IF) experiment was performed to investigate the role of the causative gene in neuron development. The large consanguineous family confirms the phenotype-causative relationship with homozygous frameshift variant (NM_004713.6:c.2618del) as revealed by ES. Linkage analysis of the family showed a significant single-point LOD of 4.5 locus. Through collaboration in GeneMatcher, four additional unrelated families' likely pathogenic NEMF variants for a spectrum of central neurological disorders, two homozygous splice-site variants (NM_004713.6:c.574+1G>T and NM_004713.6:c.807-2A>C) and a homozygous frameshift variant (NM_004713.6: c.1234_1235insC) were subsequently identified and segregated with all affected individuals. We further revealed that knockdown (KD) of Nemf leads to impairment of axonal outgrowth and synapse development in cultured mouse primary cortical neurons. Our study demonstrates that disease-causing biallelic NEMF variants result in central nervous system impairment and other variable features. NEMF is an important player in mammalian neuron development.

Anti-oxidant and Antiproliferative Activities of Mongolian Medicinal Plant Extracts and Structure Isolation of Gnetin-H Compound.

BACKGROUND: Reactive oxygen species are involved in the etiology and progress of many kinds of diseases such as cancer, cardiovascular diseases, inflammatory and neurodegenerative disorders. Epidemiological studies reported that fruits, vegetables, and wines containing a high percentage of phenolics and flavonoids showed a positive impact in treating inflammatory diseases, reducing cancer risk, and increasing life expectancy. OBJECTIVE: Some Mongolian medicinal plants were studied for their antioxidant activity and anticancer effects. METHODS: Selected Mongolian medicinal plant extracts were examined for their antioxidant activity by the DPPH-radical scavenging assay, the content of phenolics and flavonoids by Folin-Ciocalteu and the Dowd method, respectively, and anti-cancer activities in human hepatoma cell line HepG2 cells by MTT assay. RESULTS: Methanol extract from Hippophae rhamnoides L. leaf and ethanol extract from Artemisia macrocephala Jacq. ex Bess. showed the highest efficiency to scavenge free radicals. Ethanol extracts from Hippophae rhamnoides L. grain and Paeonio anomala L. leaf showed the highest total phenolics content, whereas Hippophae rhamnoides L. fruit methanol extract and ethanol extract from Caragana leucophloea pojark. mentioned the highest flavonoids content. The Artemisia macrocephala Jacq. ex Bess seed wallet and Paeonia anomala L. seed wallet showed the most potent antiproliferative effects against human liver cancer HepG2 cell line. Gnetin-H compound was isolated from the Paeonio anomala L. seed wallet extract, and its molecular structure was determined by 1H and 13C NMR spectrum and IR spectroscopy methods. CONCLUSION: The screening study on anti-oxidative effects of 21 extracts from 15 Mongolian medicinal plants showed anti-oxidative activities and was rich in phenolics and flavonoids. Among these, methanol extract of the Hippophae rhamnoides L. leaf showed a better anti-oxidative effect than the ethanol extract. Artemisia macrocephala Jacq. ex Bess and Paeonia anomala L. seed wallet mentioned the best anti-cancer effects. Gnetin-H, methyl gallate, ethylgallate were the major components in the extract from the Paeonio anomala L. seed wallet. Finally, the molecular structure of gnetin-H was determined by NMR and IR spectroscopy. Further investigation, especially in vivo antioxidant activity, is needed to justify the use of a natural source of antioxidants to prevent the progression of diseases such as cancer.

Epidemiological and Clinical Features of SARS-CoV-2: A Retrospective Study from East Karachi, Pakistan.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to almost every country on the globe, and each country is reporting the symptomatic presentation of their patients to give better insight into the various clinical presentations of SARS-CoV-2. However, the epidemiological literature from Pakistan is scanty. Methods We retrospectively analyzed data from 412 patients who were residents of East Karachi and tested positive for SARS-CoV-2 between February 26 to April 24, 2020. Patients' demographics, symptoms, travel and contact history, and outcomes were recorded. All statistical analysis was performed using the Statistical Package for the Social Sciences (SPSS) version 22 (IBM SPSS Statistics for Windows, IBM Corp, Armonk, NY). Results Most of the patients were male (64.6%), the majority (43.3%) belonging to the 21- to 40-year age group. Most of the patients (65.5%) were residents of Gulshan Iqbal. A total of 15.8% of the patients were admitted to the hospital, and 3.9% of patients expired. The three most common presenting symptoms were fever (74.8%), cough (60.4%), and flu (35.5%). The majority of patients (89.3%) gave a history of contact with SARS-CoV-2 patients. Conclusion The number of SARS-CoV-2 cases is rapidly increasing in Karachi, Pakistan. There is a need to educate the population about the most common sign and symptoms of the virus so that individuals can identify these symptoms and get themselves tested. The concerned authorities should devise an adequate and effective plan to flatten the infectivity curve.

A founder RDH5 splice site mutation leads to retinitis punctata albescens in two inbred Pakistani kindreds.

Background: Retinitis punctate albescens (RPA) is a rare form of retinal dystrophy characterized by congenital stationary night blindness and a characteristic fundus appearance. Missense or nonsense mutations in RDH5 in homozygous or heterozygous state have been implicated in RPA.Material and methods: Two consanguineous Pakistani kindreds with the highly variable manifestation of RPA were studied. Whole-exome sequencing was applied to the index subjects in both families. Sanger sequencing of the candidate RDH5 variant was carried out. Pathogenicity of the detected variant was assessed through bioinformatics tools.Results: The ophthalmic examination through full-field electroretinogram of affected patients in both families was consistent with RPA. A novel splice donor variant at the first exon/intron boundary of RDH5 (NM_002905.3: c.-33 + 2dup) segregated in recessive fashion with the clinical phenotype in both families. One of the heterozygous variant carriers was also observed to have a milder expression of retinal flecks. Haplotype analysis surrounding the splice variant and pattern of runs of homozygosity were suggestive of common ancestry in these families.Conclusion: This is the first report of any pathogenic splice variant at first exon/intron boundary implicated in RPA and suggests another mechanism through which RDH5 variants could be associated with eye phenotype. This study also highlights the importance of a thorough phenotypic evaluation of heterozygous mutation carriers who may exhibit milder symptoms.

Outcomes of Harmonic Scalpel and Electrocautery in Patients Who Underwent Modified Radical Mastectomy.

Objective This study aimed to compare the mean operative time, total analgesic required, and the mean number of drainage days in harmonic scalpel versus electrocautery in breast cancer patients undergoing modified radical mastectomy (MRM). Methodology This retrospective cross-sectional study was conducted in the Department of General Surgery, Jinnah Postgraduate Medical Center (JPMC). The duration of the study was six months, from January 2018 until July 2018. A total of 194 females with biopsy-proven breast cancer undergoing MRM were included in the study. They were divided into two groups. In group 'A', a harmonic scalpel was used, and in group 'B', electrocautery was used for hemostasis. Results The mean age of the participants was 48.68 ±10.04 years. The mean operative time was 102.13 ±2.04 minutes. The mean number of days of drainage was 1.27 ±2.63. The mean analgesia amount was 30.72 ±3.25 mg. In the harmonic scalpel group, the mean operative time was 100.43 ±0.89 minutes, whereas, in the electrocautery group, it was 103.86 ±1.12 minutes with a significant difference (p=0.001). In the harmonic scalpel group, the mean number of drainage days was 8.90 ±0.42, whereas, in the electrocautery group, it was 13.58 ±1.26 with a statistically significant difference (p=0.001). In the harmonic scalpel group, the mean analgesia amount was 1,800.5 ±353.55 mg, whereas, in the electrocautery group, it was noted to be 2,006.25 ±289.43 with a statistically significant difference (p=0.001). Conclusion This study concludes that compared with standard electrocautery, harmonic scalpel dissection is associated with significant benefits in decreasing postoperative drainage and blood loss during operations after MRM for breast cancer.