Comprehensive update on the monkeypox outbreak.

Monkeypox (MPX) was first reported in 1970 in humans and outbreaks were restricted and highly localised to endemic regions of western and central Africa. However, after the first reported case in the UK in early May, 2022, the pattern of epidemic spreading in the geographical regions was much larger compared to past, posing a risk MPX might become entrenched beyond endemic areas. This virus is less transmissible than SARS-CoV-2, as it transmitted mainly through personal, close, often skin-to-skin contact with infectious MPX rash, body fluids, or scabs from an individual with MPX. Infections usually present with chills, fever, fatigue, muscle aches, headache, sore throat, skin lesions, and lymphadenopathy. Currently, there are no antivirals approved for MPX. However, an antiviral drug called "tecovirimat," approved for the treatment of smallpox, has been made accessible to treat MPX. Moreover, to prevent MPX, there are two vaccines available which are approved by FDA: Bavarian Nordic JYNNEOS, and ACAM2000 vaccine. Contact tracing is absent in case of MPX outbreak and there is lack of information from the data systems in rapid manner. Additionally, test capacity needs to be increased. Like SARS-CoV-2, global MPX outbreak demand for vaccines far exceeds availability.

Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia

Background Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health. Methods A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 16 S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens. Results No significant (p>0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p<0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7%) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1. Conclusions Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.

Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia.

BACKGROUND: Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health. METHODS: A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens. RESULTS: No significant (p > 0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p < 0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1. CONCLUSIONS: Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.

Tanneries impact on groundwater quality: a case study of Kasur city in Pakistan.

Leather industry is the second largest export-earning sector of Pakistan. However, because of poor waste management, this industry has been continuously polluting the environment. In this paper, the impact of tanneries on the groundwater quality of Kasur city (i.e., the second largest leather producing city) is examined. The study is conducted in the following three phases: (I) water samples collection, (II) determination of physio-chemical properties, and (III) application of data mining techniques. In phase I, groundwater samples were collected from various sources such as hand pumps, motor pumps, and tube wells. In phase II, several physio-chemical properties such as (i) total dissolved solids (TDS), (ii) pH, (iii) turbidity, (iv) electrical conductivity (EC), (v) total hardness (TH), (vi) total alkalinity (TA), (vii) nitrates, (viii) chromium, (ix) fluoride, and (x) chloride were estimated. The estimated values of all these foregoing parameters are then compared with the Punjab Environmental Quality Standards for Drinking Water (PEQSDW). In phase III, principle component analysis and cluster analysis of the estimated parameters were performed to elucidate the relation between various parameters and to highlight the highly vulnerable sites, respectively. The results exhibit that most of the sampling collections sites are at the threshold of losing quality water. Moreover, it is also found that Mangal Mandi carries the worst groundwater quality among all sampling locations. Overall, it is concluded that serious attention is due from the water and wastewater authorities to further investigate and monitor the groundwater quality of Kasur before the country strikes with another pandemic after COVID-19.

Characteristics and comparisons of acute stroke in "recovered" to "active COVID-19 and "pre-pandemic" in Qatar database.

Understanding the relationship of COVID-19 to stroke is important. We compare characteristics of pre-pandemic stroke (PPS), cases in acute COVID infection (CS) and in patients who have recovered from COVID-19 infection (RCS). We interrogated the Qatar stroke database for all stroke admissions between Jan 2020 and Feb 2021 (PPS) to CS and RCS to determine how COVID-19 affected ischemic stroke sub-types, clinical course, and outcomes prior to, during and post-pandemic peak. There were 3264 cases admitted (pre-pandemic: 3111, stroke in COVID-19: 60 and recovered COVID-19 stroke: 93). Patients with CS were significantly younger, had more severe symptoms, fever on presentation, more ICU admissions and poor stroke recovery at discharge when compared to PPS and RCS. Large vessel disease and cardioembolic disease was significantly higher in CS compared to PPS or RCS. There was a significant decline in stroke mimics in CS. Stroke in RCS has characteristics similar to PPS with no evidence of lasting effects of the virus on the short-term. However, CS is a more serious disease and tends to be more severe and have a poor prognosis.

Desert boil strikes hard: An outbreak of cutaneous leishmaniasis in Sindh, Pakistan.

Amidst the ongoing wave of COVID in Pakistan, multiple cities of interior province of Sindh were struck by a new epidemic. This disfiguring disease known as the Desert Boil or Cutaneous Leishmaniasis has affected nearly 4400 people and daily 100-150 cases are being reported in men, women and children of all age. Public health authorities have declared a health emergency in various cities and are trying to curtail this epidemic.

Epidemiology, Clinico-Pathological Characteristics, and Comorbidities of SARS-CoV-2-Infected Pakistani Patients.

SARS-CoV-2 is a causative agent for COVID-19 disease, initially reported from Wuhan, China. The infected patients experienced mild to severe symptoms, resulting in several fatalities due to a weak understanding of its pathogenesis, which is the same even to date. This cross-sectional study has been designed on 452 symptomatic mild-to-moderate and severe/critical patients to understand the epidemiology and clinical characteristics of COVID-19 patients with their comorbidities and response to treatment. The mean age of the studied patients was 58 ± 14.42 years, and the overall male to female ratio was 61.7 to 38.2%, respectively. In total, 27.3% of the patients had a history of exposure, and 11.9% had a travel history, while for 60% of patients, the source of infection was unknown. The most prevalent signs and symptoms in ICU patients were dry cough, myalgia, shortness of breath, gastrointestinal discomfort, and abnormal chest X-ray (p < 0.001), along with a high percentage of hypertension (p = 0.007) and chronic obstructive pulmonary disease (p = 0.029) as leading comorbidities. The complete blood count indicators were significantly disturbed in severe patients, while the coagulation profile and D-dimer values were significantly higher in mild-to-moderate (non-ICU) patients (p < 0.001). The serum creatinine (1.22 µmol L-1; p = 0.016) and lactate dehydrogenase (619 µmol L-1; p < 0.001) indicators were significantly high in non-ICU patients, while raised values of total bilirubin (0.91 µmol L-1; p = 0.054), C-reactive protein (84.68 mg L-1; p = 0.001), and ferritin (996.81 mg L-1; p < 0.001) were found in ICU patients. The drug dexamethasone was the leading prescribed and administrated medicine to COVID-19 patients, followed by remdesivir, meropenem, heparin, and tocilizumab, respectively. A characteristic pattern of ground glass opacities, consolidation, and interlobular septal thickening was prominent in severely infected patients. These findings could be used for future research, control, and prevention of SARS-CoV-2-infected patients.

Ischemic stroke in patients that recover from COVID-19: Comparisons to historical stroke prior to COVID-19 or stroke in patients with active COVID-19 infection.

BACKGROUND AND PURPOSE: Understanding the relationship of COVID-19 to stroke is important. We compare characteristics of pre-pandemic historical stroke (Pre-C), cases in acute COVID infection (Active-C) and in patients who have recovered from COVID-19 infection (Post-C). METHODS: We interrogated the Qatar stroke database for all stroke admissions between Jan 2019 and Feb 2020 (Pre-C) to Active-C (Feb2020-Feb2021) and Post-C to determine how COVID-19 affected ischemic stroke sub-types, clinical course, and outcomes prior to, during and post-pandemic peak. We used the modified Rankin Scale (mRS) to measure outcome at 90-days (mRS 0-2 good recovery and mRS 3-6 as poor recovery). For the current analysis, we compared the clinical features and prognosis in patients with confirmed acute ischemic stroke. RESULTS: There were 1413 cases admitted (pre-pandemic: 1324, stroke in COVID-19: 46 and recovered COVID-19 stroke: 43). Patients with Active-C were significantly younger, had more severe symptoms, fever on presentation, more ICU admissions and poor stroke recovery at discharge when compared to Pre-C and Post-C. Large vessel disease and cardioembolic disease was significantly more frequent in Active-C compared to PRE-C or post-C. CONCLUSIONS: Stroke in Post-C has characteristics similar to Pre-C with no evidence of lasting effects of the virus on the short-term. However, Active-C is a more serious disease and tends to be more severe and have a poor prognosis.

Ability of Essential Oil Vapours to Reduce Numbers of Culturable Aerosolised Coronavirus, Bacteria and Fungi.

Transmission of pathogens present in the indoor air can occur through aerosols. This study evaluated the efficacy of an evaporated mix of essential oils to reduce the numbers of culturable aerosolized coronavirus, bacterium and fungus. The essential oil-containing gel was allowed to vaporize inside a glass chamber for 10 or 20 min. Aerosols of a surrogate of SARS-CoV-2, murine hepatitis coronavirus MHV-1, Escherichia coli or Aspergillus flavus spores were produced using a collision nebuliser and passed through the essential oil vapours, then collected on a six-stage Andersen sampler. The six-stages of the impact sampler capture aerosols in sizes ranging from 7 to 0.65 µm. The number of culturable microbes present in the aerosols collected in the different stages were enumerated and compared to the number of culturable microbes in control microbial aerosols that were not exposed to the evaporated essential oils. After 10 and 20 min evaporation, the essential oils reduced the numbers of culturable aerosolized coronavirus by 48% (log10 reduction = 0.3; p = 0.002 vs. control) and 53% (log10 reduction = 0.3; p = 0.001 vs. control), respectively. The essential oils vaporised for 10 min, reduced the number of viable E. coli by 51% (log10 reduction = 0.3; p = 0.032 vs. control). The Aspergillus flavus spores were mostly observed in the larger aerosols (7.00 µm to 2.10 µm) and the essential oils vaporised for 10 min reduced the number of viable spores by 72% (log10 reduction = 0.6; p = 0.008 vs. control). The vapours produced by a gel containing naturally occurring essential oils were able to significantly reduce the viable numbers of aerosolized coronavirus, bacteria and fungal spores. The antimicrobial gel containing the essential oils may be able to reduce aerosol transmission of microbes when used in domestic and workplace settings.

A New Numerical Scheme for Time Fractional Diffusive SEAIR Model with Non-Linear Incidence Rate: An Application to Computational Biology

In this paper, we propose a modified fractional diffusive SEAIR epidemic model with a nonlinear incidence rate. A constructed model of fractional partial differential equations (PDEs) is more general than the corresponding model of fractional ordinary differential equations (ODEs). The Caputo fractional derivative is considered. Linear stability analysis of the disease-free equilibrium state of the epidemic model (ODEs) is presented by employing Routh–Hurwitz stability criteria. In order to solve this model, a fractional numerical scheme is proposed. The proposed scheme can be used to find conditions for obtaining positive solutions for diffusive epidemic models. The stability of the scheme is given, and convergence conditions are found for the system of the linearized diffusive fractional epidemic model. In addition to this, the deficiencies of accuracy and consistency in the nonstandard finite difference method are also underlined by comparing the results with the standard fractional scheme and the MATLAB built-in solver pdepe. The proposed scheme shows an advantage over the fractional nonstandard finite difference method in terms of accuracy. In addition, numerical results are supplied to evaluate the proposed scheme’s performance.

SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021.

The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the world's largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 that began in March 2021. In Pakistan, during the third wave until now only 12 SARS-CoV-2 genomes have been collected and among these nine are from Islamabad. This highlights the need for more genome sequencing to allow surveillance of variants in circulation. In fact, more genomes are available among travellers with a travel history from Pakistan, than from within the country itself. We thus aimed to provide a snapshot assessment of circulating lineages in Lahore and surrounding areas with a combined population of 11.1 million. Within a week of April 2021, 102 samples were sequenced. The samples were randomly collected from two hospitals with a diagnostic PCR cutoff value of less than 25 cycles. Analysis of the lineages shows that the Alpha variant of concern (first identified in the UK) dominates, accounting for 97.9 % (97/99) of cases, with the Beta variant of concern (first identified in South Africa) accounting for 2.0 % (2/99) of cases. No other lineages were observed. In depth analysis of the Alpha lineages indicated multiple separate introductions and subsequent establishment within the region. Eight samples were identical to genomes observed in Europe (seven UK, one Switzerland), indicating recent transmission. Genomes of other samples show evidence that these have evolved, indicating sustained transmission over a period of time either within Pakistan or other countries with low-density genome sequencing. Vaccines remain effective against Alpha, however, the low level of Beta against which some vaccines are less effective demonstrates the requirement for continued prospective genomic surveillance.

Antiviral effect of multipurpose contact lens disinfecting solutions against coronavirus.

PURPOSE: To evaluate the antiviral potential of five multipurpose disinfecting solutions against coronavirus (mouse hepatitis virus, a surrogate for SARS-CoV-2 human corona virus). METHODS: Test solutions (Biotrue, renu Advanced [Bausch and Lomb], ACUVUE RevitaLens [Johnson and Johnson Vision], cleadew [Ophtecs corp.] or AOSept Plus [Alcon]) were mixed with the coronavirus mouse hepatitis virus at 104 plaque forming units (PFU)/mL as the final concentration and incubated at room temperature for the specified disinfection time. Surviving virus from each sample was then quantified by standard plaque forming unit assay and the reduction of PFU for each disinfectant was compared to the phosphate buffer saline (PBS) treated negative control. A regimen test was also conducted using Biotrue. RESULTS: The three multipurpose disinfecting solutions Biotrue (containing PHMB and polyquaternium-1), renu Advanced (PHMB, polyquaternium-1 and alexidine) and ACUVUE RevitaLens (polyquaternium-1 and alexidine) did not kill the coronavirus at the manufacturers recommended disinfection time in the stand alone test. After treatment, the virus's titer (3.8 ± 0.2 log10 for Biotrue, 3.7 ± 0.1 log10 for renu and 3.7 ± 0.2 log10 for RevitaLens) was similar to the negative control (3.7 ± 0.1 log10; p ≥ 0.996). AOSept Plus (hydrogen peroxide) and cleadew (povidone iodine) significantly (p < 0.001) reduced the numbers of coronaviruses to below the detection limit (i.e. killed 3.7 ± 0.1 log10 viruses compared to control). However, there was a significant reduction (p = 0.028) in numbers of coronaviruses attached to lenses when using the regimen test with Biotrue. CONCLUSIONS: This study shows that oxidative contact lens disinfecting solutions (i.e. those containing povidone-iodine or hydrogen peroxide) provide superior antiviral activity against a coronavirus surrogate of SARS-CoV-2, unless the full regimen test (rub, rinse, disinfect) is used.

Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.

The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organizations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1565 positive samples (172 per 100 000 population) from 1376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6 % of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. In total, 1035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region. Furthermore, 100 genetically distinct UK lineages were detected demonstrating local evolution, at a rate of ~2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.

A Case of COVID-19 Induced Thrombotic Thrombocytopenic Purpura.

Thrombotic Thrombocytopenic Purpura (TTP) is a challenging thrombotic diathesis which requires prompt diagnosis and therapeutic intervention in order to avoid life-threatening consequences. There are two forms of TTP, congenital and acquired, with the acquired form constituting about 90% of cases. Both forms are associated with a deficiency of ADAMTS-13, a metalloproteinase enzyme responsible for cleaving ultra-large von Willebrand factor (uLvWF), preventing its pathologic accumulation. Within the last year, many of the diverse and serious effects of the COVID-19 virus have come to recognition, with some of the most dire consequences involving devastating vascular and hematologic complications. As with many viruses, it seems that the endothelium and the vasculature are often prime targets. Here, we report a case of a 30 year old male who was diagnosed with TTP approximately one week after a positive COVID-19 test result. He responded appropriately to plasma exchange (PLEX), caplacizumab, and steroids. We believe it is important to investigate a potential link between these two conditions, as TTP has significant morbidity and mortality risk if left unattended. We hope that our report will contribute to a better understanding of this potential link.

Re-infection with a different SARS-CoV-2 clade and prolonged viral shedding in a hematopoietic stem cell transplantation patient.

Immunocompromised patients who have a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection pose many clinical and public health challenges. We describe the case of a hematopoietic stem cell transplantation patient with lymphoma who had a protracted illness requiring three consecutive hospital admissions. Whole genome sequencing confirmed two different SARS-CoV-2 clades. Clinical management issues and the unanswered questions arising from this case are discussed.

Monitoring the Impact of COVID-19 Lockdown on the Production of Nitrogen Dioxide (NO2) Pollutants Using Satellite Imagery: A Case Study of South Asia

Among the numerous anthropogenic pollutants, nitrogen dioxide (NO2) is one of the leading contaminants mainly released by burning fossil fuels in industrial and transport sectors. This study evaluates the impact of COVID-19 lockdown on the growing trend of NO2 emissions in South Asia. Satellite imagery data of Sentinel-5 Precursor with Tropomi instrument was employed in this study. The analysis was performed using time series data from February–May 2019 and February–May 2020. The time frame from February–May 2020 was further divided into two sub-time-frames, i.e., from 1 February–20 March (pre-lockdown) and from 21 March–May 2020 (lockdown). Results show the concentration of NO2 pollutants over the region declined by 6.41% from February–May 2019 to February–May 2020. Interestingly, an increasing trend of NO2 concentration by 6.58% occurred during the pre-lockdown phase in 2020 (1 February–20 March) compared to 2019 (February–May). However, the concentration of NO2 pollutants reduced considerably by 21.10% during the lockdown phase (21 March–10 May) compared to the pre-lockdown phase in 2020. Furthermore, the country-specific detailed analysis demonstrates the significant impact of COVID-19-attributed lockdown on NO2 concentration in South Asia.