Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics

Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values-indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus.

Smell Outcome and Seropositivity Titre in Post-COVID-19 Patients

INTRODUCTION

The aims of the study were to perform an olfactory assessment on patients active and post-COVID-19 using the culturally adapted Malaysian version Sniffin' Sticks identification smell test (mSS-SIT), to evaluate the patient olfactory outcome using a Malay short version of the Questionnaire of Olfactory Disorders-Negative Statements (msQOD-NS), as well as to evaluate seropositive titre (IgG) response using automated serology method.

METHODS

Score for mSS-SIT was performed during the hospitalization, when patients had tested positive for SARS-CoV-2 (during COVID-19), and repeated after they had tested negative (after COVID-19). Also, each patient completed msQOD-NS and serology SARS-CoV-2 antibodies blood test was evaluated.

RESULTS

During COVID-19, 2 of our patients were anosmia (6.5%), 22 (70.9%) were hyposmia, and 7 (22.6%) were normosmia. We repeated mSS-SIT on these same patients after COVID-19, and none of these subjects were hyposmia or anosmia, as they achieved a score >12. All our patients had scored 21 using msQOD-NS, meaning no impact on quality of life as they had regained their normal olfactory function. In this study also, we obtained no correlation between smell test and seropositivity titre COVID-19, and antibody levels gradually decreased over time till 6 months and remained stable up to 12 months.

CONCLUSION

From this study, we know full recovery of the sense of smell can be expected post-COVID-19 infection and COVID-19 antibody persists in the body up to 12 months of infection.

Seroprevalence of acute dengue in a Malaysian tertiary medical centre

Objectives:

The aims of this study were to determine the seroprevalence of acute dengue in Universiti Kebangsaan Malaysia (UKM) Medical Centre and its correlation with selected haematological and biochemical parameters.

Methods:

This cross-sectional study was conducted from January to June 2015. A patient was serologically diagnosed with acute dengue if the dengue virus IgG, IgM or NS-1 antigen was reactive.

Results:

Out of 1,774 patients suspected to have acute dengue, 1,153 were serologically diagnosed with the infection, resulting in a seroprevalence of 64.9%. Dengue-positive patients had a lower mean platelet count (89 × 10⁹/L) compared to the dengue-negative patients (171 × 10⁹/L) (p<0.0001). The mean total white cell count was also lower in the dengue-positive cases (4.7 × 10⁹/L vs. 7.2 × 10⁹/L; p<0.0001). The mean haematocrit was higher in patients with acute dengue (42.5% vs. 40.0%; p<0.0001). Likewise, the serum alanine transaminase level was also higher in patients with acute dengue (108 U/L vs. 54 U/L; p<0.0001).

Conclusions:

Dengue is very prevalent in UKM Medical Centre as most patients suspected to have acute dengue had serological evidence of the infection. The platelet count was the single most likely parameter to be abnormal (i.e. low) in patients with acute dengue.

INFLUENZA VACCINATION UPTAKE AMONG HEALTHCARE WORKERS AT A MALAYSIAN TEACHING HOSPITAL

Annual influenza vaccination is the most important preventive strategy against influenza illness in healthcare workers (HCWs), who could acquire influenza from and transmit influenza to patients and other HCWs. Despite the well established benefits and strong recommendations for influenza vaccination for all HCWs, influenza vaccination uptake at the Universiti Kebangsaan Malaysia Medical Centre (UKMMC) for the past 3 years has been low and is decreasing. We aimed to determine the factors associated with influenza vaccination uptake among HCWs at UKMMC. We conducted a cross sectional study via questionnaire among 211 randomly selected HCWs, consisting of 106 HCWs who were vaccinated in 2011 and 105 HCWs who were not vaccinated in 2010 or 2011. We had a 100% response rate. Influenza vaccination uptake was significantly associated with age and previous vaccination history, with older HCWs being more likely to be vaccinated (adjusted OR = 12.494; 95% CI:6.278-24.863; p < 0.001) and HCWs with previous vaccination history being more likely to be vaccinated (adjusted OR = 1.038; 95% CI:1.001-1.077; p = 0.045). Influenza vaccination uptake was not associated with gender (p = 0.926) or job category (p = 0.220). Publicity at the workplace was the main source of information about the vaccine (51.2% of respondents), followed by colleagues (29.9%). Despite the low uptake, 85.3% of respondents believed influenza vaccination was important for disease prevention. The most common reason given for vaccination was protection against influenza infection (73.6%). The most common reason for not having the vaccine was time constraints (56.2%). An evidenced-based strategy needs to be developed to improve vaccine uptake or having mandatory vaccination.

Hepatitis C virus genotyping methods: evaluation of AmpliSens(®) HCV-1/2/3-FRT compared to sequencing method

BACKGROUND

Hepatitis C virus (HCV) genotyping is important for treatment and epidemiological purposes. The objective of this study was to evaluate the performance of AmpliSens(®) HCV-1/2/3-FRT kit in comparison to sequencing method for genotyping.

METHODS

A total of 17 samples collected from December 2009 to January 2011 were analyzed. Reverse transcriptase polymerase chain reaction (PCR) was performed, followed by sequencing technique. Results were analyzed based on sequence information in GenBank. A second genotyping method (AmpliSens(®) HCV-1/2/3-FRT) was done, which differentiates HCV genotypes by means of real-time hybridization-fluorescence detection.

RESULTS

From 17 samples, four were untypeable by AmpliSens(®) HCV-1/2/3-FRT. Eleven of 13 (84.6%) results showed concordant genotypes. A specimen that was determined as genotype 3a by sequencing was genotype 1 by the AmpliSens(®) HCV-1/2/3-FRT. Another specimen that was genotype 1 by sequencing was identified as genotype 3 by AmpliSens(®) HCV-1/2/3-FRT.

CONCLUSION

HCV genotyping with AmpliSens(®) HCV-1/2/3-FRT using real-time PCR method provides a much simpler and more feasible workflow with shorter time compared to sequencing method. There was good concordance compared to sequencing method. However, more evaluation studies would be required to show statistical significance, and to troubleshoot discordant results. AmpliSens(®) HCV-1/2/3-FRT does differentiate between genotype but not until subtype level.

Community-acquired methicillin-resistant Staphylococcus aureus in a Malaysian tertiary centre

Abstract. Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is a pathogen recognized to be distinct in both phenotype and genotype from hospital-acquired MRSA. We have identified CA-MRSA cases in Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia, including their antibiotic susceptibility patterns and genotypic characteristics. Cases were identified during January to December 2009 from routine clinical specimens, where culture and antibiotic susceptibility results yielded pauci-resistant MRSA isolates suspected as being CA-MRSA. The patients' clinical data were collected and their specimens were sent for molecular confirmation and analysis. Five cases of CA-MRSA were identified, which had a multi-sensitive pattern on antibiotic susceptibility tests and were resistant to only penicillin and oxacillin. All cases were skin and soft-tissue infections, including diabetic foot with gangrene, infected scalp hematoma, philtrum abscess in a healthcare worker, thrombophlebitis complicated with abscess and infected bedsore. All five cases were confirmed MRSA by detection of mecA. SCCmec typing (ccr and mec complex) revealed SCCmec type IV for all cases except the infected bedsore case. Panton-Valentine leukocidin gene was positive in all isolates. As clinical features among methicillin-sensitive Staphylococcus aureus, CA-MRSA and "nosocomial CA-MRSA" are indistinct, early recognition is necessary in order to initiate appropriate antibiotics and infection control measures. Continual surveillance of pauci-resistant MRSA and molecular analysis are necessary in order to identify emerging strains as well as their epidemiology and transmission, both in the community and in healthcare setting.