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Properties of Coronavirus and SARS-CoV-2

Malik YA

Malays J Pathol, 2020 Apr;42(1):3-11.
PMID: 32342926

were identified beginning with the discovery of SARS-CoV in 2002. With the recent detection of SARS-CoV-2, there are now seven human coronaviruses. Those that cause mild diseases are the 229E, OC43, NL63 and HKU1, and the pathogenic species are SARS-CoV, MERS-CoV and SARS-CoV-2 Coronaviruses (order Nidovirales, family Coronaviridae, and subfamily Orthocoronavirinae) are spherical (125nm diameter), and enveloped with club-shaped spikes on the surface giving the appearance of a solar corona. Within the helically symmetrical nucleocapsid is the large positive sense, single stranded RNA. Of the four coronavirus genera (α,β,γ,δ), human coronaviruses (HCoVs) are classified under α-CoV (HCoV-229E and NL63) and β-CoV (MERS-CoV, SARS-CoV, HCoVOC43 and HCoV-HKU1). SARS-CoV-2 is a β-CoV and shows fairly close relatedness with two bat-derived CoV-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21. Even so, its genome is similar to that of the typical CoVs. SARS-CoV and MERS-CoV originated in bats, and it appears to be so for SARS-CoV-2 as well. The possibility of an intermediate host facilitating the emergence of the virus in humans has already been shown with civet cats acting as intermediate hosts for SARS-CoVs, and dromedary camels for MERS-CoV. Human-to-human transmission is primarily achieved through close contact of respiratory droplets, direct contact with the infected individuals, or by contact with contaminated objects and surfaces. The coronaviral genome contains four major structural proteins: the spike (S), membrane (M), envelope (E) and the nucleocapsid (N) protein, all of which are encoded within the 3' end of the genome. The S protein mediates attachment of the virus to the host cell surface receptors resulting in fusion and subsequent viral entry. The M protein is the most abundant protein and defines the shape of the viral envelope. The E protein is the smallest of the major structural proteins and participates in viral assembly and budding. The N protein is the only one that binds to the RNA genome and is also involved in viral assembly and budding. Replication of coronaviruses begin with attachment and entry. Attachment of the virus to the host cell is initiated by interactions between the S protein and its specific receptor. Following receptor binding, the virus enters host cell cytosol via cleavage of S protein by a protease enzyme, followed by fusion of the viral and cellular membranes. The next step is the translation of the replicase gene from the virion genomic RNA and then translation and assembly of the viral replicase complexes. Following replication and subgenomic RNA synthesis, encapsidation occurs resulting in the formation of the mature virus. Following assembly, virions are transported to the cell surface in vesicles and released by exocytosis.
Covid-19 variants: Impact on transmissibility and virulence

Malik YA

Malays J Pathol, 2022 Dec;44(3):387-396.
PMID: 36591708

The genetic evolution of SARS-CoV-2 began in February 2020, with G614 spike protein strains superseding D614 strains globally. Since then with each subsequent mutations, the SARS-CoV-2 variants of concern, namely Alpha, Beta, Gamma, Delta and Omicron, superseded the previous one to become the dominant strain during the pandemic. By the end of November 2022, the Omicron variant and its descendent lineages account for 99.9% of sequences reported globally. All five VOCs have mutations located in the RBD of the spike protein, resulting in increased affinity of the spike protein to the ACE2 receptors resulting in enhanced viral attachment and its subsequent entry into the host cells. In vitro studies showed the mutations in spike protein help increase the viral fitness, enhancing both transmissibility and replication. In general, Alpha, Beta, Gamma, and Delta variants, were reported with higher transmissibility of 43-90%, around 50%, 170-240%, or 130-170% than their co-circulating VOCs, respectively. The Omicron however was found to be 2.38 times and 3.20 times more transmissible than Delta among the fully-vaccinated and boostervaccinated households. Even the SARS-Cov-2 Omicron subvariants appear to be inherently more transmissible than the ones before. With the broader distribution, enhanced evasion, and improved transmissibility, SARS-CoV-2 variants infection cause severe diseases due to immune escape from host immunity and faster replication. Reports have shown that each subsequent VOC, except Omicron, cause increased disease severity compared with those infected with other circulating variants. The Omicron variant infection however, appears to be largely associated with a lower risk of hospitalisation, ICU admission, mechanical ventilation, and even a shorter length of hospital stay. It has been shown that the relatively much slower replication of the Omicron variants in the lung, resulted in a less severe disease.
Fulltext Antibody and immune memory persistence post infant hepatitis B vaccination

Hudu SA, Malik YA, Niazlin MT, Harmal NS, Adnan A, Alshrari AS, et al.

Patient Prefer Adherence, 2013;7:981-6.
PMID: 24101865 DOI: 10.2147/PPA.S49776

This study aimed to evaluate the level of hepatitis B immunity among undergraduate students 23 years after commencement of the nationwide hepatitis B childhood immunization program in Malaysia.
Fulltext Naturally occurring hepatitis B virus surface antigen mutant variants in Malaysian blood donors and vaccinees

Hudu SA, Harmal NS, Saeed MI, Alshrari AS, Malik YA, Niazlin MT, et al.

Eur J Clin Microbiol Infect Dis, 2015 Jul;34(7):1349-59.
PMID: 25792010 DOI: 10.1007/s10096-015-2358-1

Hepatitis B virus surface mutants are of enormous importance because they are capable of escaping detection by serology and can infect both vaccinated and unvaccinated populations, thus putting the whole population at risk. This study aimed to detect and characterise hepatitis B-escaped mutants among blood donors and vaccinees. One thousand serum samples were collected for this study from blood donors and vaccinees. Hepatitis B surface antigen, antibodies and core antibodies were tested using a commercial enzyme-linked immunosorbent assay (ELISA) kit. DNA detection was performed via nested polymerase chain reaction (PCR), and the S gene was sequenced and analysed using bioinformatics. Of the 1,000 samples that were screened, 5.5% (55/1,000) were found to be HBsAg-negative and anti-HBc- and HBV DNA-positive. All 55 isolates were found to belong to genotype B. Several mutations were found across all the sequences from synonymous and non-synonymous mutations, with the most nucleotide mutations occurring at position 342, where adenine was replaced by guanine, and cytosine at position 46 was replaced by adenine in 96.4% and 98% of the isolates, respectively. Mutation at position 16 of the amino acid sequence was found to be common to all the Malaysian isolates, with 85.7% of the mutations occurring outside the major hydrophilic region. This study revealed a prevalence of 5.5% for hepatitis B-escaped mutations among blood donors and vaccinated undergraduates, with the most common mutation being found at position 16, where glutamine was substituted with lysine.
Performance of ULV formulations (Pesguard 102/Vectobac 12AS) against three mosquito species

Yap HH, Chong AS, Adanan CR, Chong NL, Rohaizat B, Malik YA, et al.

J Am Mosq Control Assoc, 1997 Dec;13(4):384-8.
PMID: 9474567

Adulticidal and larvicidal performances of a water-based pyrethroid microemulsion Pesguard PS 102 (AI d-allethrin and d-phenothrin, both at 5.0% w/w) and Vectobac 12AS, an aqua-suspension Bacillus thuringiensis israelensis (B.t.i.) formulation (AI 1,200 ITU/mg) were assessed against mosquitoes Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus using a Leco ULV Fog Generator Model 1600 and a Scorpion 20 ULV AirBlast Sprayer. Laboratory-cultured mosquito adults and larvae were used for efficacy assessment. For trials using Leco, both pyrethroid and bacterial formulations were dispersed both singly and in combination with Pesguard PS 102 at a dosage of 0.2 liters/ha and B.t.i. at a dosage of 1.0 liter/ha. Similar trials with the Scorpion were also conducted with Pesguard PS 102 at a dosage of 0.2 liters/ha and a higher dosage of B.t.i. (1.5 liters/ha). Experiments were conducted in a football field (200 x 100 m) where five check points at 10, 25, 50, 75, and 100 m downwind from the spray nozzle were chosen for efficacy assessments. Knockdown and mortality were scored at 1 and 24 h postspraying. Results from both trials showed that mortality values varied with distance from spray nozzle. For trials with Leco, fogging with the combination of Pesguard PS 102 and B.t.i. provided larvicidal mortality of > 80% for both Aedes species and of > 60% for Cx. quinquefasciatus larvae at several check points, depending on wind conditions. Complete mortality of adult Aedes mosquitoes at 24 h posttreatment was also achieved, while mortality values for Culex adults reached > 90% under strong wind conditions. As for trials with the Scorpion 20, high adult and larval mortalities were also achieved, with > 90% mortality at some check points. The above study demonstrated the possibility of achieving both larvicidal and adulticidal effects when using a combination of B.t.i. and Pesguard PS 102 in ULV space spray.
An Overview of Hepatitis B Virus Surface Antigen Mutant in the Asia Pacific

Hudu SA, Malik YA, Niazlin MT, Harmal NS, Sekawi Z

Curr Issues Mol Biol, 2014;16:69-78.
PMID: 24014801

Hepatitis B virus infection is a serious health problem worldwide, and more than 350 million people are chronic carriers, constituting a major global threat. Southeast Asia and the Western Pacific have the highest levels of endemicity in the world, with an estimated seroprevalence ranging between 2% and 31%. Mutations in the hepatitis B surface antigen (HBsAg) have been reported in many parts of the world but are most common in Asian infants; such mutants have several clinical effects, such as the development of hepatocellular carcinoma. Diagnostic failures by commercial assays have reduced the diagnostic effectiveness of HBsAg detection. For example the substitution of an amino acid in the major hydrophilic region of the S gene reduces the binding of hepatitis B surface antibodies leading to immune escape. The safety of blood transfusion may be compromised by current screening tests due to escape from being neutralised by antibodies induced by HBsAg mutants, and undetectable levels of viral surface protein. Data on the epidemiology of HBsAg mutation in Asia Pacific are scant; however, this manuscript has reviewed the available information on the epidemiology of HBsAg mutation in Asia Pacific.
Field efficacy of a new repellent, KBR 3023, against Aedes albopictus (SKUSE) and Culex quinquefasciatus (SAY) in a tropical environment

Yap HH, Jahangir K, Chong AS, Adanan CR, Chong NL, Malik YA, et al.

J Vector Ecol, 1998 Jun;23(1):62-8.
PMID: 9673931

Two new repellent formulations, KBR 3023 10% and 20% from Bayer AG, Germany, were evaluated together with DEET 10% and 20% as standard repellent formulations. Evaluation was based on two separate field studies: a daytime study (0900-1700 hr) in a forested orchard on Penang Island and a nighttime study (2100-0100 hr) in a squatter residential area on the adjacent mainland of peninsular Malaysia. Both studies were carried out by exposing humans with bare arms and legs to mosquitoes landing/biting for an eight hour period. Right arms and legs of the human baits were treated with different repellent formulations (KBR 3023 10%, 20% and DEET 10%, 20%) and the left limbs were left untreated to act as controls. The daytime study indicated that all four formulations were equally effective (P < 0.05) as repellents against the predominant Aedes albopictus with greater than 88.5% reduction in landing/biting in the first four hours and not less than 65.0% in the next four hours of the assessment period. In the night study, all four formulations were also found to be equally effective (P < 0.05) in repelling Culex quinquefasciatus, the predominant species. All four formulations provided complete protection against Cx. quinquefasciatus in the first two hours of exposure. The percentage reduction values were maintained above 90.0% for the next six hours of the assessment period. In conclusion, both the KBR 3023 and DEET formulations were found to be equally effective (P < 0.05) in providing a long-lasting reduction in human-mosquito contact in both the day and night field studies.
Fulltext Isolated hepatitis B core antibody positive among vaccinated cohort in Malaysia

Hudu SA, Malik YA, Niazlin MT, Harmal NS, Alshrari AS, Sekawi Z

Ann Saudi Med, 2013;33(6):591-4.
PMID: 24413864 DOI: 10.5144/0256-4947.2013.591

BACKGROUND AND OBJECTIVES: Hepatitis B core antibodies (anti-HBc) are detected in almost every patient with previous exposure to hepatitis B virus (HBV). However, with this marker alone, one cannot understand the activity of the disease; therefore, this study aimed to identify the implication of isolated hepatitis B core antibody and evaluate the effect of hepatitis B vaccine booster in isolated anti-HBc among adults who received the HBV vaccine as infants.
DESIGN AND SETTINGS: A prospective cohort study of vaccinated undergraduate students of University Putra Malaysia.
PATIENTS AND METHODS: A total of 408 undergraduate students who received infant hepatitis B vaccination volunteered for this study; 5 mL of venous blood was taken from the volunteers. Hepatitis B surface antigen (HBsAg) and core antibodies were tested using a commercially available enzyme-linked immunosorbent assay kit according to the manufacturer's instructions (DRG international Inc., USA). Molecular detection of hepatitis B viral DNA was performed using nested polymerase chain reaction.
RESULTS: The prevalence of isolated anti-HBc among the vaccinated cohort was found to be 5.0%, out of which 80% had a hepatitis B surface antibodies (anti-HBs) titer higher than 10 IU/L, while 20% had less than 10 IU/L anti-HBs titer. All the anti-HBc positivesubjects had detectable hepatitis B viral DNA in their serum. Anamnestic response was found to be 100% among isolated anti-HBc with negative antibody.
CONCLUSION: Isolated anti-HBc developed protective levels of anti-HBs after a single dose of recombinant hepatitis B vaccination. HBV DNA was detected in all isolated anti-HBc indicating occult chronic HBV infection with undetectable HBsAg.
Molecular and serological detection of occult hepatitis B virus among healthy hepatitis B surface antigen-negative blood donors in Malaysia

Hudu SA, Harmal NS, Saeed MI, Alshrari AS, Malik YA, Niazlin MT, et al.

Afr Health Sci, 2016 Sep;16(3):677-683.
PMID: 27917199

BACKGROUND: Occult hepatitis B infections are becoming a major global threat, but the available data on its prevalence in various parts of the world are often divergent.
OBJECTIVE: This study aimed to detect occult hepatitis B virus in hepatitis B surface antigen-negative serum using anti-HBc as a marker of previous infection.
PATIENT AND METHODS: A total of 1000 randomly selected hepatitis B surface antigen-negative sera from blood donors were tested for hepatitis B core antibody and hepatitis B surface antibody using an ELISA and nested polymerase chain reaction was done using primers specific to the surface gene (S-gene).
RESULTS: Of the 1000 samples 55 (5.5%) were found to be reactive, of which 87.3% (48/55) were positive for hepatitis B surface antibody, indicating immunity as a result of previous infection however, that does not exclude active infection with escaped mutant HBV. Nested PCR results showed the presence of hepatitis B viral DNA in all the 55 samples that were positive for core protein, which is in agreement with the hepatitis B surface antibody result.
CONCLUSION: This study reveals the 5.5% prevalence of occult hepatitis B among Malaysian blood donors as well as the reliability of using hepatitis B core antibody in screening for occult hepatitis B infection in low endemic, low socioeconomic settings.
Molecular phylogeny of modern coxsackievirus A16

Perera D, Yusof MA, Podin Y, Ooi MH, Thao NT, Wong KK, et al.

Arch Virol, 2007;152(6):1201-8.
PMID: 17308978

A phylogenetic analysis of VP1 and VP4 nucleotide sequences of 52 recent CVA16 strains demonstrated two distinct CVA16 genogroups, A and B, with the prototype strain being the only member of genogroup A. CVA16 G-10, the prototype strain, showed a nucleotide difference of 27.7-30.2% and 19.9-25.2% in VP1 and VP4, respectively, in relation to other CVA16 strains, which formed two separate lineages in genogroup B with nucleotide variation of less than 13.4% and less than 16.3% in VP1 and VP4, respectively. Lineage 1 strains circulating before 2000 were later displaced by lineage 2 strains.

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