The latest research progress of novel coronavirus "Omicron sub-variant BA.5"

Since the outbreak of COVID-19, severe acute respiratory syndrome coronavirus 2 genome is still mutating, forming a variety of variants with strong transmission capacity, causing the spread of the epidemic worldwide, posing a serious threat to people's physical and mental health, and posing a major challenge to global public health. Omicron remains the main variant in several outbreaks worldwide, accounting for about 99% of the global genetic sequence. Recently, the World Health Organization announced that the subvariant of Omicron BA.5 has been found in more than 100 countries and regions around the world, causing the global epidemic rebound. However, there are few studies on the subvariant BA.5. This article reviews the latest research progress in epidemiology, infectivity, pathogenicity, vaccine and monoclonal antibody protection against Omicron subvariant BA.5, in order to provide reference for scientific prevention and control of Omicron subvariant BA.5.

Isolation, identification, and S1 gene sequencing of two strains of Avian Infectious bronchitis virus

Objective: Epidemiology and genetic variations of the infectious bronchitis virus(IBV) in Fujian province were studied. Method: Two strains of virus isolated from the diseased chickens in Fujian in 2021 were identified by chicken embryo pathogenicity test, electron microscope observation, and RT-PCR. S1 genes of the isolates were cloned, sequenced, and analyzed using biological software. Result: The two IBV strains were code named FJ-NP01 and FJ-FZ01. The full length of S1 of FJ-NP01 was 1 629 nt encoding 543 amino acids, and that of FJ-FZ01, 1 620 nt encoding 540 amino acids. The S1 gene cleavage site of FJ-FZ01 was HRRRR, same as all reference strains of genotype I branch;while that of FJ-NP01 HRRKR differed from the reported site of IBV isolated from genotype IV but same as that of TC07-2 reference strain of genotype VI. The homology of nucleotide and amino acid between the two isolates was 83.2% and 79.6%, respectively, but merely 75.7%-76.3%and 77.1%-83.5% with the Mass-type conventional vaccines H120 and H52, respectively. Further analysis showed that FJ-NP01was from a recombination event between CK CH GD LZ12-4 and L-1148, the homology of nucleotide acid between 1438-1506 nt of FJ-NP01 with CK CH GD LZ12-4 was 97%, and 95.9% between the other nucleotide acid of S1 gene with L-1148. Conclusion: It appeared that the IBV epidemic experienced in the province was complex in nature and that the existing Mass vaccines would not provide sufficient immune protection to deter the spread.

Genetic risk factors associated with SARS-CoV-2 susceptibility in multiethnic populations

Susceptibility to infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes the disease COVID-19, may be understood more clearly by looking at genetic variants and their associations to susceptibility phenotype. I conducted a genome-wide association study of SARS-CoV-2 susceptibility in a multiethnic set of three populations (European, African, and South Asian) from a UK BioBank clinical and genomic dataset. I estimated associations between susceptibility phenotype and genotyped or imputed SNPs, adjusting for age at enrollment, sex, and the ten top principal components of ancestry. Three genome-wide significant loci and their top associated SNPs were discovered in the European ancestry population: SLC6A20 in the chr3p21.31 locus (rs73062389-A;P=2.315 x 10-12), ABO on chromosome 9 (rs9411378-A;P=2.436 x 10-11) and LZTFL1 on chromosome 3 (rs73062394;P=4.4 x 10-11);these SNPs were not found to be significant in the African and South Asian populations. A multiethnic GWAS may help elucidate further insights into SARS-CoV-2 susceptibility.

Genetic pattern of the COVID-19 course and reinfection

A new coronavirus infection (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) broke out at the end of 2019 in Wuhan (China). The disease has become a global pandemic and claimed more than 6 million lives after spreading rapidly around the world. Issues related to the complicated course of COVID-19 mechanisms continue to be the subject of active study. It is known that morbidity and mortality increase dramatically with increasing age and concomitant diseases, including obesity, diabetes, cancer, and cardiovascular diseases. Although most infected people recover, even young and otherwise healthy patients can get sick with this disease. In this regard, an urgent task is to search for specific genetic factors that can explain the predisposition of people to infection and the development of a severe COVID-19 form. Human genetic determinants can provide the scientific basis for disease prediction and the development of personalized therapies to counteract the epidemic. In addition, cases of repeated infection with SARS-CoV-2 are increasingly being registered, which occurs 1-6 months after initial infection on average and depends on the virus genome structure. Studies conducted on sequencing viral genomes have shown that some patients were re-infected with the same strain of coronavirus, while others were different. This, in turn, causes researchers concerns about the effectiveness of immunity after infection and vaccine reliability. The genetic characteristics of a person and a virus commonly determine the tendency for reinfection. It is difficult to determine the true COVID-19 reinfection prevalence, which is explained by the low detectability of asymptomatic reinfection and the fact that many patients with a mild course of the disease were not tested at an early stage of the pandemic. Therefore, the true prevalence of reinfection with COVID-19 does not reflect the current reality. There are many more cases of reinfection than are described in the literature. In this regard, the true contribution of a virus' genetic features to reinfection of COVID-19 can be determined only after population studies, and when developing immunization programs against a COVID-19, it is necessary to take into account the prevalence of reinfection in the population.

Studying mutations of SARS-CoV-2 different variants (alpha, beta, delta, gamma, omicron)

Being pushed by natural selection, random genetic drift, gene editions, and receptor immunity response, viruses develop constantly through mutations affecting different genes and leading to genetic diversity and producing new variants. In order to know well how a mutation could have an impact on the possibility of being infected, on transmission, and on aggressivity of SARS-CoV-2 it would be important to study these mutations. To be able to carry out a comparative study between variants and undergone mutations over many countries in the world, we've dealt with many genomic sequences that have been rapidly accumulated in the GenBank since January 2020, and published by many laboratories over the world. These sequences allowed us to establish phylogenetical trees using a strong bioinformatic tool, just enhanced to study Covid which is MEGA version 11. Distribution of shifted sequences of different variants over the world within phylogenetical trees shows that the overwhelming majority of detected mutations are accumulated in the 5 known variants Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), Gamma (P.1) et Omicron (B.1.1.529), especially within their most variable genes, structural genes of which are N (Nucleocapsid protein) and S (Spike glycoprotein) added to functional ones ORF (Open Reading Frame : ORF1ab, ORF3a);hence, variants holding these mutations are the most dominant and the most infectious this time in the world.

Risk assessment of public health emergencies concerned in the mainland of China, January 2023

Objective: To assess the risk of public health emergencies occurring in the mainland of China or possibly imported from outside China in January 2023. Methods: Based on various data and departmental notification information on domestic and foreign public health emergencies reports and surveillance of key infectious diseases, the expert consultation method was used and experts from provincial (autonomous regions and municipalities directly under the central government) centers for disease prevention and control were invited to participate in the assessment by video conference. Results: The number of public health emergencies reported in January 2023 is expected to increase or be similar to that reported in December 2022. The COVID-19 rebound in the northern hemisphere is likely to continue in January 2023 due to immune escape of BQ, XBB and other possible emerging Omicron variants' subtypes. The increased migration of people in Chinese mainland during the Spring Festival in 2023 could increase the risk of the spread of the SARS-CoV-2 among uninfected people. The level of influenza virus activity is likely to increase in January, and influenza A is likely to dominate. January 2023 remains risky month for nonoccupational carbon monoxide poisoning. Conclusion: Special attention is given to COVID-19, and general attention is given to seasonal influenza and nonoccupational carbon monoxide poisoning.

The response of local governments and public health centers to COVID-19: looking for infectious disease control due to the change of trend and mutations of the virus

Public Health Centers of Japan. of which there are 468 across the country as of April 2022. are at the core of health crisis management. responding to natural disasters and infectious diseases according to the Community Health Act (1994). Under the Infectious Diseases Control La these centers have made repeated efforts to respond to COV1D-19 from the first to the seventh waves while epidemic dynamics changed. variants emerged. and pathogenicity fluctuated. All centers essentially play a common role in infectious disease control (answering questions and consultations. testing, registering cases, coordinating healthcare. transporting confirmed patients, following up with patients and close contacts. carrying out epidemiological investigations. issuing notifications for recommendations on hospital stays and work restrictions. etc.). 'forever, due to the varying number of cases and healthcare resources depending on the region, the actual work was not identical, and local governments. which operate the centers. took different appreoclws. Looking back on the epidemic, the first, second, and third waves saw travel restrictions implemented across the country, and were characterized by a demand for testing that exceeded capacity. At that time. COVID-19 was a threat to the respiratory system, no effective treatment or vaccination was available. and the number of healthcare institutions diagnosing and treating cases was inadequate. The fourth wave saw the Alpha variant ripping through nursing homes putting a significant burden on healthcare. while the fifth wave saw the Delta variant spreading mainly from Tokyo after the Olympics. The sixth and seventh waves came with the highly. Contagious Omicron variant. leading to skyrocketing patient numbers and the public health capacity quickly being overwhelmed. Local governments considered ways to reduce the burden on Public Health Centers, including outsourcing. Over this 2.5 year period, numerous advisories were issued by the Ministry of Health, Labor, and Welfare (MHLW), and the Japanese Association of Public Health Center Directors has advocated actively on behalf of the centers. Given that Japan is a disaster-prone country, Public Health Centers in Japan are expected to play a pivotal role in crisis preparedness, responses to, and recovery from natural disasters and infectious diseases. As a coordination hub to protect lives and maintain health, here we strongly suggest that public health centers implement the lessons learned from COVID-19 to collaborate with healthcare institutions and long-term care facilities, and evolve into a sustainable social framework to advance pandemic preparedness in their respective communities.

COVID-19 and the pathologies of Australia's regulatory state

The COVID-19 pandemic has elicited a wide range of national responses with an even wider range of outcomes in terms of infections and mortalities. Australia is a rare success story, keeping deaths comparatively low, and infections too, until the Omicron wave. What explains Australia's success? Typical explanations emphasise leaders' choices. We agree, but argue that leaders' choices, and whether these are implemented effectively, is shaped by the legacy of state transformation. Decades of neo-liberal reforms have hollowed out state capacity and confused lines of control and accountability, leaving Australia unprepared for the pandemic. Leaders thus abandoned plans and turned to ad hoc, simple to implement emergency measures - border closures and lockdowns. These averted large-scale outbreaks and deaths, but with diminishing returns as the Delta variant took hold. Conversely, Australia's regulatory state has struggled to deliver more sophisticated policy responses, even when leaders were apparently committed, including an effective quarantine system, crucial for border controls, and vaccination programme, essential for exiting the quagmire of lockdowns and closed borders, leading to a partial return to top-down governing. The Australian experience shows that to avoid a public health catastrophe or more damaging lockdowns in the next pandemic, states must re-learn to govern.

Comparison of the clinical characteristics of the first and second waves of COVID-19 in a public hospital in Peru

During the COVID-19 pandemic, doctors faced an unprecedented mass admission of patients with viral atypical pneumonia. The objective of the study was to compare the clinical characteristics of the first and second waves of the pandemic. An analytical observational study was carried out on patients with COVID-19 pneumonia who were admitted to Hospital Carrion de Huancayo, Peru located at more than 3000 meters above sea level. Two study periods were determined, group one represented by the first wave characterized by massive restriction and strict quarantine and the second wave where productive activities had already normalized to a great extent. Of a total of 252 patients with COVID-19, the average age was 56 years in the first wave and 52 years in the second wave, the male sex was more frequent in both 74% and 57%, mortality was 27% and 23%, the time of illness was 8 days and 10 days, respectively. On the other hand, the percentage of use of antibiotics, ivermectin and hydroxychloroquine was higher in the first wave. The use of corticosteroids and prolonged hospital stay was more frequent in the second wave. Comparison of both waves shows differences in age, mortality and time of illness, which may be due to the new molecular variants of SARS-COV-2.

A statistical analysis of COVID-19 pandemic based on the temporal evolution of entropy in different countries

Objective: Currently the Covid-19 pandemic is studied with great expectations by several epidemiological models with the aim of predicting the future behaviour of the pandemic. Determining the level of disorder in the pandemic can give us insight into the societal reactions to the pandemic the socio-economic structures and health systems in different countries.

The genetic characteristics of human coronavirus OC43 in cases of severe acute respiratory infection

Human coronavirus (HCoV) is one of the important pathogens of human respiratory tract infection. in order to clarify the genetic characteristics of HCoV-0C43 in severe acute respiratory infection (SARI) cases at the molecular level, a total of 374 samples obtained from SARI cases in Henan Province, China, in 2019 were screened for the nucleic acids of HCoV -0C43 by real - time polymerase chain reaction (PCR). Reverse transcription-PCR amplification and sequencing of spike (5) RNA-dependent RNA polymerase (12dRp) and nucleocapsid (N) was carried out in samples with positive detection of the nucleic acids of FICoV-0C43. Upon. combination Of 42 representative sequences obtained from the GenBank database, phylogenetic trees were constructed based on three full-length sequences of S, RdRp and N genes. The FICoV -0C43 strains obtained from SARI cases were genotyped and the genetic characteristics of three target genes were analyzed. Variations in the amino acids of S protein (an important antigen of HCoV-0C43) were also analyzed. Results showed that 15 (4.01%) out of 374 samples from SARI cases were positive for FICoV-0C43, and the full-length sequences of S, RdRp and N genes were obtained from 4 out of 15 samples. Based on the phylogenetic trees of these three target genes, three strains belonged to the U genotype and one strain belonged to the H genotype. Analysis of the amino - acid variations of S protein indicated that there were three special sites of amino - acid variation (L272P, P5165 and 5902A) among the G genotype strains in 2019, including the three strains in our study and USA /MN306041/SC0810/2019. Another special variation in amino acids (N484D) was found among the II genotype strains in 2019, including one strain in our study and USA/MN306043/SC0841/2019. Based on the genotype identification and genetic characteristics of HCoV-0C43 strains from SARI cases in Henan Province in 2019, baseline data for the study of molecular epidemiology of HCoV 0C43 in China have been provided.

Prevalent mutations in the Delta variants of SARS CoV2 circulating in India

In this study SARS-CoV-2 genome encoding for spike protein of Delta lineage circulating upto December 2022 in India were downloaded from NCBI and GISAID and aligned against the reference sequence MN908947.3. The mutational profiles of these sequences were estimated using online software available. The most frequent non-synonymous mutational events were D614G, L452R, T478K, P681R, D950N, T19R, G142D, A222V, T95I and V1061V.

Special issue: New coronavirus (2019-nCoV or SARS-CoV-2) and the outbreak of the respiratory illness (COVID-19): part-XIX. (Special issue: New coronavirus (2019-nCoV or SARS-CoV-2) and the outbreak of the respiratory illness (COVID-19): part-XIX.)

This special issue consists of 64 papers on various aspects of COVID-19 research, including outbreaks and spread, evolution of new variants, detection and diagnosis, pathology, disease manifestations, and current treatment interventions (such as antivirals, steroids and vaccines).

SARS-CoV-2 mutation hotspots incidence in different geographic regions

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is RNA virus with a positive-sense single-strand that belongs to the beta-coronavirus group that causes COVID-19 (Coronavirus Disease 2019) which originally emerged in China. Viruses with RNA genomes are known by a high mutation rate potential. The mutation rate determines genome variability and evolution of the virus;therefore, allowing viruses to evade the immune system, gain more infectivity potentials, virulence modifications, and probably resistance development to antivirals. A total of 311 SARS-CoV-2 virus whole genome sequences have been retrieved from the GISAID database from 1st of January 2020 to 31th of August 2020. The sequences were analyzed for sequence purity and multiple sequence alignment together with reference sequence was conducted through using Clustal Omega that is imbedded in Jalview software and Blast tools. We recorded the occurrence of 4 newly incident high frequently occurring mutations in all six geographic regions, namely at positions 2416, 18877, 23401, and 27964. The majority of all recorded hotspots were detected in Asia, Europe, and North America. The findings of our study suggest that the SARS-CoV-2 is in continuous evolution. For the impact of these mutations, further investigations are required and to understand whether these mutations would lead to the appearance of Drug-resistance viral strains, strains with increased infectivity and pathogenicity, and also their effect on the vaccine development and immunogenesis.

Health intervention with vaccine candidates as a temporary strategy to confront COVID-19, Cuba, 2021

Introduction: The Health Surveillance System reported in December 2019 cases with pneumonia in the city of Wuhan, China. The new disease, caused by SARS-CoV-2, was named COVID-19. On March 11, 2020, the first three imported cases were diagnosed in Cuba. The gradual introduction of different viral variants caused several outbreaks. It became necessary to look for alternatives that would allow epidemiological control to be achieved.

Evolving faces of SARS-CoV-2 with the emergence of diverse variants

Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in December 2019, scientists have tracked five variants of concern (VOC) of SARS-CoV-2. The variants such as B.1.1.7 and B.1.617.2 primarily originated independently from the United Kingdom and India, respectively, and subsequently became dominant across the globe. The adaptability of these variants depends on their relative survival fitness to the positive selection pressure acting on them. Antiviral drugs and vaccine usage might act as a selective environment, thus, facilitating the positive selection resulting in the rapid emergence of new variants with higher fitness and survival value. The recently emerged VOC, the omicron variant (B.1.1.529), was first reported from South African samples, and it has a large number of mutations some of which are concerning as per the preliminary evidence. Owing to the dynamism of mutations in the SARS-CoV-2 genome, we may expect many unexpected events as far as the emergence of variants, virulence, and transmissibility is concerned. However, as an evolutionary trade-off strategy, the virulence of SARS-CoV-2 might get reduced with an increase in the transmissibility to attain a wider host range. The intermingling of vaccinated and unvaccinated individuals provides the virus opportunity to amplify by infecting the unvaccinated individuals and causing breakthrough infections. Moreover, the prevalence of different variants of SARS-CoV-2 has been different in different geographic zones as far as the cases and causalities are concerned. Sustained viral surveillance and monitoring with region-wise variant-specific preventive strategies are required to prevent and contain the outbreak of emerging variants of SARS-CoV-2.

A cross-sectional study on omicron - knowledge and practice among COVID recovered adults in Chengalpattu district

Introduction: India is one of the top three countries in the world with more than 10 million confirmed cases. Ever since the emergence of this COVID-19 pandemic, many SARS-CoV-2 mutations have been identified all over the globe and the latest to this addition is the Omicron variant of COVID-19. Only when there is adequate knowledge about the pandemic, we can handle the situation with ease. The main aim of the study is to assess the prevalence of knowledge and awareness about COVID-19 among COVID-19 recovered adults in the rural population of Chengalpattu district and to assess the prevalence of standard practising methods followed by them. Methodology: It is a cross-sectional study. It used a semi-structured questionnaire that had three segments like sociodemographic profile, awareness related to COVID-19 and practice related to COVID-19. Scores were given to knowledge and practice related questions and the cumulative score for the same was taken into consideration.

Influenza-like illness and etiological surveillance in Zhenjiang, Jiangsu, 2013-2020

Objective: To understand the epidemiological and etiological characteristics of influenza-like illness (ILI) in Zhenjiang, Jiangsu province, during 2013-2020, and provide scientific basis for the prevention and control of influenza.

Molecular analysis and genome sequencing of SARS-CoV-2 during second wave 2021 revealed variant diversity in India

SARS-CoV-2 variants rapid emergence has posed critical challenge of higher transmission and immune escape causing serious threats to control the pandemic. The present study was carried out in confirmed cases of SARS-CoV-2 patients to elucidate the prevalence of SARS-CoV-2 variant strain. We performed RT-PCR using extracted RNA from the nasopharyngeal swabs of suspected Covid-19 patients. Confirmed positive cases with CT< 25 were subjected to whole-genome sequencing to track the prevalence of the virus in the Malwa region of Punjab. The presence of B.1, B.1.1.7, B.1.351, B.1.617.1, B.1.617.2, AY.1 and other unidentified variants of SARS-CoV-2 was found in the studied population. Among all the variants, B.1.1.7 (UK variant) and B.1.617.2 (delta-Indian variant) was found to be the most dominant variant in the population and was found majorly in Patiala followed by Ludhiana, SBS Nagar, Mansa and Sangrur. In addition to this, sequencing results also observed that the dominant trait was more prevalent in male population and age group 21-40 years. The B.1.1.7 and B.1.617.2 variant of SARS-CoV-2 is replacing the wild type (Wuhan Strain) and emerging as the dominant variant in Punjab.

Global public health responses: lessons learned from the COVID-19 pandemic between march 2020 and 2021

Between March 2020 to March 2021, SARS-CoV-2 (COVID-19) exposed the readiness and reactivity of global healthcare systems. Analyzing various countries in each continent showed a delayed strict response to the novel respiratory virus had more considerable consequences with COVID-19 related cases, intensive care unit admissions and deaths than nations with strict and swift lockdown procedures. It is a stark reminder for countries to dedicate public health protocols and have unified government responses and supply chains that can quickly adapt to minimize damage to their citizens' social, economic, and physical health and well-being. This is already relevant with the rise of variant strains, particularly with the impact of the rising wave of the COVID-19 and its variants.