Sub-lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology.

During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru, compared with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub-lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub-lineages to emerge. A mutation profile was also obtained for each sub-lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub-lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.

The emergence of human metapneumovirus G gene duplication in hospitalized patients with respiratory tract infection, India, 2016-2018.

BACKGROUND: Human metapneumovirus (HMPV) belongs to the family Pneumoviridae. It is one of the emerging respiratory viruses causing both upper and lower respiratory tract illnesses. HMPV has two genotypes: A and B. These genotypes are classified into lineage A1, A2, B1 and B2. Lineage-A2 is further classified as A2a, A2b and A2c. Similarly, B2 is classified as B2a and B2b. Studies have shown the circulation of A2b, B1 and B2 lineages in India. However, a limited amount of data is available on the current circulating genotypes of HMPV in India. METHODS: Throat swab samples positive for HMPV by real-time RT- PCR, archived at Manipal Institute of Virology as a part of a hospital-based acute febrile illness surveillance study, was used from April 2016 to August 2018 by purposive sampling method. We performed the conventional reverse transcriptase-polymerase chain reaction for twenty samples targeting the G gene and then subjected them to sequencing. Phylogenetic analysis was done using MEGA X software by the Maximum Likelihood method. RESULTS: All the twenty sequences belonged to the A2c subgroup. Phylogenetic analysis showed that strains from the study have genetic relation with circulating strains in Japan, China and Croatia. Seven out of the twenty sequences showed 180-nucleotide duplication and eleven sequences showed 111-nucleotide duplication. Two sequences did not show any duplications. CONCLUSION: In the current study, we report that A2c is the sub-lineage in India from April 2016 to August 2018. This study is the first retrospective study reporting the circulation of the A2c sub-lineage among adults in India with 180- and 111-nucleotide duplications in the G gene of human metapneumovirus.

An update on genetic analysis of porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) in South America: identification of ORF5 sequences of lineage 1A, 1C and 1G.

Data regarding PRRSV-2 in South America are scant and a coordinated criterion for molecular characterization is needed. A phylogenetic analysis was performed using a dataset of 76 ORF5 sequences from South America, and results showed the identification of lineage 5 in the early 2000s and the predominance of lineage 1 at least since 2013. Lineage 1 sequences were further classified into sub-lineages according to a recent molecular characterization study of PRRSV-2 in United States. Our results revealed the recent identification in Uruguay of PRRSV-2 ORF5 sequences of lineage 1 sub-lineage C. Two additional sub-lineages were identified in South America, 1G in Chile and 1A in Peru. Continuous updating the molecular epidemiology of circulating viruses with coordinated investigations among countries is required to control and prevent the emergence of genetic variants of PRRSV-2.

Characterization of antigenic variant infectious bursal disease virus strains identified in South Korea.

Infectious bursal disease (IBD) is one of the most important immunosuppressive diseases of young chickens, causing considerable economic losses to the poultry industry. More than 30 years ago, an antigenic variant (av) pathotype of the IBD virus (IBDV) was reported to originate in, and subsequently spread among, poultry farms in the USA. Recently, a novel avIBDV lineage was identified in China and was shown to exhibit clear differences in its pathogenicity as well as molecular characteristics compared with the previously isolated variant strains. In this study, we conducted a passive surveillance of chicken carcasses submitted to our research division from June-December 2019, and detected the IBDV strains by reverse transcription PCR. Five avIBDV strains were isolated, and their pathogenicity was determined by necropsy and molecular analysis. Additionally, a coinfection field case involving an avIBDV strain and a very virulent IBDV (vvIBDV) strain was identified. Multiple sequence alignment and phylogenetic analysis of partial viral protein 1 (VP1) and hypervariable region (hv) VP2 genes revealed that those strains originated from two different avIBDV lineages. The co-occurrence of two sub-groups of avIBDVs in South Korea confirms for the first time the evolution of antigenic variant IBDV strains, and highlights the urgency for the development of new strategies for IBDV intervention in South Korea.RESEARCH HIGHLIGHTS Five avIBDV strains were identified in South Korea by passive surveillance test in 2019.A coinfection between two IBDV strains from different genogroups was reported in a field case.By phylogenetic analysis, Korean avIBDVs belonged to two distinct lineages of antigenic variant genogroup.

Post-pandemic memory T cell response to SARS-CoV-2 is durable, broadly targeted, and cross-reactive to the hypermutated BA.2.86 variant.

Ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has given rise to recombinant Omicron lineages that dominate globally (XBB.1), as well as the emergence of hypermutated variants (BA.2.86). In this context, durable and cross-reactive T cell immune memory is critical for continued protection against severe COVID-19. We examined T cell responses to SARS-CoV-2 approximately 1.5 years since Omicron first emerged. We describe sustained CD4+ and CD8+ spike-specific T cell memory responses in healthcare workers in South Africa (n = 39) who were vaccinated and experienced at least one SARS-CoV-2 infection. Spike-specific T cells are highly cross-reactive with all Omicron variants tested, including BA.2.86. Abundant nucleocapsid and membrane-specific T cells are detectable in most participants. The bulk of SARS-CoV-2-specific T cell responses have an early-differentiated phenotype, explaining their persistent nature. Overall, hybrid immunity leads to the accumulation of spike and non-spike T cells evident 3.5 years after the start of the pandemic, with preserved recognition of highly mutated SARS-CoV-2 variants.

Corrigendum: SARS-CoV-2 Omicron variants: burden of disease, impact on vaccine effectiveness and need for variant-adapted vaccines.

[This corrects the article DOI: 10.3389/fimmu.2023.1130539.].

SARS-CoV-2 Omicron variants: burden of disease, impact on vaccine effectiveness and need for variant-adapted vaccines.

The highly transmissible Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in late 2021. Initial Omicron waves were primarily made up of sub-lineages BA.1 and/or BA.2, BA.4, and BA.5 subsequently became dominant in mid-2022, and several descendants of these sub-lineages have since emerged. Omicron infections have generally caused less severe disease on average than those caused by earlier variants of concern in healthy adult populations, at least, in part, due to increased population immunity. Nevertheless, healthcare systems in many countries, particularly those with low population immunity, have been overwhelmed by unprecedented surges in disease prevalence during Omicron waves. Pediatric admissions were also higher during Omicron waves compared with waves of previous variants of concern. All Omicron sub-lineages exhibit partial escape from wild-type (Wuhan-Hu 1) spike-based vaccine-elicited neutralizing antibodies, with sub-lineages with more enhanced immuno-evasive properties emerging over time. Evaluating vaccine effectiveness (VE) against Omicron sub-lineages has become challenging against a complex background of varying vaccine coverage, vaccine platforms, prior infection rates, and hybrid immunity. Original messenger RNA vaccine booster doses substantially improved VE against BA.1 or BA.2 symptomatic disease. However, protection against symptomatic disease waned, with reductions detected from 2 months after booster administration. While original vaccine-elicited CD8+ and CD4+ T-cell responses cross-recognize Omicron sub-lineages, thereby retaining protection against severe outcomes, variant-adapted vaccines are required to expand the breadth of B-cell responses and improve durability of protection. Variant-adapted vaccines were rolled out in late 2022 to increase overall protection against symptomatic and severe infections caused by Omicron sub-lineages and antigenically aligned variants with enhanced immune escape mechanisms.

Prediction models for neutralization activity against emerging SARS-CoV-2 variants: A cross-sectional study.

Objective: Despite extensive vaccination campaigns to combat the coronavirus disease (COVID-19) pandemic, variants of concern, particularly the Omicron variant (B.1.1.529 or BA.1), may escape the antibodies elicited by vaccination against SARS-CoV-2. Therefore, this study aimed to evaluate 50% neutralizing activity (NT50) against SARS-CoV-2 D614G, Delta, Omicron BA.1, and Omicron BA.2 and to develop prediction models to predict the risk of infection in a general population in Japan. Methods: We used a random 10% of samples from 1,277 participants in a population-based cross-sectional survey conducted in January and February 2022 in Yokohama City, the most populous municipality in Japan. We measured NT50 against D614G as a reference and three variants (Delta, Omicron BA.1, and BA.2) and immunoglobulin G against SARS-CoV-2 spike protein (SP-IgG). Results: Among 123 participants aged 20-74, 93% had received two doses of SARS-CoV-2 vaccine. The geometric means (95% confidence intervals) of NT50 were 65.5 (51.8-82.8) for D614G, 34.3 (27.1-43.4) for Delta, 14.9 (12.2-18.0) for Omicron BA.1, and 12.9 (11.3-14.7) for Omicron BA.2. The prediction model with SP-IgG titers for Omicron BA.1 performed better than the model for Omicron BA.2 (bias-corrected R 2 with bootstrapping: 0.721 vs. 0.588). The models also performed better for BA.1 than for BA.2 (R 2 = 0.850 vs. 0.150) in a validation study with 20 independent samples. Conclusion: In a general Japanese population with 93% of the population vaccinated with two doses of SARS-CoV-2 vaccine, neutralizing activity against Omicron BA.1 and BA.2 were substantially lower than those against D614G or the Delta variant. The prediction models for Omicron BA.1 and BA.2 showed moderate predictive ability and the model for BA.1 performed well in validation data.

Genetic diversity of Mycobacterium tuberculosis isolates from the central, eastern and southeastern Ethiopia.

Introduction: The population structure of Mycobacterium tuberculosis complex (MTBC) in Ethiopia is diverse but dominated by Euro-American (Lineage 4) and East-African-Indian (Lineage 3) lineages. The objective of this study was to describe the genetic diversity of MTBC isolates in Central, Eastern and Southeastern Ethiopia. Methods: A total of 223 MTBC culture isolates obtained from patients referred to Adama and Harar TB reference laboratories were spoligotyped. Demographic and clinical characteristics were collected. Results: Six major lineages: Euro-American (Lineage 4), East-African-Indian (Lineage 3), East Asian (Lineage 2), Indo-Oceanic (Lineage 1), Mycobacterium africanum (Lineage 5 and Lineage 6) and Ethiopian (Lineage 7) were identified. The majority (94.6 %) of the isolates were Euro-American and East-African-Indian, with proportions of 75.3 % and 19.3 %, respectively. Overall, 77 different spoligotype patterns were identified of which 42 were registered in the SITVIT2 database. Of these, 27 spoligotypes were unique, while 15 were clustered with 2-49 isolates. SIT149/T3_ETH (n = 49), SIT53/T1 (n = 33), SIT21/CAS1_Kili (n = 24) and SIT41/Turkey (n = 11) were the dominant spoligotypes. A rare Beijing spoligotype pattern, SIT541, has also been identified in Eastern Ethiopia. The overall clustering rate of sub-lineages with known SIT was 71.3 %. Age group (25-34) was significantly associated with clustering. Conclusion: We found a heterogeneous population structure of MTBC dominated by T and CAS families, and the Euro-American lineage. The identification of the Beijing strain, particularly the rare SIT541 spoligotype in Eastern Ethiopia, warrants a heightened surveillance plan, as little is known about this genotype. A large-scale investigation utilizing a tool with superior discriminatory power, such as whole genome sequencing, is necessary to gain a thorough understanding of the genetic diversity of MTBC in the nation, which would help direct the overall control efforts.

Sub-lineages of Taenia solium Asian Genotype Recorded in North India.

PURPOSE: Porcine cysticercosis is a neglected zoonotic disease of significant veterinary and medical importance owing to its economic impact and public health significance. The present study aimed at genetic characterization of Taenia solium metacestodes in slaughtered pigs of Haryana (North India). METHODS: A total of 213 (160 and 53 from Chandigarh and Hisar, respectively) slaughtered pigs intended for human consumption were screened for the presence of T. solium metacestodes. The retrieved metacestodes were confirmed molecularly based on the partial amplification of mitochondrial cytochrome c oxidase subunit 1 (CO1) gene. Evolutionary divergence, haplotype and nucleotide diversities and neutrality indices of the retrieved isolates were also assessed. RESULTS: Out of the 213 pigs, 2 (0.94%) revealed the presence of metacestodes involving 1 pig each from Chandigarh (0.62%) and Hisar (1.9%). The sequences obtained after custom sequencing were submitted to GenBank under the accession numbers LC661682-83. The present study haplotype clustered with haplotypes of Asian origin and showed variation from other haplotypes by 1-23 mutational steps. However, the present study isolates also showed nucleotide polymorphisms (A198T, A199G, A201T, G204A, T206A, C210T, T212G, T213A, T216G/A, T217C, T221C, C524T, G994A) at different positions, which indicated the presence of sub-lineages. Low nucleotide diversity (π = 0.020) and negative value of Tajima's D (- 1.304) observed for the haplotypes under consideration was indicative of purifying selection and recent population expansion. CONCLUSIONS: Our study confirms the circulation of T. solium Asian genotype (with distinct sub-lineages) in study area and recommends strict control measures to contain the zoonotic disease.

Strategies to tackle SARS-CoV-2 Mu, a newly classified variant of interest likely to resist currently available COVID-19 vaccines.

Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have recently been reported in many countries. These have exacerbated the coronavirus disease 2019 (COVID-19)-induced global health threats and hindered COVID-19 vaccine development and therapeutic progress. This commentary discusses the potential risk of the newly classified Mu variant of interest, seeming a highly vaccine-resistant variant, and the approaches that can be adopted to tackle this variant based on the available evidence. The SARS-CoV-2 B.1.621 (Mu variant) lineage has shown approximately ten times higher resistance to neutralizing sera obtained from COVID-19 survivors or BNT161b2-vaccinated people than the parenteral B.1 lineage. Several urgent and long-term strategic plans, including quick genomic surveillance for uncovering the genetic characteristics of the variants, equitable global mass vaccination, booster dose administration if required, and strict implementation of public health measures or non-pharmaceutical interventions, must be undertaken concertedly to restrict further infections, mutations, or recombination of the SARS-CoV-2 virus and its deadly strains.

Molecular epidemiology and multidrug resistance of Mycobacterium tuberculosis complex from pulmonary tuberculosis patients in the Eastern region of Ghana.

BACKGROUND: Tuberculosis (TB) and drug-resistant TB (DR-TB) continue to persist as a serious public health challenges in Ghana. Although several research has evaluated the drug resistance of Mycobacterium tuberculosis complex (MTBc) strains across the country, there is a paucity of data on its magnitude as well as the various lineages circulating in the Eastern region of Ghana. OBJECTIVE: This study therefore evaluated the distribution of the various lineages of MTBc in the Eastern region of the country and the associated drug resistance. MATERIALS AND METHODS: One hundred and forty-three (143) patients with pulmonary TB attending the Eastern Regional Hospital, Koforidua/Ghana were included in the study. The BACTEC MGIT 960 tube media was used for both sputum culture and drug susceptibility of streptomycin (STR), isoniazid (INH), rifampicin (RIF) and Ethambutol (ETH). Isolates were initially typed using IS6110, followed by large sequence polymorphisms analysis and spoligotyping. RESULTS: The majority [108 (75.5%)] of the 143 patients were male gender and the 45-54 years [46 (32.2%)] age range had the highest frequency. Forty-one (28.7%) of the 143 isolates were IS6110 negative. Of the 102 spoligotyped isolates, the main sub-lineages included 45 (44.1%) Cameroon and 23 (22.5%) Ghana. SITs 61 and 53 represented the major cluster with 22/102 (21.6%) and 13/102 (12.7%) isolates respectively, while 59/65 (90.8%) isolates belonged to Lineage 4 with 27/65 (41.5%) LAM10_CAM. MDR-TB occurred in 26/79 (32.9%) isolates, and was not associated with neither gender [20/58 (34.5%) male vs 6/21 (28.6%) female, OR = 1.31; 95%CI, 0.44-3.92; p = 0.624)] nor age. No association was found between MDR-TB and the major sub-lineages [8/25 (32%) Cameroon (OR = 0.94; 95%CI, 0.34-2.59; p = 0.920) and 5/11 (45.5%) Ghana (OR = 1.87; 95%CI, 0.51-6.80; p = 0.489)], or previously treated [8/23 (34.8%), OR = 0.89; 95%CI, 0.32-2.48; p = 0.823)] patients. CONCLUSION: Despite the serious threat posed by MDR in the study area, no sub-lineage was shown to be associated with drug resistance. Nonetheless, a sustained surveillance of drug resistance pattern is advocated. A lower proportion of M. africanum was observed in the Eastern region of Ghana and will require further evaluation.

Chikungunya Manifestations and Viremia in Patients WhoPresented to the Fever Clinic at Bangkok Hospital for Tropical Diseases during the 2019 Outbreak in Thailand.

Chikungunya virus is an Alphavirus belonging to the family Togaviridae that is transmitted to humans by an infected Aedes mosquito. Patients develop fever, inflammatory arthritis, and rash during the acute stage of infection. Although the illness is self-limiting, atypical and severe cases are not uncommon, and 60% may develop chronic symptoms that persist for months or even for longer durations. Having a distinct periodical epidemiologic outbreak pattern, chikungunya virus reappeared in Thailand in December 2018. Here, we describe a cohort of acute chikungunya patients who had presented to the Bangkok Hospital for Tropical Diseases during October 2019. Infection was detected by a novel antigen kit and subsequently confirmed by real-time RT-PCR using serum collected at presentation to the Fever Clinic. Other possible acute febrile illnesses such as influenza, dengue, and malaria were excluded. We explored the sequence of clinical manifestations at presentation during the acute phase and associated the viral load with the clinical findings. Most of the patients were healthy individuals in their forties. Fever and arthralgia were the predominant clinical manifestations found in this patient cohort, with a small proportion of patients with systemic symptoms. Higher viral loads were associated with arthralgia, and arthralgia with the involvement of the large joints was more common in female patients.

Neutralization antibody response to booster/priming immunization with new equine influenza vaccine in Japan.

Equine influenza (EI) vaccine has been widely used. However, the causative EI virus (H3N8) undergoes continuous antigenic drift, and the vaccine strains must be periodically reviewed and if necessary, updated to maintain vaccine efficacy against circulating viruses. In 2016, the Japanese vaccine was updated by replacing the old viruses with the Florida sub-lineage Clade (Fc) 2 virus, A/equine/Yokohama/aq13/2010 (Y10). We investigated the virus neutralization (VN) antibody response to Fc2 viruses currently circulating in Europe, after booster or primary immunization with the new vaccine. These European viruses have the amino acid substitution A144V or I179V of the hemagglutinin. In horses that had previously received a primary course and bi-annual boosters with the old vaccine booster, immunization with the updated vaccine increased the VN antibody levels against the European Fc2 viruses as well as Y10. There were no significant differences in the VN titers against Y10 and the Fc2 viruses with A144V or I179V substitution in horses that had received a primary course of the updated vaccine. However, a mixed primary course where the first dose was the old vaccine and the second dose was the updated vaccine, reduced VN titers against the European viruses compared to that against Y10. In summary, the new vaccine affords horses protective level of VN titers against the Fc2 viruses carrying A144V or I179V substitution, but our results suggest that the combination of the old and new vaccines for primary immunization would not be optimum.