Papers in Virology

Review Microbiology

Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants

Anshumali Mittal, Arun Khattri, Vikash Verma

Summary: This review focuses on the emerging SARS-CoV-2 variants, the structural basis for antibody-mediated neutralization, and the identification of escape mutations for designing escape-resistant antibody therapeutics and vaccines.

PLOS PATHOGENS (2022)

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Review Virology

The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2

Grigorios D. Amoutzias, Marios Nikolaidis, Eleni Tryfonopoulou, Katerina Chlichlia, Panayotis Markoulatos, Stephen G. Oliver

Summary: This review discusses the evolution of the coronavirus subfamily and its importance for human and animal health. The impact of point mutations, insertions/deletions, and recombination events on the evolution of coronaviruses is highlighted. The potential direction for the development of next-generation vaccines and the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic are also discussed.

VIRUSES-BASEL (2022)

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Article Virology

Distinctive Roles of Furin and TMPRSS2 in SARS-CoV-2 Infectivity

Rachid Essalmani, Jaspreet Jain, Delia Susan-Resiga, Ursula Andreo, Alexandra Evagelidis, Rabeb Mouna Derbali, David N. Huynh, Frederic Dallaire, Melanie Laporte, Adrien Delpal, Priscila Sutto-Ortiz, Bruno Coutard, Claudine Mapa, Keith Wilcoxen, Etienne Decroly, Tram Nq Pham, Eric A. Cohen, Nabil G. Seidah

Summary: The spike protein of SARS-CoV-2 plays a crucial role in infecting the lungs and other tissues by binding to the ACE2 receptor. Cleavage of the spike protein at S1/S2 and S2' sites is important for viral entry and fusion. This study identifies the fusion activation site S2' as KPSKR815 down arrow and demonstrates that its cleavage is enhanced by ACE2 engagement. The combination of furin and TMPRSS2 inhibitors shows promise as potent antivirals against SARS-CoV-2.

JOURNAL OF VIROLOGY (2022)

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Review Virology

COVID-19 vaccinations: The unknowns, challenges, and hopes

Kawthar Mohamed, Piotr Rzymski, Md Shahidul Islam, Rangarirai Makuku, Ayesha Mushtaq, Amjad Khan, Mariya Ivanovska, Sara A. Makka, Fareeda Hashem, Leander Marquez, Orsolya Cseprekal, Igor Salerno Filgueiras, Dennyson Leandro M. Fonseca, Essouma Mickael, Irene Ling, Amanuel Godana Arero, Sarah Cuschieri, Kseniia Minakova, Eduardo Rodriguez-Roman, Sunny O. Abarikwu, Attig-Bahar Faten, Giulia Grancini, Otavio Cabral-Marques, Nima Rezaei

Summary: Vaccines have brought hope to the world in controlling the COVID-19 pandemic, despite facing challenges and uncertainties such as longevity, asymptomatic spread, long-term side effects, global access and distribution, compliance with hygiene guidelines, emerging variants, and vaccine resistance. Reports show a significant decrease in the risk of COVID-19-related infection and hospitalizations, indicating the positive impact of vaccination.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Letter Virology

A third booster dose may be necessary to mitigate neutralizing antibody fading after inoculation with two doses of an inactivated SARS-CoV-2 vaccine

Lei Yue, Tianhong Xie, Ting Yang, Jian Zhou, Hongbo Chen, Hailian Zhu, Hua Li, Hong Xiang, Jie Wang, Huijuan Yang, Hong Zhao, Xingchen Wei, Yuhao Zhang, Zhongping Xie

JOURNAL OF MEDICAL VIROLOGY (2022)

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Review Virology

Potency of BNT162b2 and mRNA-1273 vaccine-induced neutralizing antibodies against severe acute respiratory syndrome-CoV-2 variants of concern: A systematic review of in vitro studies

Maryam Noori, Seyed Aria Nejadghaderi, Shahnam Arshi, Kristin Carson-Chahhoud, Khalil Ansarin, Ali-Asghar Kolahi, Saeid Safiri

Summary: This study systematically reviewed 36 recent in vitro studies to evaluate the effectiveness of neutralizing antibodies induced by BNT162b2 and mRNA-1273 vaccines against SARS-CoV-2 variants. The results showed that the B.1.351 variant had the lowest sensitivity to neutralizing antibodies, while the B.1.1.7 variant had the highest sensitivity.

REVIEWS IN MEDICAL VIROLOGY (2022)

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Article Virology

SARS-CoV-2 T Cell Responses Elicited by COVID-19 Vaccines or Infection Are Expected to Remain Robust against Omicron

Syed Faraz Ahmed, Ahmed Abdul Quadeer, Matthew R. McKay

Summary: The study assessed the impact of Omicron mutations on known T cell epitopes and found that T cell responses to this new variant remain robust.

VIRUSES-BASEL (2022)

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Article Virology

The puzzling mutational landscape of the SARS-2-variant Omicron

Jacques Fantini, Nouara Yahi, Philippe Colson, Henri Chahinian, Bernard La Scola, Didier Raoult

Summary: The recently emerging SARS-CoV-2 variant omicron has a unique set of mutations and exhibits decreased affinity for the ACE-2 receptor compared to the delta variant. The omicron variant is predicted to be less pathogenic but may evade neutralizing antibodies generated by current vaccines, suggesting a potential decrease in vaccine effectiveness.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Editorial Material Virology

Monkeypox: A potential global threat?

Zhilong Yang

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Virology

Characteristics of the first 1119 SARS-CoV-2 Omicron variant cases, in Marseille, France, November-December 2021

Linda Houhamdi, Philippe Gautret, Van Thuan Hoang, Pierre-Edouard Fournier, Philippe Colson, Didier Raoult

Summary: Between November 28, 2021, and December 31, 2021, a total of 1119 cases of SARS-CoV-2 Omicron variant were diagnosed at the Institut Hospitalo-Universitaire Mediterranee Infection in Marseille, France. Among the 825 patients with known vaccination status, 46.4% were vaccinated, with 91.9% of them having received at least two doses of the vaccine. Interestingly, 26.3% of the cases developed SARS-CoV-2 infection within 21 days after the last dose of vaccine, suggesting early production of antibodies. There were 21 hospitalized patients, one in intensive care, and one patient who received a vaccine booster dose died.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Review Virology

Quantifying the risk of SARS-CoV-2 reinfection over time

Eamon O. Murchu, Paula Byrne, Paul G. Carty, Cillian De Gascun, Mary Keogan, Michelle O'Neill, Patricia Harrington, Mairin Ryan

Summary: The study found that SARS-CoV-2 reinfection is not common, with a relatively low risk of reinfection, and there is no evidence to suggest an increase in reinfection risk over time. Whole genome sequencing in a subset of patients showed a low population-level risk of reinfection, with no evidence of waning immunity for up to 7 months following primary infection.

REVIEWS IN MEDICAL VIROLOGY (2022)

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Article Microbiology

Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75

Qian Wang, Sho Iketani, Zhiteng Li, Yicheng Guo, Andre Yanchen Yeh, Michael Liu, Jian Yu, Zizhang Sheng, Yaoxing Huang, Lihong Liu, David D. Ho

Summary: The newly emerged SARS-CoV-2 Omicron subvariant BA.2.75 exhibits moderate resistance to neutralization by sera from vaccinated/boosted individuals compared to the currently circulating BA.2, but is more sensitive than BA.4/5. BA.2.75 shows heightened resistance to class 1 and class 3 monoclonal antibodies targeting the spike-receptor-binding domain, while gaining sensitivity to class 2 antibodies. The resistance is mainly conferred by two mutations. BA.2.75 also shows slight resistance to a therapeutic antibody with potent activity against all Omicron subvariants. Additionally, BA.2.75 exhibits higher binding affinity to the host receptor ACE2 compared to other Omicron subvariants.

CELL HOST & MICROBE (2022)

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Article Virology

Twin combination of Omicron and Delta variants triggering a tsunami wave of ever high surges in COVID-19 cases: A challenging global threat with a special focus on the Indian subcontinent

Ranjan K. Mohapatra, Ruchi Tiwari, Ashish K. Sarangi, Sanjay K. Sharma, Rekha Khandia, G. Saikumar, Kuldeep Dhama

Summary: The emergence of the Omicron variant of SARS-CoV-2 has resulted in a massive surge in COVID-19 cases worldwide, surpassing even the Delta variant in infectivity. The simultaneous presence of Omicron and Delta variants is leading to a tsunami-like wave of high COVID-19 cases globally.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Review Biochemical Research Methods

The screening value of RT-LAMP and RT-PCR in the diagnosis of COVID-19: systematic review and meta-analysis

Ruiyang Pu, Sha Liu, Xiaoyu Ren, Dian Shi, Yupei Ba, Yanbei Huo, Wenling Zhang, Lingling Ma, Yanyan Liu, Yan Yang, Ning Cheng

Summary: This systematic review evaluates the test accuracy of RT-LAMP and RT-PCR for diagnosing COVID-19. The overall sensitivity of RT-PCR and RT-LAMP was found to be 0.96 and 0.92, respectively, with false-negative rates of 0.06 and 0.12. Subgroup analysis suggests that mixed sampling and multiple target gene diagnosis methods have better diagnostic value. The study shows that RT-PCR and RT-LAMP have high value in diagnosing COVID-19, but there is still a false-negative rate of about 6%-12%.

JOURNAL OF VIROLOGICAL METHODS (2022)

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Review Virology

COVID-19 vaccines mix-and-match: The concept, the efficacy and the doubts

Ronak Rashedi, Noosha Samieefar, Niloofar Masoumi, Sahar Mohseni, Nima Rezaei

Summary: The search for effective vaccines against SARS-CoV-2 began during the COVID-19 pandemic, with full vaccination considered essential to overcoming the crisis. Challenges have included adverse reactions leading to vaccine discontinuation in some countries, difficulties in vaccine supply in poorer regions, and reduced effectiveness due to new variants. The mix-and-match strategy of using heterologous vaccines may offer a solution by improving immune response and addressing shortages.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Microbiology

Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses

Alexandra Tauzin, Shang Yu Gong, Guillaume Beaudoin-Bussieres, Dani Vezina, Romain Gasser, Lauriane Nault, Lorie Marchitto, Mehdi Benlarbi, Debashree Chatterjee, Manon Nayrac, Annemarie Laumaea, Jeremie Prevost, Marianne Boutin, Geremy Sannier, Alexandre Nicolas, Catherine Bourassa, Gabrielle Gendron-Lepage, Halima Medjahed, Guillaume Goyette, Yuxia Bo, Josee Perreault, Laurie Gokool, Chantal Morrisseau, Pascale Arlotto, Renee Bazin, Mathieu Dube, Gaston De Serres, Nicholas Brousseau, Jonathan Richard, Roberta Rovito, Marceline Cote, Cecile Tremblay, Giulia C. Marchetti, Ralf Duerr, Valerie Martel-Laferriere, Daniel E. Kaufmann, Andres Finzi

Summary: The study found that extending the interval between doses to 16 weeks significantly increased humoral responses in non-infected individuals, reaching similar levels as previously infected individuals. Compared to a shorter interval, a longer interval between vaccine doses resulted in stronger immune responses.

CELL HOST & MICROBE (2022)

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Article Microbiology

Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75

Yunlong Cao, Weiliang Song, Lei Wang, Pan Liu, Can Yue, Fanchong Jian, Yuanling Yu, Ayijiang Yisimayi, Peng Wang, Yao Wang, Qianhui Zhu, Jie Deng, Wangjun Fu, Lingling Yu, Na Zhang, Jing Wang, Tianhe Xiao, Ran An, Lu Liu, Sijie Yang, Xiao Niu, Qingqing Gu, Fei Shao, Xiaohua Hao, Bo Meng, Ravindra Kumar Gupta, Ronghua Jin, Youchun Wang, Xiaoliang Sunney Xie, Xiangxi Wang

Summary: The newly emerged SARS-CoV-2 Omicron subvariant, BA.2.75, has shown a growth advantage over other circulating variants in India. This study reveals that BA.2.75 has a higher affinity for the host receptor ACE2 and exhibits increased low-pH-endosomal cell entry. It also demonstrates reduced evasion of humoral immunity from certain convalescent plasma, while showing a distinct neutralizing antibody escape pattern. These findings suggest that BA.2.75 may become the dominant variant following BA.4/BA.5.

CELL HOST & MICROBE (2022)

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Letter Virology

Detection of SARS-CoV-2 Omicron (B.1.1.529) variant has created panic among the people across the world: What should we do right now?

Md. Rabiul Islam, Md. Jamal Hossain

JOURNAL OF MEDICAL VIROLOGY (2022)

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Review Virology

The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity

Yongbing Zhou, Huilin Zhi, Yong Teng

Summary: As of November 2021, multiple variants of concern (VOCs) of SARS-CoV-2, including Alpha, Beta, Gamma, Delta, and Omicron, have emerged and become dominant strains in many countries. Omicron is categorized into five main lineages (BA.1, BA.2, BA.3, BA.4, BA.5) and several sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) as of August 2022. Compared to previous VOCs, Omicron lineages have the highest number of spike protein mutations, with a total of 50 mutations throughout the genome. Early data suggests that the Omicron BA.2 sublineage is more infectious and exhibits more immune escape than the early wild-type strain, previous VOCs, and BA.1. Recent global surveillance data indicate that BA.4/BA.5 has higher transmissibility than BA.1, BA.1.1, and BA.2, and BA.4/BA.5 is becoming the dominant strain in many countries globally.

JOURNAL OF MEDICAL VIROLOGY (2023)

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Review Virology

Epidemiologic characteristics of cases with reinfection, recurrence, and hospital readmission due to COVID-19: A systematic review and meta-analysis

Sahar Sotoodeh Ghorbani, Niloufar Taherpour, Sahar Bayat, Hadis Ghajari, Parisa Mohseni, Seyed Saeed Hashemi Nazari

Summary: Studies have shown cases of COVID-19 patients testing positive for the virus again after recovery, with higher reinfection rates in males and more frequent recurrence in females. Uncertainty regarding long-term immunity after SARS-Cov-2 infection indicates the possibility of reinfection and recurrence post-recovery. Efforts like mass vaccination and proper disease management can help control the frequent occurrence of the disease.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Virology

Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants

The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2

Distinctive Roles of Furin and TMPRSS2 in SARS-CoV-2 Infectivity

COVID-19 vaccinations: The unknowns, challenges, and hopes

A third booster dose may be necessary to mitigate neutralizing antibody fading after inoculation with two doses of an inactivated SARS-CoV-2 vaccine

Potency of BNT162b2 and mRNA-1273 vaccine-induced neutralizing antibodies against severe acute respiratory syndrome-CoV-2 variants of concern: A systematic review of in vitro studies

SARS-CoV-2 T Cell Responses Elicited by COVID-19 Vaccines or Infection Are Expected to Remain Robust against Omicron

The puzzling mutational landscape of the SARS-2-variant Omicron

Monkeypox: A potential global threat?

Characteristics of the first 1119 SARS-CoV-2 Omicron variant cases, in Marseille, France, November-December 2021

Quantifying the risk of SARS-CoV-2 reinfection over time

Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75

Twin combination of Omicron and Delta variants triggering a tsunami wave of ever high surges in COVID-19 cases: A challenging global threat with a special focus on the Indian subcontinent

The screening value of RT-LAMP and RT-PCR in the diagnosis of COVID-19: systematic review and meta-analysis

COVID-19 vaccines mix-and-match: The concept, the efficacy and the doubts

Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses

Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75

Detection of SARS-CoV-2 Omicron (B.1.1.529) variant has created panic among the people across the world: What should we do right now?

The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity

Epidemiologic characteristics of cases with reinfection, recurrence, and hospital readmission due to COVID-19: A systematic review and meta-analysis

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