Introduction of SARS-COV-2 C.37 (WHO VOI lambda) from Peru to Italy

Evolution of SARS-CoV-2 Variants: Implications on Immune Escape, Vaccination, Therapeutic and Diagnostic Strategies

The COVID-19 pandemic caused by SARS-CoV-2 is associated with a lower fatality rate than its SARS and MERS counterparts. However, the rapid evolution of SARS-CoV-2 has given rise to multiple variants with varying pathogenicity and transmissibility, such as the Delta and Omicron variants. Individuals with advanced age or underlying comorbidities, including hypertension, diabetes and cardiovascular diseases, are at a higher risk of increased disease severity. Hence, this has resulted in an urgent need for the development of better therapeutic and preventive approaches. This review describes the origin and evolution of human coronaviruses, particularly SARS-CoV-2 and its variants as well as sub-variants. Risk factors that contribute to disease severity and the implications of co-infections are also considered. In addition, various antiviral strategies against COVID-19, including novel and repurposed antiviral drugs targeting viral and host proteins, as well as immunotherapeutic strategies, are discussed. We critically evaluate strategies of current and emerging vaccines against SARS-CoV-2 and their efficacy, including immune evasion by new variants and sub-variants. The impact of SARS-CoV-2 evolution on COVID-19 diagnostic testing is also examined. Collectively, global research and public health authorities, along with all sectors of society, need to better prepare against upcoming variants and future coronavirus outbreaks.

Effectiveness of the BBIBP-CorV vaccine in preventing infection and death in health care workers in Peru 2021

BACKGROUND

During 2021, Peru started the vaccination against SARS-CoV-2 using the BBIBP-CorV inactivated virus vaccine for health care workers (HCW). We aim to evaluate the effectiveness of the BBIBP-CorV vaccine to prevent SARS-CoV-2 infection and deaths among HCWs.

METHODS

Retrospective cohort study, from February 9 to June 30, 2021, using national registries of health care workers, laboratory tests for SARS-CoV-2 and deaths. We calculated the vaccine effectiveness for preventing laboratory-confirmed SARS-CoV-2 infection, COVID-19-mortality, and all-cause mortality among partially immunized and fully immunized HCWs. An extension of Cox proportional hazards regression was used to model the mortality results, and Poisson regression was used to model SARS-CoV-2 infection.

RESULTS

The study included 606,772 eligible HCWs, the mean age was 40 (IQR: 33.0, 51.0). In fully immunized HCW, the effectiveness for preventing all-cause mortality was 83.6 (95% CI: 80.2 to 86.4), 88.7 (95% CI: 85.1 to 91.4) for preventing COVID-19 mortality, and 40.3 (95% CI 38.9 to 41.6) for preventing SARS-CoV-2 infection.

CONCLUSION

The BBIBP-CorV vaccine showed high levels of effectiveness for preventing all-cause and COVID-19 deaths among fully immunized HCW. These results were consistent within different subgroups and sensitivity analyses. However, the effectiveness for preventing infection was suboptimal in this particular setting.

Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage C.37 (Lambda) has spread rapidly in Peru and other Latin American countries. However, most studies in Peru have focused on Lima, the capital city, without knowing the dynamics of the spread of the variant in other departments. Cusco, Peru, is one of the most popular departments in the country for tourists, so the introduction of new variants of SARS-CoV-2 might occur despite closure of the borders. Therefore, in this work, we analyzed the variants circulating in Cusco. The aim of this work was to better understand the distribution of SARS-CoV-2 lineages circulating in Cusco and to characterize the genomes of these strains. To this end, 46 SARS-CoV-2 genomes from vaccinated and unvaccinated patients were sequenced in the first half of 2021. The genomes were analyzed using phylogenetic and natural selection methods. Phylogenetic trees from Cusco showed dominance of the Lambda lineage over the variants of concern (VOCs), and there was no clustering of variants by district. Natural selection analysis revealed mutations, mainly in the spike protein, at positions 75, 246, 247, 707, 769, and 1020. In addition, we found that unvaccinated patients accumulated more new mutations than did vaccinated patients, and these included the F101Y mutation in ORF7a, E419A in NSP3, a deletion in S (21,618-22,501), and a deletion in ORF3a (25,437-26,122).

Host genetic diversity and genetic variations of SARS-CoV-2 in COVID-19 pathogenesis and the effectiveness of vaccination

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the outbreak of coronavirus disease 2019 (COVID-19), has shown a vast range of clinical manifestations from asymptomatic to life-threatening symptoms. To figure out the cause of this heterogeneity, studies demonstrated the trace of genetic diversities whether in the hosts or the virus itself. With this regard, this review provides a comprehensive overview of how host genetic such as those related to the entry of the virus, the immune-related genes, gender-related genes, disease-related genes, and also host epigenetic could influence the severity of COVID-19. Besides, the mutations in the genome of SARS-CoV-2 __leading to emerging of new variants__ per se affect the affinity of the virus to the host cells and enhance the immune escape capacity. The current review discusses these variants and also the latest data about vaccination effectiveness facing the most important variants.

Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a highly infectious agent associated with unprecedented morbidity and mortality. A failure to stop growth of COVID-19-linked morbidity rates is caused by SARS-CoV-2 mutations and the emergence of new highly virulent SARS-CoV-2 strains. Several acquired SARS-CoV-2 mutations reflect viral adaptations to host immune defence. Mutations in the virus Spike-protein were associated with the lowered effectiveness of current preventive therapies, including vaccines. Recent in vitro studies detected diminished neutralisation capacity of vaccine-induced antibodies, which are targeted to bind Spike receptor-binding and N-terminal domains in the emerging strains. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. The vaccine effectiveness is yet to be examined against new mutant strains of SARS-CoV-2 originating in Europe, Nigeria, Brazil, South Africa, and India. To prevent the loss of anti-viral protection in vivo, often defined as antibody resistance, it is required to target highly conserved viral sequences (including Spike protein) and enhance the potency of antibody cocktails. In this review, we assess the reported mutation-acquiring potential of coronaviruses and compare efficacies of current COVID-19 vaccines against 'parent' and 'mutant' strains of SARS-CoV-2 (Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).

COVID-19 pandemic: the delta variant, T-cell responses, and the efficacy of developing vaccines

Background

The mayhem COVID-19 that was ushered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) was declared pandemic by the World Health Organization in March 2020. Since its initial outbreak in late 2019, the virus has affected hundreds of million adults in the world and killing millions in the process. After the approval of newly developed vaccines, severe challenges remain to manufacture and administer them to the adult population globally in quick time. However, we have witnessed several mutations of the virus leading to ‘waves’ of viral spread and mortality. WHO has categorized these mutations as variants of concern (VOCs) and variants of interest (VOIs). The mortality due to COVID-19 has also been associated with various comorbidities and improper immune response. This has created further complications in understanding the nature of the SARS-CoV2–host interaction that has fuelled doubts in the efficacy of the approved vaccines. Whether there is requirement of booster dose and whether the impending wave could affect the children are some of the hotly debated topics.

Materials and Methods

A systematic literature review of PubMed, Medline, Scopus, Google Scholar was utilized to understand the nature of Delta variant and how it alters our T-cell responses and cytokine production and neutralizes vaccine-generated antibodies.

Conclusion

In this review, we discuss the variants of SARS-CoV2 with specific focus on the Delta variant. We also specifically review the T-cell response against the virus and bring a narrative of various factors that may hold the key to fight against this marauding virus.

SARS-CoV-2 infections in households in a peri-urban community of Lima, Peru: A prospective cohort study

Background

We assessed the prevalence and incidence of SARS‐CoV‐2 infections in a prospective study of households in Lima, Peru.

Methods

Households with a child, a young adult 18–50 years, and an adult age >50 years in peri‐urban Lima were followed with twice‐a‐week household visits during a 2‐month period. Nasal swabs and saliva specimens were collected twice weekly, and nasopharyngeal swabs were collected weekly from each participant, regardless of symptoms. Laboratory‐confirmed SARS‐CoV‐2 infection was defined by two RT‐PCR tests from any of the collected specimens within a week. Blood samples collected at enrollment and end of follow‐up were tested with rapid serological tests. We calculated the prevalence and incidence of laboratory‐confirmed SARS‐CoV‐2 infections.

Results

We enrolled 132 participants from 44 households: 44 children, 44 young adults, and 44 older adults. A total of 13 SARS‐CoV‐2 infections were detected in eight households, for an overall period prevalence of 9.85% (95% confidence interval [CI]: 5.35–16.25). Most (61.54%) infections were symptomatic. Eight of 11 (72.73%) SARS‐CoV‐2 detections corresponded to the Lambda variant. During 218.79 person‐months at risk of follow‐up, there were six new SARS‐CoV‐2 infections detected (2.74 per 100 person‐month, 95% CI: 1.25–6.04). At enrollment, 59 of 128 participants tested had positive SARS‐CoV‐2 IgG serology (46.09%, 95% CI: 37.25–55.12). Five of six new infections occurred among participants with negative baseline serology.

Conclusions

We demonstrated high incidence of SARS‐CoV‐2 infections in households, especially among subjects without evidence of prior infection, most of them not detected by the Ministry of Health system.

Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy

The SARS-CoV-2 variant of concern (VOC) "Delta" is currently defined by PANGOLIN as a cluster of 33 different AY sublineages. Delta (in particular B.1.617.2) is largely and rapidly replacing the Alpha VOC as the dominant clade in most countries. To date, variations in the Spike protein of the Delta VOC have largely been limited. We report here the results of a genomic surveillance programme from Northern Italy. We identified several Delta sublineages harbouring mutations previously reported in GISAID at extremely low frequencies and in different combinations. Two patients (one of them vaccinated) tested positive for a Delta sublineage harbouring S71F, T250I, T572I and K854N. More patients tested positive for G769 V plus C1248F, A352S, and R158G and C1248F, respectively. Genomic surveillance of Delta variants should be encouraged to anticipate immune escape and deploy countermeasures.

SARS-CoV-2 Lambda (C.37): An emerging variant of concern?

Many SARS-CoV-2 variants have high infectivity and transmissibility. The viral genome data show that the COVID-19 curves of daily case numbers were shaped by the emergence of the variants, including Alpha 202012/01 GRY (B.1.1.7; the U.K.), Beta GH/501Y.V2 (B.1.351, B.1.351.2, and B.1.351.3; South Africa), Gamma GR/501Y.V3 (P.1, P.1.1, and P.1.2; Japan, Brazil), Eta G/484K.V3 (B.1.525; Nigeria, the U.K.), Delta G/478K.V1 (B.1.617.2, AY.1, AY.2, and AY.3; India), Iota GH/253G.V1 (B.1.526; the U.S.A.), and Kappa G/452R.V3 (B.1.617.1; India). The Lambda (C.37) variant was reported in Peru initially; this has spread to 41 countries in four continents. Seven out of eight mutations in this variant are associated with the viral spike protein, akin to mutations in the other variants. These mutations have implications for effectiveness of the vaccines and neutralizing antibodies in immunized subjects and those previously infected with the virus and are thought to facilitate the viral invasion into host cells and help the virus evade the host immune system. Widespread dissemination of the viral variants may cause severe clinical consequences, lengthy hospitalizations, and unfavorable prognoses. Healthcare systems will be stretched, and health workers will be fatigued. Fast, equitable, and widespread vaccination with strict adherence to hygiene protocols will control the rising curves of the pandemic due to the new variants.

Extracellular pH, osmolarity, temperature and humidity could discourage SARS-CoV-2 cell docking and propagation via intercellular signaling pathways

The COVID-19 pandemic and its virus variants continue to pose a serious and long-lasting threat worldwide. To combat the pandemic, the world's largest COVID-19 vaccination campaign is currently ongoing. As of July 19th 2021, 26.2% of the world population has received at least one dose of a COVID-19 vaccine (1.04 billion), and one billion has been fully vaccinated, with very high vaccination rates in countries like Israel, Malta, and the UEA. Conversely, only 1% of people in low-income countries have received at least one dose with examples of vaccination frequency as low as 0.07% in the Democratic Republic of Congo. It is thus of paramount importance that more research on alternate methods to counter cell infection and propagation is undertaken that could be implemented in low-income countries. Moreover, an adjunctive therapeutic intervention would help to avoid disease exacerbation in high-rate vaccinated countries too. Based on experimental biochemical evidence on viral cell fusion and propagation, herein we identify (i) extracellular pH (epH), (ii) temperature, and (iii) humidity and osmolarity as critical factors. These factors are here in discussed along with their implications on mucus thick layer, proteases, abundance of sialic acid, vascular permeability and exudate/edema. Heated, humidified air containing sodium bicarbonate has long been used in the treatment of certain diseases, and here we argue that warm inhalation of sodium bicarbonate might successfully target these endpoints. Although we highlight the molecular/cellular basis and the signalling pathways to support this intervention, we underscore the need for clinical investigations to encourage further research and clinical trials. In addition, we think that such an approach is also important in light of the high mutation rate of this virus originating from a rapid increase.

Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy

The Delta variant of concern of severe acute respiratory syndrome coronavirus 2 is dominant worldwide. We report a case cluster caused by Delta sublineage B.1.617.2 harboring the mutation E484K in Italy during July 11–July 29, 2021. This mutation appears to affect immune response and vaccine efficacy; monitoring its appearance is urgent.