Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia

Objectives

To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia.

Methods

A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument.

Results

Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.1.468 (n = 10), B.1 (n = 5), B.1.1 (n = 2), B.1.1.398 (n = 2), and B.6 (n = 1). Other unique amino acid mutations found in our samples were present in A58T on non-structural protein (NSP3) (70%), P323L on NSP12 (95%), Q57H on NS3 protein (75%), and D614G on S (100%).

Conclusion

The SARS-CoV-2 lineage B.1.468 may be the main virus variant circulating in North Sumatra at the beginning of the emergence of COVID-19 cases in this province.

Examination with Cross-Correlation Analysis of the Time-Lagged Relationship Between COVID-19 Cases of Turkey and Some Countries

Amaç: Bu çalışmada, Dünya’da COVID-19 vaka sayısında üçüncü dalganın yaşandığı dönemde Türkiye’ye en fazla ziyaretçinin geldiği ülkeler ile Türkiye’nin günlük bir milyon kişi başına düşen COVID-19 vaka sayıları arasındaki gecikmeli ilişkinin incelenmesi amaçlanmıştır.Yöntem: Bütün ulaşım yolları dahil olmak üzere Türkiye’ye en fazla ziyaretçinin geldiği ilk 30 ülke çalışma kapsamına alınmıştır. Vaka sayıları arasındaki gecikmeli ilişki çapraz korelasyon analizi kullanılarak belirlenmiştir.Bulgular: Ukrayna (r=0,80), Polonya (r=0,81), Makedonya (r=0,78), Romanya (r=0,77), Sırbistan (r=0,76), Bulgaristan (r=0,73), Avusturya (r=0,71), Moldova (r=0,71), Birleşik Krallık (r=0,53), Fransa (r=0,52), Belçika (r=0,57), Amerika Birleşik Devletleri (r=0,57), Ürdün (r=0,81), Libya (r=0,74) ve Lübnan’da (r=0,64) vaka sayılarının pik yapmasından haftalar sonra Türkiye’de de pik gerçekleştirdiği ve gecikmeli ilişkinin olduğu saptanmıştır. Türkiye’de vaka sayılarının Almanya (r=0,69), Azerbaycan (r=0,93), Irak (r=0,88), İran (r=0,87) ve Hollanda (r=0,77) ile benzer zaman aralıklarında benzer bir trend sergilediği tespit edilmiştir. Sonuçlar istatistiki açıdan anlamlıdır (p<0,05).Sonuç: Türkiye’de vaka sayılarında üçüncü dalganın yaşandığı dönemde, çalışma kapsamında gecikmeli ilişki tespit edilen ülkelerden gelen ziyaretçilerin hastalığın toplum içerisinde yayılımında etkisi olabilir. Bu bakımdan vaka sayılarında ciddi artışların olduğu ülkelerden Türkiye’ye gelen ziyaretçilerin ülkeye girişlerine izin verilmemesi, karantinada kalma koşulu ile girişine izin verilmesi, ülkeye girişten sonra semptom takibinin yapılması gibi farklı çözümler ile farklı ülkelerden hastalığın taşınması kısmi olarak engellenebilir. 

Lessons from SARS-CoV-2 in India: A data-driven framework for pandemic resilience

India experienced a massive surge in SARS-CoV-2 infections and deaths during April to June 2021 despite having controlled the epidemic relatively well during 2020. Using counterfactual predictions from epidemiological disease transmission models, we produce evidence in support of how strengthening public health interventions early would have helped control transmission in the country and significantly reduced mortality during the second wave, even without harsh lockdowns. We argue that enhanced surveillance at district, state, and national levels and constant assessment of risk associated with increased transmission are critical for future pandemic responsiveness. Building on our retrospective analysis, we provide a tiered data-driven framework for timely escalation of future interventions as a tool for policy-makers.

COVID mortality in India: National survey data and health facility deaths

India’s national COVID death totals remain undetermined. Using an independent nationally representative survey of 0.14 million (M) adults, we compared COVID mortality during the 2020 and 2021 viral waves to expected all-cause mortality. COVID constituted 29% (95%CI 28-31%) of deaths from June 2020-July 2021, corresponding to 3.2M (3.1-3.4) deaths, of which 2.7M (2.6-2.9) occurred in April-July 2021 (when COVID doubled all-cause mortality). A sub-survey of 57,000 adults showed similar temporal increases in mortality with COVID and non-COVID deaths peaking similarly. Two government data sources found that, when compared to pre-pandemic periods, all-cause mortality was 27% (23-32%) higher in 0.2M health facilities and 26% (21-31%) higher in civil registration deaths in ten states; both increases occurred mostly in 2021. The analyses find that India’s cumulative COVID deaths by September 2021 were 6-7 times higher than reported officially.

Immunology and Technology of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccines

We have experienced an enormous cohesive effort of the scientific community to understand how the immune system reacts to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and how to elicit protective immunity via vaccination. This effort resulted in the development of vaccines in record time with high levels of safety, efficacy, and real-life effectiveness. However, the rapid diffusion of viral variants that escape protective antibodies prompted new studies to understand SARS-CoV-2 vulnerabilities and strategies to guide follow-up actions to increase, and maintain, the protection offered by vaccines. In this review, we report the main findings on human immunity to SARS-CoV-2 after natural infection and vaccination; we dissect the immunogenicity and efficacy of the different vaccination strategies that resulted in products widely used in the population; and we describe the impact of viral variants on vaccine-elicited immunity, summarizing the main discoveries and challenges to stay ahead of SARS-CoV-2 evolution. SIGNIFICANCE STATEMENT: This study reviewed findings on human immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), analyzed the immunogenicity and efficacy of the various vaccines currently used in large vaccination campaigns or candidates in advanced clinical development, and discussed the challenging task to ensure high protective efficacy against the rapidly evolving SARS-CoV-2 virus. This manuscript was completed prior to the emergence of the Omicron variant and to global vaccine boosting efforts.

Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants

Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.

Analysis of SARS-COV2 spike protein variants among Iraqi isolates

The ongoing pandemic of COVID-19 caused by the SARS-COV2 virus has triggered millions of deaths around the globe. Emerging several variants of the virus with increased transmissibility, the severity of disease, and the ability of the virus to escape from the immune system has a cause for concerns. Here, we compared the spike protein sequence of 91 human SARS CoV2 strains of Iraq to the first reported sequence of SARS-CoV2 isolate from Wuhan Hu-1/China. The strains were isolated between June 2020 and March 2021. Twenty-two distinct mutations were identified within the spike protein regions which were: L5F, L18F, T19R, S151T, G181A, A222V, A348S, L452 (Q or M), T478K, N501Y, A520S, A522V, A570D, S605A, D614G, Q675H, N679K, P681H, T716I, S982A, A1020S, D1118H. The most frequently mutations occurred at the D614G (87/91), followed by S982A (50/91), and A570D (48/91), respectively. In addition, a distinct shift was observed in the type of SARS-COV2 variants present in 2020 compared to 2021 isolates. In 2020, B.1.428.1 lineage was appeared to be a dominant variant (85%). However, the diversity of the variants increased in 2021, and the majority (73%) of the isolated were appeared to belong to B.1.1.7 lineage (VOC/alpha variants). To our knowledge, this is the first major genome analysis of SARS-CoV2 in Iraq. The data from this research could provide insights into SARS-CoV2 evolution, and can be potentially used to recognize the effective vaccine against the disease.

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.