SARS-CoV-2

Last Reviewed
January 21, 2021

SARS-CoV-2 Coronavirus

In December 2019, the novel coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was identified in China. As the name indicates, the virus is related to the SARS coronavirus (SARS-CoV) that caused deadly outbreaks in 2002-2003.

However, it is not the same virus.

The SARS-CoV-2 virus is a betacoronavirus, similar to MERS-CoV and SARS-CoV, both of which have their origins in bats. On February 5, 2020, the JAMA published a study focused on genetic sequencing data, which found the SARS-CoV-2 coronavirus shares 79.5% of the genetic sequence with SARS-CoV and has 96.2% homology to a bat coronavirus.

The coronavirus that causes COVID-19 is mutating, and that's to be expected. Many viruses do as they spread throughout the world, stated the U.S. CDC on December 22, 2020.

A new variant strain of SARS-CoV-2 that contains a series of mutations has been described in the United Kingdom (UK) and has become highly prevalent in London and southeast England. At present, the variant is referred to as “SARS-CoV-2 VUI 202012/01” or “B.1.1.7.” Based on these mutations, this variant strain has been predicted to potentially be more rapidly transmissible than other circulating strains of SARS-CoV-2.

And in South Africa, another variant of SARS-CoV-2 (501Y.V2 or B.1.351) emerged independently of VOC 202012/01. This variant shares some mutations with VOC 202012/01. Furthermore, cases attributed to this variant have been detected outside of South Africa, stated the U.S. CDC on December 30, 2020.

SARS-CoV-2 Mutations and Variants

The US Centers for Disease Control and Prevention (CDC) reported (144) cases of the SARS-CoV-2 betacornavirus B.1.1.7 lineage confirmed in the USA as of January 20, 2021. The states of California and Florida have reported the most coronavirus variant cases.

On January 21, 2021, the European Centre for Disease Prevention and Control issued its first update regarding the spread of new SARS-CoV-2 variants of concern in the EU/EEA.

Viruses constantly change through mutation, and new variants of a virus are expected to occur over time. Sometimes new variants emerge and disappear. Other times, new variants emerge and start infecting people, says the U.S. CDC.

The WHO stated researchers had isolated the virus causing pneumonia in December 2019 and found it a strain of β-coronavirus (CoV). The virus showed a high nucleotide sequence homology with two SARS-like bat coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21 (88% homology), and with SARS-CoV (79.5% homology), while only 50% homology with the Middle East respiratory syndrome coronavirus.

During 2020, the numbers of people infected with SARS-CoV-2 cases have varied from country to country, with multiple studies attempting to clarify the clinical differences.

The original strain, detected in Wuhan's city, China, in December 2019, is the L virus strain. The virus then mutated into the S strain at the beginning of 2020. V and G strains were followed by Strain G mutated yet further into strains GR, GH, and GV. Several other infrequent mutations were collectively grouped as strain O.

The most recent mutation to emerge is the GV strain, which has so far been isolated to Europe, where it has become increasingly common.

A few example studies are as follows:

In April 2020, a study's findings suggested that the virus is evolving and European, North American, and Asian strains might coexist, each of them characterized by a different mutation pattern. These researchers characterized (8) novel recurrent mutations of SARS-CoV-2, with 2891, 3036, 14408, 23403, and 28881 positions predominantly observed in Europe, whereas those located at positions 17746, 17857, and 18060 are exclusively present in North America.

The WHO published an analysis on June 2, 2020, which found several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. The evolutionary analysis indicated structured transmission, with the possibility of multiple introductions into the population.

And a study published on July 22, 2020, classified 28 countries into (3) clusters showing different fatality rates of COVID-19. In correlation analyses, they identified that ORF1ab 4715L and S protein 614G variants, which are in strong linkage disequilibrium, showed significant positive correlations with fatality rates (r = 0.41, P = 0.029 and r = 0.43, P = 0.022, respectively).

On August 13, 2020, EuroSurveillance published a report which found 'Since the first genomes were published in January 2020, the number of available sequences has rapidly increased to more than 63,000 complete genome sequences available in GISAID as on July 10, 2020.'

'The subsampled distribution of clades and lineages over time in the WHO European Region. There was an initial period in January 2020 when the 19A/L/V/O clades were more prevalent in total than the 20A/G clades. However, this could partially affect small numbers of sequenced viral genomes in Europe early in the pandemic and the widespread sampling strategy focusing on East Asia's travel history cases.

The 20A/G clades are characterized by the spike protein D614G mutation suggested increasing transmissibility but not pathogenicity. After this initial stage, the 20B/GR clade increased rapidly, stabilized around 30% between March and May 2020, and increased further to become the most frequent clade in June 2020Thehe 20C/Gclades' trajectories differ slightly depending on the nomenclature applied. The Nextstrain 20C clade peaked at ca 20% of the sequences in early April 2020 and has since then slowly declined and almost disappeared, while the GISAID GH clade peaked at ca 30% in May 2020 has rapidly declined since then. Different delays could partially explain the changing trends at the end of the data series from sampling to publication for different countries with different clade distributions.'

A study published on October 28, 2020, supported the WHO's recent finding that 'A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic.'

On October 28, 2020, a non-peer-reviewed study reported a variant of the SARS-CoV-2 coronavirus emerged in early summer 2020 has since spread to multiple European countries. The variant, known as A222V, was first observed in Spain has been at transmission frequencies above 40% since July 2020. Outside of Spain, this variant's frequency has increased to 40-70% in Switzerland, Ireland, United Kingdom, Norway, Latvia, the Netherlands, and France.

A study published on November 12, 2020, found the D614G variant transmits significantly faster and displayed increased competitive fitness than the wild-type virus in hamsters. These data show that the D614G substitution significantly enhances SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human cells and animal models.

This strain is named VUI-202012/01 (the first “Variant Under Investigation” in December 2020 and is defined by a set of 17 changes or mutations. One of the most significant is an N501Y mutation in the spike protein that the virus uses to bind to the human ACE2 receptor. Changes in this part of spike protein may, in theory, result in the virus becoming more infectious and spreading more easily between people.

On December 18, 2020, the South African government announced that it had also seen the emergence of a new strain in a scenario similar to that in the UK. The South African variant also has the N501Y mutation and several other mutations but emerged completely independently of the UK strain and is not related to it, confirmed by the WHO on December 21, 2020.

Public Health England confirmed on December 21, 2020, and a novel variant has been identified, B.1.1.7, which has spread rapidly within the UK. When examined in the national phylogeny, the Kent cluster is part of a larger cluster, which is phylogenetically very distinct from the rest of the UK dataset. Much less is known about the other spike variants present in this cluster, except for D614G, which is well characterized and already highly prevalent in the UK.

In a non-peer-reviewed study published on December 23, 2020, in the three most heavily affected England regions (South East, East of England, and London), the researchers estimated that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2.

'Their significance cannot be judged at present,' stated PHE.

Additionally, on December 28, 2020, PHE published version #2 of its report, which concluded, 'The findings from the analysis of data on SGTF cases showed a roughly similar spatial distribution of cases as observed from a mapping of genomic data. SGTF cases were mostly observed in the South East, London parts of the South West regions, and Cumbria.'

'However, in regions with relatively high and consistent coverage, the findings can be used as a proxy for the burden of VOC 201212/01 infection.'

'Investigation of novel SARS-COV-2 variant Preliminary results from the cohort study found no statistically significant difference in hospitalization and 28-day case fatality between cases with the variant (VOC 201212/01) and wild-type comparator cases. There was also no significant difference in the likelihood of reinfection between variant cases and the comparator group.'

Prior work on variants with N501Y suggests they may bind more tightly to the human angiotensin-converting enzyme 2 (ACE2) receptor. It is unknown whether that tighter binding, if true, translates into any significant epidemiological or clinical differences, says the CDC.

The U.S. CDC stated on December 28, 2020, 'Since November 2020, the UK has reported a rapid increase in COVID-19 cases and has been linked to a different version—or variant—of the SARS-CoV-2 virus.'

The Imperial College of London and others published Update #42: Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data on December 31, 2020. This Update concluded by stating 'we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20-year-olds among reported VOC than non-VOC cases.'

On January 15, 2021, the CDC published the following update:

In the United Kingdom (UK), a new variant called B.1.1.7 has emerged with many mutations. This variant spreads more easily and quickly than other variants. There is no evidence that it causes more severe illness or increased death risk. This variant was first detected in September 2020 and is now highly prevalent in London and southeast England. It has since been detected in numerous countries worldwide, including the United States and Canada.

In South Africa, another variant called 1.351 has emerged independently of the UK's variant. This variant, originally detected in early October, shares some mutations with the UK's variant. There have been cases caused by this variant outside of South Africa, but it has not been detected in the US.

In Brazil, a variant called P.1 emerged and was identified in four travelers from Brazil, who were tested during routine screening at Haneda airport outside Tokyo, Japan. This variant contains additional mutations that may affect its ability to be recognized by antibodies. This variant has not been detected in the US.

These variants seem to spread more easily and quickly than other variants, leading to more cases of COVID-19. There is no evidence that these variants cause more severe illness or increased death risk.

SARS-CoV-2 Symptoms

People infected with this new betacoronavirus have reported a wide range of symptoms – ranging from mild symptoms to severe illness - often appearing 2-14 days after exposure to the SARS-CoV-2 virus, says the U.S. CDC.

Specifically, studies published in JAMA on June 18, 2020, and in PLOS on October 1, 2020, found that the loss of taste and smell may be common symptoms among those in the early stages of SARS-CoV-2 coronavirus infection. And the seropositivity for the SARS-CoV-2 virus was 3 times more likely in study participants with smell loss (OR 2.86; 95% CI 1.27–6.36; p < 0.001) compared with those with taste loss.

SARS-CoV-2 Transmission Patterns

Based on what is currently known about this coronavirus, the transmission occurs much more commonly through respiratory droplets than through fomites. The SARS-CoV-2 virus appears to spread more efficiently than influenza, but not as efficiently as measles, which is highly contagious, says the CDC.

The virus spread from person-to-person happens most frequently among close contacts, living together at home or a nursing facility.

On October 5, 2020, the CDC published a website change that states, 'There is evidence that people with COVID-19 seem to have infected others who were more than 6 feet away under certain conditions. These transmissions occurred within enclosed spaces that had inadequate ventilation. Sometimes the infected person was breathing heavily, for example, while singing or exercising.'

'This kind of spread is referred to as 'airborne transmission' and is an important way that infections like tuberculosis, measles, and chickenpox are spread.'

'Under these circumstances, scientists believe that the amount of infectious smaller droplets and particles produced by the people with COVID-19 became concentrated enough to spread the virus to other people,' says the CDC.

A study published in Emerging Infectious Diseases on June 23, 2020, suggests that SARS-CoV-2 generally maintains infectivity at a respirable particle size over short distances, in contrast to either betacoronavirus, SARS-1, and MERS.

On November 10, 2020, the CDC published a virus transmission review that found up to 70% of fine particles could be reduced by wearing face masks when inside. No data was disclosed regarding the benefits of wearing a face mask when outside.

Furthermore, at this time, the risk of the SARS-CoV-2 virus spreading from animals to people is considered to be low, says the CDC.

Who Is At Higher-Risk For SARS-CoV-2 Infection

There are currently limited data and information about the impact of underlying medical conditions and whether they increase the risk of severe illness from COVID-19. 'Based on what we know at this time, older people with the following conditions might be at an increased risk for severe illness from COVID-19.'

The CDC says children who are medically complex, who have serious genetic, neurologic, metabolic disorders, and congenital (since birth) heart disease might be at increased risk for severe illness from COVID-19. Like adults, children with obesity, diabetes, asthma, chronic lung disease, or immunosuppression might be at increased risk of severe illness from COVID-19.

On June 18, 2020, the director of the U.S. NIH, Dr. Francis S. Collins, wrote a posting that stated: 'the findings (of studies) suggest that people with blood type A face a 50% greater risk of needing oxygen support or a ventilator should they become infected with the novel coronavirus. In contrast, people with blood type O appear to have a 50% reduced risk of severe COVID-19.

SARS-CoV-2 Antibody Duration

Questions regarding the robustness, functionality, and longevity of the antibody response to the virus remain unanswered. A study published on October 28, 2020, found SARS-CoV-2 antibodies were detectable after 5-months.

The U.S. NIH director Dr. Francis S. Collins’s weekly blog highlight SARS-CoV-2 antibody detection after 4-months.

A study published by the U.S. CDC in 2007 found 'among patients who had the original severe acute respiratory syndrome (SARS-1), SARS-specific antibodies were maintained for an average of 2-years, and significant reduction of immunoglobulin G–positive percentage and titers occurred in the 3rd year post-infection.

SARS-CoV-2 Immunity Responses

Humoral immune responses to SARS-CoV-2 are mediated by antibodies directed to viral surface glycoproteins, mainly the spike glycoprotein and the nucleocapsid protein (figure 3). Such antibodies neutralize viral infection of human cells and tissues expressing angiotensin-converting enzyme 2 (ACE2).

Initial reports on cellular immunity to SARS-CoV-2 have consisted of case reports with small numbers of patients, which have indicated that the proportion of CD38+, HLA-DR+ T cells (both CD4+ and CD8+) increases during the first 7–10 days of COVID-19 symptoms and begins to return to baseline around day 20.

Overall, the current data show that CD4+ T-cell and CD8+ T-cell responses occur in most patients infected by SARS-CoV-2 within 1–2 weeks after symptom onset and produce mainly Th1 cytokines. The frequency of CD4+ T cells targeted to the spike glycoprotein correlates with neutralizing antibody titers, suggesting that the T-cell response might also vary among individuals with different disease severities. 

SARS-CoV-2 Seasonality

In theory, antibodies induced by coronavirus infections might have broad coronavirus-recognizing characteristics. To examine this, researchers announced on September 24, 2020, and they performed an additional enzyme-linked immunosorbent assay, this time using the complete nucleocapsid protein of SARS-CoV-2, including the more inter-species-conserved N-terminal region to allow detection of broadly recognizing antibodies.

Our serological study is unique because it avoids previous epidemiologic studies' sampling bias based on symptoms-based testing protocols5. In our study, the months of June, July, August, and September 2020 show the lowest prevalence of infections for all four seasonal coronaviruses (Fig. 1d; Wilcoxon signed-rank test, P = 0.004), confirming the higher prevalence in winter in temperate countries, and SARS-CoV-2 might share this feature in the post-pandemic era.

However, these researchers could not identify strain variation, which could play a role in susceptibility to reinfection. HCoV-NL63, HCoV-OC43, and HCoV-HKU1 all show different co-circulating genetic clusters. The situation is even more complicated for HCoV-229E, which shows continuous genetic drift.

SARS-CoV-2 Sunlight and Swimming

The U.S. CDC published updated various considerations as some USA communities consider opening public beaches. On July 30, 2020, the CDC stated 'evidence suggests that COVID-19 cannot be spread to humans through most recreational water.'

Previously, on June 12, 2020, the US Department of Homeland Security Science and Technology (S&T) Directorate added a new calculator that estimates the natural decay of the SARS-CoV-2 virus in the air, such as when visiting a breach, and found the coronavirus was least stable in the presence of sunlight. This new S&T research has been featured in the Oxford Academic Journal of Infectious Diseases, with the most recent – Airborne SARS-CoV-2 is Rapidly Inactivated by Simulated Sunlight.

SARS-CoV-2 Vaccine Candidates

The SARS-CoV-2 vaccine development efforts include platforms such as nucleic acid, virus-like particle, peptide, viral vector (replicating and non-replicating), recombinant protein, live attenuated virus, an inactivated virus approaches. Detailed vaccine development information can be found on this webpage.

SARS-CoV-2 Diagnostic Tests

The COVID-19 tests most people discuss are RT-PCR, the nasal-swab test that detects viral RNA, and various antibody tests that detect if you have an immune response due to past exposure to the SARS-CoV-2 virus. For updated news, please visit 'Tests.'

SARS-CoV-2 Oral Infection and Preventions

A non-peer-reviewed study published on October 27, 2020, examined RNA that, compared with other oral tissues, cells of the salivary glands, tongue, and tonsils carry the most RNA linked to proteins (ACE2 receptor) that coronavirus needs to infect cells. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibiting ACE2 expression and SARS-CoV-2 RNA.

Matched nasopharyngeal and saliva samples found distinct viral shedding dynamics and viral burden in saliva correlated with COVID-19 symptoms, including taste loss. Upon recovery, this cohort exhibited salivary antibodies against SARS-CoV-2 proteins.

According to a study published on September 17, 2020, nasal rinses and mouthwashes directly impact the major sites of reception and transmission of human coronaviruses (HCoV), which may provide an additional protection level against the virus. Common over‐the‐counter nasal rinses and mouthwashes - gargles were tested for their ability to inactivate high concentrations of HCoV using contact times of 30 s, 1 min, and 2 min.

A 1% baby shampoo nasal rinse solution inactivated HCoV greater than 99.9% with a 2‐min contact time, said these researchers. Several over‐the‐counter mouthwash/gargle products, including Listerine and Listerine‐like products, were highly effective at inactivating infectious virus with greater than 99.9% even with a 30‐second contact time. And, according to Penn State College of Medicine researchers, some of these products might be useful for reducing the viral load, or amount of virus, in the mouth after infection.

In a previous study published on August 25, 2020, mouthwashes are widely-used solutions due to their ability to reduce the number of microorganisms in the oral cavity. Although there is still no clinical evidence that they can prevent the transmission of SARS-CoV-2, preoperative antimicrobial mouth rinses with chlorhexidine gluconate, cetylpyridinium chloride, povidone-iodine, and hydrogen peroxide have been recommended to reduce the number of microorganisms in aerosols and drops during oral procedures.

On October 30, 2020, a Letter to the Editor discussed methylene blue as an anti-COVID-19 mouthwash in dental practice. In the case of SARS-CoV-2, the salivary gland could be a major source of the virus in saliva (Liu et al.). Therefore, we suggest repeated use of mouth wash every five to ten minutes during dental procedures to decrease the viral load of freshly secreted saliva. Based on the facts, diluted MB appears to be a potentially effective preprocedural mouthwash in dental practice. 0.5% MB oral rinse therapy has already yielded results as a potent, safe, and cost-effective alternative to other mouthwashes.

SARS-CoV-2 and Pets

The U.S. CDC says a small number of pets worldwide, including cats and dogs, have been reported by the OiE on November 27, 2020, to be infected with the virus that causes COVID-19, mostly after close contact with people with COVID-19. It appears that the virus that causes COVID-19 can spread from people to animals in some situations.

If a person inside the household becomes sick, isolate that person from everyone else, including pets. This is a rapidly evolving situation, and information will be updated as it becomes available.

SARS-CoV-2 Coronavirus FAQs

NOTE: This page's content is sourced from the CDC, WHO, clinicaltrials.gov, and the Precision Vax network of websites. This information was last fact-checked by healthcare providers, such as Dr. Robert Carlson.