Sexually Transmitted Infections (STIs) continue to be a significant global health concern, affecting millions of people each year, irrespective of geographical location or economic status. While the spotlight often falls on diseases like HIV and syphilis due to their severe consequences and historical significance, other STIs such as chlamydia, gonorrhoea, and human papillomavirus (HPV) also pose substantial threats to public health worldwide.


STI Trends and Insights

While syphilis and HIV have historically been central to STI discussions, it’s crucial to address the wide spectrum of STIs affecting populations globally. Diseases like chlamydia, often asymptomatic, can lead to infertility if untreated. HPV, the most common STI, is a leading cause of cervical cancer, underscoring the importance of vaccination and regular screenings.

  • Chlamydia: A common STI caused by infection with the bacterium Chlamydia trachomatis. The WHO estimated that in 2020 there were 5 million new infections worldwide among adults aged 15 to 49 years.
  • Syphilis: Despite being one of the oldest known STIs, syphilis cases have surged, particularly in high-income countries, with an increase in Europe of 70% from 2010 to 2017 and cases are still rising with an increase of 34% between 2021 to 2022.
  • Human Papillomavirus (HPV): The WHO estimates that nearly all sexually active individuals will get at least one type of HPV at some point in their lives. Whilst in 90% of people the body controls the infection by itself, persistent HPV infection with high-risk HPV types is a leading cause of cervical cancer.
  • Trichomoniasis: The most common non-viral STI. Caused by the protozoan Trichomonas vaginalis which specifically targets the urogenital tract. There were an estimated 156 million new cases of vaginalis infection among people aged 15–49 years old globally in 2020 with approximately one third of infections in the WHO African Region.


Gonorrhoea- An Urgent Threat

Caused by the bacteria Neisseria gonorrhoeae, cases of Gonorrhoea have increased significantly. In the UK whilst there was an increase of 13% in the number of sexual health screens between 2021 and 2022, there was a larger increase in diagnoses of gonorrhoea (50%), which may either reflect more targeted testing of people more likely to have an STI, or an increase in STI transmission in the community. A recent publication from the European Centre for Disease Prevention and Control (ECDC) confirms the worrying trend across Europe with the number of reported cases of gonorrhoea rising by 48% compared to the previous year.

Alongside the increasing incidence is the concern over antibiotic-resistant gonorrhoea which has emerged as a significant public health challenge, with the US CDC identifying it as an “urgent threat” and estimating that there are 550,000 drug-resistant infections per year.


The Interconnectedness of STIs and Other Health Risks

The relationship between different STIs can exacerbate health outcomes. For example, genital ulcers from syphilis can increase the risk of acquiring HIV, a phenomenon seen with other ulcerative STIs as well. Two types of HPV (HPV 16 and HPV 18) are responsible for approximately 70% of cervical cancer cases. Moreover, co-infections can complicate treatment and disease management, highlighting the need for comprehensive testing and prevention strategies.


The Importance of Comprehensive STI Testing and Prevention

With more than 1 million sexually transmitted infections acquired every day worldwide, the majority of which are asymptomatic, testing is vital to reduce the transmission. Beyond the successful models of HIV and syphilis testing in pregnant women, there’s a pressing need to enhance screening and prevention for other STIs. Approaches include:

  • Expanded Testing: Point-of-care (POC) tests and integrated screening programs to include a broader range of STIs, making it easier to identify and treat diseases early. Increased screening for chlamydia and gonorrhoea has been shown to reduce incidence rates, particularly in high-risk populations.
  • Vaccination: Promoting vaccines, especially against HPV, can significantly reduce the incidence of cervical cancer and other HPV-related diseases. The WHO recommends HPV vaccination for girls aged 9-14 to prevent cervical cancer, with studies showing vaccine efficacy of nearly 100% for certain HPV types.
  • Education and Awareness: Increasing awareness about the importance of safe sex practices and regular testing can help reduce the transmission of STIs.
  • Integrated Health Services: Combining STI screening with other health services can improve access to testing and treatment, especially in LMICs where healthcare resources are limited.


Conclusion: A Call for Global Action Against STIs

The data underscores the critical need for a global response to the STI epidemic that encompasses not only HIV and syphilis but also other prevalent infections like chlamydia, gonorrhoea, and HPV. By investing in comprehensive strategies that include education, vaccination, and accessible testing, the global community can make significant strides in reducing the burden of STIs and safeguarding public health.


STI Biospecimens from Logical Biological

Logical Biological can provide a wide variety of serum, plasma and swabs for the research and development of STI tests and manufacture of control material. All specimens can be provided according to your custom specifications and are supplied with patient demographic information. A variety of testing methods can be utilised to confirm positivity for the disease marker requested and provide titre values.

Popular products available include:

Marker Matrix
HIV Plasma, Serum
HIV O (Human Immunodeficiency Virus Subtype O) Plasma, Serum
Syphilis Plasma, Serum, Swab, PBMC, Urine
Syphilis IgM Plasma, Serum
Gonorrhoea IgM Plasma
Neisseria gonorrhoeae Swab, Urine, Plasma
Chlamydia trachomatis Swabs, Urine
Chlamydia trachomatis IgA/ IgG/ IgM Plasma, Serum
Trichomonas vaginalis Swab, Urine
Trichomonas vaginalis IgM Plasma
HPV (Human Papillomavirus) Swab
HPV (Human Papillomavirus) IgG Plasma

A full range of infectious disease products available can be found in our product table

Sexually transmitted infection (STI) cases across the world are an ever present and ever-increasing issue, not only to adults but to a foetus. Two diseases of particular importance are HIV and Syphilis (caused by the bacterium Treponema pallidum).

How big a threat are STIs in today’s world?

The most recent figures show that in the US, Syphilis cases have tripled between 2013 and 2018 , which includes 5,726 pregnant women. Between 2008 and 2018 Europe also saw a 50% increase in Syphilis and Canada’s cases have more than doubled. In these high-income countries men are disproportionately  affected, however, in low to middle income countries (LMIC), syphilis is endemic to the general population and makes up over 90% of worldwide case numbers. This also means high numbers of infections in pregnant women, leading to increased cases of congenital Syphilis.

Syphilis is classed as an ulcerative STI, which means it causes genital ulcers. These ulcers facilitate the acquisition of HIV during intercourse, increasing the chance of transmission five-fold. Coinfections of Syphilis and HIV can increase the HIV viral load and HIV can accelerate the natural history of Syphilis. This means that individuals suffering from a coinfection will more frequently develop neurosyphilis than those with syphilis alone. In LMIC countries such as Tanzania, Uganda, and Ethiopia, the number of HIV positive patients with Syphilis are nearly 10%, and in Ghana, it is as high as 14.8%.


What does Syphilis mean for pregnant women?

Globally, Congenital syphilis is the second leading cause of preventable stillbirths and there are a plethora of other complications that can arise from untreated congenital Syphilis, such as severe anaemia, jaundice, and ultimately blindness and deafness. In 2016, the World Health Organisation (WHO) estimated that there were 661,000 infants born with congenital Syphilis, and that approximately 40% of babies born to untreated Syphilis, or an estimated 143,000 infants, will suffer early deaths or stillbirths. This is not to say that this is inevitable, and in fact syphilis can be effectively treated with penicillin if caught early enough. This is why testing pregnant women for these infections is so important.

The World Health Organisation (WHO) ‘Prevention of Mother-to-Child Transmission of HIV/AIDS Program’ (PMTCT) aims to eliminate mother-to-child transmission of HIV and syphilis by providing technical support to member states on the uptake of antenatal services like HIV and Syphilis testing, as well as collecting and analysing regional trends.

In higher income countries, high sensitivity and high specificity tests for HIV and Syphilis are performed in labs and protocols are defined for screening of these diseases. In LMIC’s, there are often limited centralised health services or appropriate lab availability for these kinds of tests and so a point of care (POC) approach is taken, which allows for the collecting of a sample, and testing to be conducted in a single visit. POC tests for HIV have proved successful in LMIC countries, with 70-100% of pregnant women being screened. However, there is a clear deficit for pregnant women being screened for Syphilis, falling short at 40-60%. The high prevalence of syphilis in HIV infected patients indicates that there is a need to increase syphilis testing efforts.

What can be done to bridge the gap between HIV and Syphilis testing rates?

There are several combined HIV/ Syphilis POC rapid diagnostic tests (RTD) which aim to increase the rate of syphilis testing by leveraging existing HIV testing programs. To be successful the combined tests must be affordable, easy to use, and appropriate for a POC scenario. The widespread distribution of these combined tests is cheaper and more efficient than two individual tests and can allow for the early detection and treatment of HIV and Syphilis, saving both pregnant women and their unborn children.

Source: World Health Organization

Tests designed with decentralised testing and POC scenarios in mind can be visually interpreted and are easily used. Storage and distribution are big concerns and so these HIV/ syphilis POC tests are compact, have a 2-year shelf life, and can be stored across a broad temperature range. It is important to understand that these tests are only for initial screening, and if positives come back more specific alternative diagnosis methods should be used.

The importance of dual HIV/ Syphilis POC tests in LMIC’s cannot be understated. These tests are projected to allow for an additional 4.4 million women to be tested, with at least 285,000 Syphilis infections in women to be identified. Ultimately this could lead to 38,000 fewer cases of congenital syphilis, and 51,500 child mortalities being avoided.

HIV/ Syphilis Serum and Plasma from Logical Biological

Logical Biological provide a large portfolio of HIV and syphilis serum and plasma products. Testing can be performed on syphilis serum and syphilis plasma using a wide selection of methodologies including TPHA, ELISA and EIA. Available testing for HIV serum and HIV plasma includes LIA, EIA, PCR (copies/ml), Nucleic Acid Amplification, Western Blot, Ratio CD4/CD8 profiling and Chemiluminescent Immunoassay (ChLIA) (S/CO units).

All serum and plasma specimens can be provided according to your custom specifications and are supplied with demographic information available.

Table: HIV and Syphilis serum and plasma available from Logical Biological

BK polyomovirus (BKV) is a double stranded DNA virus that affects 65-90% of the adult population. Commonly a childhood infection with minimal symptoms, this virus can exist in a latent form in the renal system for a lifetime. Its significance arises if an individual becomes immunocompromised such as for recipients of kidney or bone marrow (stem cell hematopoietic) transplants (HCT). Under these circumstances tests for BKV are essential to prevent haemorrhagic cystitis, ureteral stenosis or nephropathy (BKVN) and organ rejection.


The kidney is the most common type of transplanted organ. There were 2,263 kidney transplant procedures in the UK in 2021/2022 and the US reached a record high of 25,487 in 2021. Bone marrow or stem cell transplant numbers are in the region of almost 5,000 people in the US, 4,000 annually in the UK and over 32,000 across Europe as a whole. With BKV affecting up to 15% of transplant patients and a lack of effective antiviral therapies, post-transplant screening is a key recommendation to manage the reduction of immunosuppression in patients with BKV infections.


BKV Screening

Although a kidney biopsy remains the gold standard for BKVN diagnosis, most testing is currently performed in regional or reference laboratories utilising serum, plasma, EDTA whole blood, or urine samples tested using PCR based tests. When triggered by reduced immunity, BKV reactivation causes decoy cells and viral components to be excreted in urine, viruria, then progresses across the interstitium and within a couple of weeks pass into the capillaries causing viremia.


In HCT patients, BKV testing can help to manage the diagnosis and management of hemorrhagic cystitis, with an antiviral drug. In kidney transplantation, screening for BKV DNA allows for an early intervention generally with a preemptive reduction in immunosuppression. This prevents BKVN development and subsequent graft failure.


A UK study that screened paediatric transplant patients found that 30% of them were BKV viremia positive and BKVN was found in 6.6% of cases 3 months post-transplant. This supports other studies in adults that have seen viruria and viremia from 3 months post-transplant. As a result of this, the current guidelines  for testing start at one month post-transplant, with monthly plasma screening for the first 6 months, then every 3 months until 2 years post-transplant.


 Image: Other kidney disease state serum and plasma available from Logical Biological


BKV Test Standardisation

Disparity in sample type, DNA extraction techniques, primer and probe sequences, and even the BK strain DNA used for the control, can all affect results and potentially produce clinical variability. Attempts at reducing these discrepancies have resulted in a WHO International standard to help reduce inter assay variability.


Introduced in 2016 the 1st WHO International Standard for BKV nucleic acid amplification testing (NAAT) enables worldwide harmonization of results across hospitals and institutions. As clinical laboratories worldwide use assays traceable to the WHO International standard, we will see an increased potential for establishing quantitative BKV DNA load cutoffs that can be used in a clinical setting. There is currently no definitive viral load cutoff associated with nephropathy although guidelines recommend a plasma viral load of ≥10,000 copies/ml as the threshold for clinical intervention in kidney transplantation based on a specificity of 93% for BKVN, some centers have reported that this threshold may underestimate the diagnosis of BKVN and suggest using lower viral load thresholds.


To make matters more complicated there are 12 subtypes/subgroups of BKV. Commercial diagnostic testing often uses genotype I, the Dunlop strain, as the reference sequence for primers and probes. One study looked at using these tests on BK variants and concluded a decrease in the sensitivity for patients with BKV variant infections. They urged caution when interpreting test results and being faced with a clinical discrepancy. Unfortunately, rare subtypes have been shown to be an increased risk factor for BKV induced nephropathy, namely subtypes III and IV.


BKV infections continue to be the predominant clinical issue faced by transplant providers and patients. Screening guidelines have resulted in earlier detection, improved patient outcomes and standardisation is helping reduce inter-assay variability. BKVN is however still a challenge for physicians, especially with no anti-viral currently available for the virus.


BK Virus Serum and Plasma from Logical Biological

Logical Biological provide BK Virus PCR positive serum and BK Virus PCR positive plasma with known values (IU/mL) standardised against the 1st WHO International Standard for BK Virus. We can also offer transplant serum and transplant plasma, and kidney failure samples. All serum and plasma specimens can be provided according to your custom specifications and are supplied with demographic information available.

The flu season is well and truly upon us, but is it Influenza, RSV or Covid? And does it matter?


The ‘tripledemic’ season of Influenza, COVID-19, and RSV viruses

Influenza A/B, COVID-19 with its variants and respiratory syncytial virus (RSV) are the three largest contenders responsible for respiratory infections globally. The European Centre of Disease prevention and Control and the Pan American Health Organisation have reported unusual infection spikes this year, collectively calling it a ‘triple threat’, and providing a worldwide picture of increased infections.

Global numbers for annual mortality associated with respiratory infections stands at up to 650,000 for influenza and 80,000 for RSV. The relative newness of SARS-COV-2 and its fatalities mean its numbers cannot yet be directly used in comparisons here, needless to say cumulative deaths from COVID-19 are over 6 million and continue to be recorded in great detail. Infections themselves number in the tens to hundreds of millions, some sources even estimate flu infections reach a billion cases annually, leading to between 300,000 and 800,000 hospitalizations in the U.S. alone each year. Australia’s increased flu infections this year have been an important prediction for the Northern Hemisphere flu season to be ready, and that prediction is unfortunately proving accurate.


Influenza, Covid and RSV symptoms are very similar- Is there a need to define which respiratory disease you have?

Covid Flu A/B RSV A/B symptoms

Influenza, SARS-COV-2, and RSV have incredibly similar symptoms and without medical intervention, the same treatment – namely rest, fluids and over the counter relief medication. An average, healthy infected individual will suffer for a week or two, but otherwise make a full recovery.  People suffering moderate to severe symptoms tend to self-impose an element of isolation from others, with awareness of the effectiveness of this as a prevention highlighted in the recent SARS-COV-2 pandemic. Problems arise when the young, old, or immunologically challenged are infected and need medical assistance in their recovery.

Vaccines and antiviral treatments however vary, and there is an increased interest in being able to identify which virus is responsible for specific infections. A test is the only way to be certain of which antiviral medication should be administered as soon as possible after infection.

Table source: CDC, Mayo Clinic


Combined tests offer streamlined workflow for doctors allowing viral specific diagnosis in a single test

Calls for simple, low cost, differential diagnosis combination tests for the three viruses discussed here are growing. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) or rapid lateral flow tests (LFT) that combine more than one pathogen identifier would enable the testing process to be streamlined, allowing for multiple test results from a single sample. Patient sample collection from one nasopharyngeal or mid-turbinate swab would decrease patient discomfort but also provide a financial saving and optimise clinician’s time.


Different types of combination tests available

Real-time quantitative reverse transcription PCR (rRT-PCR) testing that combines Flu A and B with COVID, is used by the Centres for Disease Control and Prevention to track disease trends. Other clinical combination testing that includes RSV is available for general diagnostic use, are FDA approved and encourage home sample collection. Further available tests, have Emergency Use Authorisation (EUA) from the FDA, but with time and increased demand we may well find more of these tests being approved. Globally companies were swift to produce combination tests for these viral respiratory diseases using TEM-PCR technology. CE-IVD marked RT-PCR and multiplex rRT-PCR tests are already available in European countries and the Middle East.

Laboratory test results are generally available between 24 to 48 hours. As with all tests needing additional equipment for sample processing and analysis, transport and storage facilities have to be considered and can add outlying costs to testing.

A limited number of lateral flow tests combining the three viral components in one test have been developed, although results are available within a 10 minute window, there are separate sample requirements, meaning it may require more than one sample extraction. Other technologies for combination testing include microfluid immunofluorescence assays, combinations remain limited to two viral components. These provide quick results, within 12 minutes, using a specific reader.

Currently there is no reliable, over the counter, rapid lateral flow test that combines these three, allowing quick, cheap testing in a clinical setting or indeed a home test.


Logical Biological Products

At Logical Biological we supply nasopharyngeal/ oropharyngeal/ nasal SARS-CoV-2, Influenza A, Influenza B and RSV swabs available in UTM, Inactivating TM, saline or dry frozen. Negative swabs and COVID-19 / pre-COVID saliva are also available. Typically, our swabs are provided together with a Ct value measured from a ‘companion swab’ taken simultaneously. We also provide serum and plasma samples from individuals infected with SARS-CoV-2, Influenza A/ B, RSV, Streptococcus A, Adenovirus, Parainfluenza and other respiratory infectious diseases.

SARS-CoV-2 Flu A/B RSV A/B products

Table: Products available from Logical Biological

Global vaccine roll out is making progress but with most countries wanting priority status and with a limited supply, how can governments best prioritise those requiring vaccination?

Vaccination strategies

Overall two vaccination strategies are in place: the first concentrates on those at highest risk, the second focuses vaccinations on people most likely to transmit the virus, known as direct and indirect vaccination strategies, respectively. Regardless of vaccine type and manufacturer, there are significant availability issues. Cell division time is a limiting factor in production, and considerations such as vaccine transport, worker health and storage capacity all contribute towards availability issues. Limited stores of reagents and chemicals involved in production have become a problem in the massive upscaling of vaccine production required for the global population.

As of writing, Israel has vaccinated its 9 million population once and is over halfway through the second dosage. The UAE is also high on the list of countries who have nearly managed to complete vaccination and has started its own vaccine manufacture.  


Countries with larger populations have different hurdles. The UK has targeted vaccinations for the old-aged, healthcare workers and those with underlying health conditions, with Norway doing similar. Studies in vaccination strategy suggest prioritising the over 60’s to minimise mortality. However, Indonesia was one of the first countries breaking from this template, focusing on vaccinations to reduce transmissions, namely the working age group 18-59. Indonesia’s population consists of only 10% over 60, whereas the UK is nearer 20%. The UK has vaccinated approximately 60% of its population, with nearly 40 million doses given, whereas the US is making astounding progress with well over 50% of the population having had the first dose; a whopping 185 million doses given. However, the overall picture is one of limited vaccine availability, with only a small proportion of the global population having been vaccinated.

Length of vaccine protection

It is unknown how long the vaccines provides protection for. Research has suggested after an asymptomatic, mild or moderate infection specific T cell immunity may be persist for around 6 months. The CEO of Pfizer has speculated that booster vaccinations for SARS-CoV-2 may be required within 12 months. 

Factors affecting vaccine efficacy:

  • age 
  • underlying health conditions 

Factors affecting vaccination strategy:

  • country specific age structure 
  • infection fatality rate
  • vaccine availability 
  • vaccine efficacy 
  • social distancing/isolation measures
  • seroprevalence

Over a dozen COVID-19 vaccines are currently approved. Types used include inactivated virus, mRNA, non-replicating viral vector and Adenovirus vectors. Whether these contrasting mechanisms provide differing outcomes regarding longevity of protection remains to be seen.  

Serology status

Serology, the study of antibodies in the blood, is relevant to vaccinations as individuals may already carry the antibodies required to fight SARS-CoV-2 through previous infection. If this is the case, should they be lower down the priority list for vaccination?



Hepatitis B Virus (HBV) is a disease known to require susceptibility status prior to vaccination, and therefore serology documentation. However, most vaccinations do not require serology paperwork. With limited supply of SARS-CoV-2 vaccines available it stands to reason the most impactful use of each dose would be given to susceptible individuals and not immune individuals. Modelling studies have advocated prioritising COVID-19 vaccinations by serostatus as well as age. There are clearly additional logistics, complexity and expense involved, and few if any governments have deprioritised citizens for vaccination on the basis of serology or positive PCR tests. Another rational approach that has not caught on would be to provide only a single dose to those who have recovered from SARS-CoV-2 infection; in Ferbruary 2021 it was reported that France intends to give only a single dose to those citizens who have recovered from COVID-19.

A SARS-CoV-2 serology test, or antibody test, is typically a lateral flow test, lab based ELISA or Chemiluminescence Immunoassay designed to detect whether an individual has ever been infected with the virus. Generally SARS-CoV-2 serology tests can detect immunoglobulins: IgG, IgM or a combination of both. There is research to indicate IgA should be included in these serology tests as it may be a more accurate marker than IgM regarding tests taken shortly after an infection. There is much activity taking place within the IVD industry to tailor such tests to areas where they might be useful, for example to develop a test identifying those who have produced adequate antibodies from the vaccine and those who would require a booster.

Time kinetics of antibody response in coronavirus disease 2019 (COVID-19). The illustration demonstrates the relative levels of host immunoglobulins (IgM, IgG, IgA) and SARS-CoV-2 viral load at different stages of COVID-19. Antibody-specific seroconversion occurs when the antibody reaches a detectable level in blood. Disclaimer: This graphic is for illustrative purposes only and does not represent actual levels of each antibody.


As scientists we support the use of serology tests and previous PCR status to inform SARS-CoV-2 vaccine prioritisation in the context of limited vaccine availability, particularly in the young and healthy who are least at risk from the virus .

Logical Biological Products

At Logical Biological we provide serum and plasma from individuals pre- and post-COVID-19 vaccination, as well as SARS-CoV-2 IgG, IgM and IgA positive serum and plasma samples. We also provide SARS-CoV-2, Influenza and RSV swabs and saliva.

Table- Products available from Logical Biological



As the pandemic has struck the predicted second wave, public struggles persist with lifestyle restrictions, but our knowledge to identify and fight the virus has significantly progressed.

With tests developed, distributed and administered satisfactorily for most symptomatic sufferers (PCR), and the vaccine roll out for the most vulnerable, science and medicine turn to consider the silent carriers of SARS-CoV-2…the asymptomatic vectors.

The case for rapid antigen testing using Lateral Flow

At present testing generally consists of Polymerase Chain Reaction (PCR ) or Lateral Flow Tests (LFT) also known as rapid or antigen tests. Writing on these previously highlighted the differences and nuances of each. Regarding asymptomatic carriers it would appear that PCR will test positive for a longer period of the infection, even if the individual is not contagious. It can also take a long time to get PCR test results, often days – making them non-suitable for detecting asymptomatic carriers in everyday social settings such as schools. Lateral flow tests are considerably quicker, providing a result in 10-30 minutes, and significantly cheaper as they do not require a laboratory.

Graph – High-Frequency Testing with Low Analytic Sensitivity versus Low-Frequency Testing with High Analytic Sensitivity

Analysis of UK mass lateral flow test events have been beneficial. It is suggested the 60% of people who had “false negative” tests in the Liverpool pilot were not contagious. As the graph shows, PCR sensitivity may be detrimental when considering the effects of extreme and unnecessary self-isolation requirements. Evaluations have shown that lateral flow tests identify 90100% of asymptomatic individuals whose samples go on to provide viable virus in cultured samples. 

Results from an American University mass testing event showed the ability to culture viable virus from a sample means the virus is capable of reinfecting, hence the individual is contagious. This study also used lateral flow tests and showed similar results to the UK. Virus samples collected were able to infect cell cultures in vitro, showing their viability. Good news indeed for identifying individuals who are asymptomatic and infectious.

Repeat testing using lateral flow tests, especially in high transition groups, medical staff, teachers and carers, with a short turn around time, will help reduce transmissions. The cost effectiveness and ease of a lateral flow test makes repeat testing an obvious option.  

Not to rapid test

Evidence from mass testing events (previous blog) has suggested lateral flow tests can miss up to approximately 60% of infected people. In the UK Liverpool study a third of people tested negative even with high viral loads, implying the individuals would be infectious, even if they were asymptomatic. A negative lateral flow test would potentially release this individual into the population to spread the disease, although this assumes positive individuals ignore the guidance to not treat a negative result as a definitive confirmation of COVID-negative status. This scenario shows how important other preventative measures are, such as social distancing and hand washing. Unfortunately Liverpool, whilst providing reams of data, is also, to date (18th Jan 2021), one of the few UK areas with increased cases of the disease, even after all the lockdown measures and mass testing. 

France has recently voiced its concerns over lateral flow tests and have insisted that any non-EU travellers must have a negative RT-PCR test; they will no longer accept a negative lateral flow test as sufficient for entry into France. This will inevitably feed into the public concern over lateral flow test results and cause many issues, not only because at present, certainly in the UK, you only qualify for an RT-PCR test if you are symptomatic. Medicines and Healthcare products Regulatory Agency (MHRA) have raised concerns about using lateral flow tests in UK schools as there is no ‘test-to-enable’, this had led to a pause on testing in UK schools. A test-to-enable would provide definitive results as to the infectiousness of an individual.

Mass testing has been touted as the way out of the crisis since it began. Now we are getting into a position to test everyone how might this affect human behaviour? People are encouraged to act as if they are positive for COVID-19, but the increase in testing means many will have a “negative” test and could decide to ignore social distancing guidance on the basis of it. This had been flagged as a major (hypothetical) problem by some highly-credentialed scientists taking issue with the UK’s lateral flow test testing program.

Most tests need a swab of some kind to collect their sample, exceptions being drooled saliva and blood samples. Sample collection can be uncomfortable but most willingly go through the procedure. Often sample collection is supervised with the individual taking the actual sample. This has implications for correct procedure sample collection, with reports from the Liverpool mass testing suggesting the test performed worse when civilians performed their own test without supervision. For others, who are unwilling or unable to undergo the stress or complexities of testing, the test may fail from the start with inadequate sample collection. As yet lateral flow tests are not readily available without symptoms at home.

Logical Biological’s View

Our view is that lateral flow tests are a cheap and easy test that when performed on a regular basis in certain settings, schools being a prime example, can identify a substantial proportion of infectious individuals, enabling them to be removed quickly from that setting. This would undoubtedly improve the safety of those associating with them in the same setting, allowing the setting to remain open for longer, to the benefit of society. However, in order to maximise the utility of such an approach a minimum test frequency guideline should be defined in each setting. This testing should be frequent, ideally daily.  

Other high risk settings are likely to include meat processing plants, university halls of residence and care homes (staff and visitors). Imagine how much safer you would be as a teacher, parent or care home resident if most asymptomatic people you or your loved ones associated with were identified and self-isolated. This would also cut chains of transmission and reduce strain on health systems. For these reasons many scientists have pushed back against the warnings from researchers with ‘unfounded criticism’ of the lateral flow test.

Currently no test can definitively assess for SARS-CoV-2 infectiousness, and to attain that ideal may take many months/years or may never happen. Heeding the prescient words of Mike Ryan at the outset of the pandemic “perfection is the enemy of the good. Speed trumps perfection”, we are frustrated at resistance from within the scientific community to the use of technologies that, despite their imperfections, are likely to have an enormous benefit to society. 

Logical Biological Products

At Logical Biological we supply nasopharyngeal/oropharyngeal/nasal SARS-CoV-2, FluA and Flu B swabs available in UTM, Inactivating TM, saline or dry frozen. Negative swabs and COVID-19 / pre-COVID saliva are also available. Typically, our swabs are provided together a Ct value measured from a ‘companion swab’ taken simultaneously. We also provide serum and plasma samples from individuals infected with SARS-CoV-2 and other respiratory infectious diseases. Samples from vaccinated individuals can be collected.

Table: Products available from Logical Biological

What are Ct values?  

In quantitative PCR (qPCR) and reverse transcriptase quantitative PCR (RT-qPCR), the cycle threshold (Ct) value is the number of nucleic acid amplification cycles required for the signal generated by the amplification of a specific target DNA to cross a set threshold. Labelling the DNA primers with a fluorescent tag is what makes this PCR ‘real time’; as the target genetic material increases with each amplification cycle so does the fluorescence signal.

The lower the amplification cycles required to meet the threshold, the higher the level of target nucleic acid (and thus virus in the case of SARS-CoV-2) in the patient sample. Therefore Ct values are inversely related to viral load. Within a specific test the Ct value result is compared to a value often known as a ‘cut-off’. A value lower than the cut-off is a positive result (for COVID-19 meaning the patient most likely has the infection), whereas a value higher than the cut-off is a negative result.


Many of Logical Biological’s COVID-19 swab samples are tested using Thermo-Fisher Taqpath, which has a positive cut-off of Ct ≤37. In that test, a sample with a Ct of 36 would be a low positive. At the other end of the range, Ct values below 20 would be considered a strong positive, and we have infrequently seen values below 15.

Ct values and COVID-19 

The course of SARS-CoV-2 infection shows viral levels vary throughout the duration of the disease, peaking a few days after symptom onset. Correspondingly RT-qPCR Ct values should alter depending on the timeline of an individuals infection. The lower the Ct values the increased probability the patient is near to peak-infection. However there are multiple practical factors unrelated to the actual infection that may also affect the Ct value achieved.

Correspondence between development of viral load during SARS-CoV-2 infection, clinical course and positivity of quantitative rRT-PCR assays (r = real-time). (Lippi et al, 2020).

qPCR/RT-qPCR Ct value variables include but are not limited to:

  1. Swabbing protocol
  2. Swabbing technique
  3. Swab type
  4. Swab brand
  5. Sample storage time
  6. Sample storage conditions
  7. UTM/VTM brand
  8. RNA extraction method
  9. PCR reagents used
  10. PCR test kit used
  11. Patient days since infection
  12. Patient viral load
  13. Environmental contamination
  14. Standard quantification curves

With so many variables any comparison of Ct values between individuals has obvious limitations.

Clinical Use of Covid-19 Ct data

Cycle threshold values are beginning to be used for COVID-19 patients as there is a suggested relationship between viral load and prognosis. Lower Ct values have been linked to a worse course of illness and poorer outcomes. Clinicians have been  encouraged to interpret the SARS-CoV-2 RT-qPCR test results and consider the Ct value where appropriate.

A positive PCR test alone does not correlate with infectivity (Tom and Mina, 2020); a positive test with high Ct value may indicate the patient is not infectious. If this information could be used to inform patient isolation decisions it could transform quarantine restrictions and take significant steps in reducing the already extensive economic consequences of the pandemic, not to mention the mental health implications of isolation. Conversely, low Ct values may indicate a high level of infectiousness, acting as a signal to healthcare professionals to ensure the patient remains isolated and avoid releasing them into the general population until their Ct value increases sufficiently. The challenge here is reliably using Ct values to determine infectiousness.

Contradictory research regarding viral load and shedding in asymptomatic cases require further investigation. Measuring asymptomatic Ct values provided evidence of little difference when compared to symptomatic cases, implying similar viral load. On the other hand, other researchers found asymptomatic cases tested had no viable SARS-CoV-2 virus and no evidence of viral transmission for these carriers. This particular study should be viewed in the context of the virus persisting undetected in a population (Wuhan) where non-pharmaceutical interventions had been used to almost eradicate the virus from the population over a relatively long period of time; selection for a weakened strain may have occurred.

Ct values and disease diagnosis test development

While the value of Ct values to clinicians is debatable, they definitely have utility in in vitro diagnostic (IVD) assay development. Assay sensitivity can be defined as the proportion of true positive samples that actually test positive. SARS-CoV-2 test makers are motivated to produce sensitive tests able to even detect virus in patient samples where the viral load is low. Lateral Flow SARS-CoV-2 antigen test manufacturers, for example, may use patient samples with known RT-qPCR Ct values to determine how the samples test in their assay. Samples with very low Ct counts (high viral loads) would be expected to test positive, but by testing samples with increasing Ct counts (lower viral loads) assay developers can assess the performance of their test, understand what viral loads correspond with a failure of their test to detect, and work to optimise assay performance where necessary.


Ct values have limited use in clinical settings. A multitude of variables impact on the viral load and a separate large set of variables impact on patient outcomes (e.g. age). Ultimately Ct values are not easily comparable between assays or patients. It is possible they can be used to assist patient prognosis in some circumstances where a full clinical history is available. 

However, in vitro diagnostic assay developers find Ct values useful as a way of quickly determining the lower limit of detection of the tests they are developing. In this way, Ct data has a great value in contributing to the development of sensitive tests. 

Available from Logical Biological

At Logical Biological we supply nasopharyngeal/oropharyngeal/nasal SARS-CoV-2, FluA and Flu B swabs available in Universal Transport Medium (UTM), Inactivating Transport Medium (ITM), saline or in dry frozen format. Negative swabs and COVID-19 / pre-COVID saliva are also available, as are serum and plasma. Typically, our swabs are provided together a Ct value measured from a ‘companion swab’ taken simultaneously. For UTM & ITM we can provide remnant samples at your preferred Ct values.

Swabs table

Table: Products available from Logical Biological

This article covers swab type and selection, transport products and medium enabling a smooth transfer of patient samples to the laboratory for analysis. Additionally, we discuss the implications of cycle thresholds and whether they should be assessed in patient prognosis.


Swabs come in all shapes and sizes and some favourites have become well known in recent months:

  • Nasal Swab: needs to be inserted at least 1cm into the naris (nostril), directed upwards. May cause sneezing.
  • Nasopharyngeal Swab: one method is to measure the distance from the corner of the nose to the front of the ear, then half it. This is the approximate distance the nasopharyngeal swab should be entering the nasal cavity. Use the medial side of the septum as a guide and gently rotate to facilitate insertion. The swab should run parallel to the palate and needs to be left in place for ‘several seconds’. Taking a sample is a skill in itself. The complexity and invasive nature of this test paired with lack of discrepancy compared to nasal swab results has lead to a shift in favour of nasal swabs. May cause sneezing and watering eyes.
  • Oropharyngeal Swab: enters through the oral cavity (mouth). This swab aims to take material from the tonsils and the oropharyngeal wall (back of the throat), and avoids touching the tongue, teeth and gums. May cause retching.  

nasopharyngeal swab, oropharyngeal swab, nasal swab

Generally the shape of these swabs are incredibly similar, essentially long shafted cotton buds. The tips can be selected to best accommodate the chosen antigen or marker of interest and the shafts chosen for access purposes. Options include long-armed pharmaceutical grade cotton buds, or perhaps Rayon or Dacron swabs are better suited if considering a dry swab. Rayon swabs are made from synthetic fibres spun from wood pulp, whereas Dacron is made from polystyrene. Swabs destined for transport medium require different properties such as polyester or foam, they can be made less or more absorbent, have different porosities and have good ‘release’ factors. Canadian researchers investigated how specific these swabs need to be especially in the current pandemic with supplies at a premium. They determined swab type had limited impact on test results.

Transport Medium

Having collected samples with wisely chosen swabs, samples must be secured in transport medium to make their way to the lab. Again there are many choices. Generally used, Universal Transport Medium (aka UTM) will protect and conserve samples. This is a well know method and low risk regarding the preservation of the sample. Examples are the BD universal viral transport system, which can accommodate storage at room temperature or at +4°C, and Copan UTM, which contains proteins for virus stablisation, plus buffer, antibiotics and antimycotics. 

Other media can provide more specific care depending on sample consistency, for example Viral Transport Medium (VTM) has specific ingredients suited to the transport of viral content. However, UTMs are also suitable for virus sample maintenance and the ingredients list of VTMs is similar. Generon outline a mix including heat inactivated fetal bovine serum, gentamicin and amphotericin B, an antifungal agent. Some recipes suggest including additional calcium and magnesium. If you are making your own sterility can be ensured by filtration or using sterile ingredients and aseptic technique upon mixing. A newer alternative is the Inactivated Transport Medium (ITM), or Molecular Transport Medium.

Inactivation – Health & Safety

It is not a large leap to identify the advantages of using ITM, and in fact there has been a call for this to take place with SARS-CoV-2 from back in April. From a UK perspective, SARS-CoV-2 is classified as Hazard Group 3 (HG3) by the UK Advisory Committee for Dangerous Pathogens. The Containment Level 3 list of requirements for low-risk handling of active HG3 infectious organisms are long and require specialist facilities, including:

  • Maintenance of a negative air pressure
  • HEPA systemic exhaust air extraction and filtration 
  • Sealable laboratory to enable fumigation

For SARS-CoV-2 research and assay development, the ability to transport and analyse inactivated viral samples potentially negates the need for such stringent containment measures. This would assist COVID-19 test developers because they would no longer need to access Containment Level 3 / BSL 3 facilities as part of their test development. Such facilities are few and far between and potentially extremely expensive to access. The CDC advises transport of inactivated COVID-19 samples in a nucleic acid extraction buffer. The nucleic acids remain intact and identifiable, the medium inactivates the protein cap (using guanidine thiocyanate and N-Lauroylsarcosine (sodium) in ethanol) and renders the virus unable to reinfect. Of course, each user will need to abide by their local risk assessments and satisfy themselves that their choice of ITM truly inactivates the virus. Inactivation may denature the antigen of interest so users would need to be sure that the ITM would be compatible with their project objectives. Users should also seek specialist advice on the containment measures required when using any ITM. Logical Biological offers SARS-CoV-2 remnant swabs inactivated in NEST Scientific ITM.

Cycle Threshold Values

With an inactivated sample safely in the lab, the molecular components are ready to be amplified and analysed. Cycle Threshold (Ct) values are important as the quantitative unit of measurement in PCR methodologies and using them in diagnostic testing can be invaluable for patient prognosis. Essentially the lower the number of amplification cycles required to reach a threshold level for the target gene is, the higher the level of target nucleic acid (and thus virus in the case of SARS-CoV-2) in the patient sample; Ct values are inversely related to viral load. Generally speaking a very high Ct value indicates a low amount of target nucleic acid in the sample, and the possibility of environmental contamination should be borne in mind. Often a Ct value of around 34 is the cut-off point for a patient to be considered positive for the infection. Many of Logical Biological’s COVID-19 swab samples are tested using Thermo-Fisher Taqpath, which has a positive cut-off of Ct ≤37. At the other end of the range we have infrequently observed Ct values as low as 9, with Ct values below 15 considered an extremely strong positive. Some Logical Biological clients wish to access a selection of swabs with a range of different Ct values, to ensure that their assay is able to detect the various different ‘strengths’ of infection. This is something we have been able to accommodate readily

SARS-COV-2 PCR Ct values have been analysed and the scientific and clinical communities are assessing if indeed Ct values, that are not often reported in clinical results, should be included and used as a marker for future prognosis. As an example please refer to Rao et al, 2020. 


Available from Logical Biological

At Logical Biological we supply nasopharyngeal/oropharyngeal/nasal SARS-CoV-2, FluA and Flu B swabs available in UTM, Inactivating TM, saline or dry. Negatives, and COVID-19 / pre-COVID saliva is also available.


Swabs table
Table: Products available from Logical Biological

At the outset of the 2019 SARS-CoV-2 / COVID-19 epidemic, diagnostic immunoassay manufacturers focused on developing anti-SARS-CoV-2 IgM & IgG tests.
While the epidemic has progressed to become a global pandemic, diagnostic test developers’ efforts have also evolved. Recently, we have noticed an increase in interest for patient material positive for Human anti-SARS-CoV-2 IgA. This article will take a look at the difference between the different immunoglobulin sub-classes and seek to understand test developers’ interest in human IgA antibodies specific to SARS-CoV-2.


SARS-CoV-2 Antibody Tests

In a recent article we have explained the reason for interest in tests to detect SARS-CoV-2 specific antibodies. Previously infected individuals may be expected to express antibodies specific to SARS-CoV-2. Therefore antibody tests have utility for serology studies that seek to understand how many in the population have previously been infected, and may also have future use as companion tests for vaccinated populations to understand if satisfactory immune responses have been generated. Furthermore, one idea early in the pandemic which hasn’t gained much traction was to mitigate some of the economic impact by identifying and liberating from freedom of movement constraints, i.e. “lockdown”, those individuals who have already been infected by the virus and may therefore be immune from future infections.


Types of Immunoglobulin

There are 5 major classes of immunoglobulins. These are IgG, IgM, IgA, IgD, and IgE, each with its own structure based around the classic antibody “Y” shape consisting of Heavy and Light chains.



The most common class of immunoglobulin, present in the largest amounts in blood and tissue fluids, and the most commonly detected type in diagnostic infectious disease tests.


The initial class of Immunoglobulin made by B cells following exposure to an antigen, commonly present as a receptor on the B cell surface. Typically the earliest class of immunoglobulin detectable before levels wane. However, the situation can vary for different infections and different individuals, e.g. in Lyme Disease and Toxoplasmosis which we have covered in previous articles.


The main class of antibody found in many bodily secretions including tears and saliva, respiratory and intestinal secretions. Typically, IgA is not as stable as IgG despite being synthesized in large amounts


IgE is present in low concentrations in the blood. IgE antibodies stimulate a histamine response when binding allergens and play a crucial role in allergy testing; allergen specific IgEs produced in response to exposure to a given allergen can be readily detected in human serum or plasma and are diagnostic of specific allergies.


IgD is present on the surface of most B cells early in their development but only limited amounts are released into circulation


Why Test for IgA?

Whereas early studies of SARS-CoV-serological responses focused on IgG and IgM responses, some papers have suggested COVID-19 IgA may be the most readily detectable of the immunoglobulins in COVID-19 patients and detection of it can serve to increase test sensitivity.

Back in March 2020 Guo et al reported that IgM and IgA appeared earlier than IgG while IgG titres were highest followed by IgA and then IgM.

In a May 2020 article, Jääskeläinen et al. analysed sera from 39 patients and determined that IgA levels were higher than IgG in most cases. In many cases, the IgA level was high enough for the patient to test positive whereas the IgG level was below the threshold for a positive test result. Euroimmun SARS-CoV-2 IgG and IgA kits were used, which are suitable for detection in serum and plasma.

In August 2020 Beavis et al showed 68 out of 82 SARS-CoV-2 PCR positive patients were positive for SARS-CoV-2 IgA whereas 55 out of 82 were positive for SARS-CoV-2 IgG. For patients tested 0, 1 or 2 days after symptom onset the vast majority were negative for IgG whereas most were positive for IgA.



Timelines of IgG and IgA results from SARS-CoV-2 PCR positive patients (from Beavis et al.)


Infantino et al., have recommended the use of IgA tests in order to enhance diagnostic sensitivity of COVID-19 serology tests. They found that IgA levels reached concentrations higher than those observed for IgG and IgM and were often positive in IgM negative patients. Therefore, IgA could shorten the amount of time needed post-infection for virus positive patients to test antibody positive.

SARS-CoV-2 IgG, IgA and IgM in SARS-CoV-2 patients who were initially IgM negative


Saliva testing

Collecting blood and converting to serum or plasma in order to detect antibodies is a fairly straightforward process, but perhaps not as straightforward as collecting saliva. Since IgA tends to be present in saliva, detection of  SARS-CoV-2 specific human IgA could theoretically be performed on saliva. Recent studies have confirmed that SARS-CoV-2 IgA is detectable in the saliva of COVID-19 patients.  Another paper in pre-print suggests that antibody levels in serum and saliva do not correlate particularly well so testing in both matrices would enhance test sensitivity even further.


Closing the serology gap

If the time window between viral infection and antibody detectability is short enough (e.g. 0-2 days post-infection) the utility of SARS-CoV-2 serology tests could greatly increase. With many countries struggling to expand molecular PCR testing capacity to the levels needed, serology tests carried out using different technology and by different laboratories/personnel to PCR tests, would be additive to the existing COVID-19 test capacity. The price per test would also likely be significantly lower. Unfortunately, it would be hard to tell from the test results exactly when the patient had become infected, especially as antibody levels post-infection vary greatly between individuals, so the utility of such a test is still in doubt.

Interestingly, SARS-CoV-2 IgA also has potential as a prognostic marker, being associated with more severe disease.



Data from several sources suggests that the detection of SARS-CoV-2 IgA in addition to the other immunoglobulins (IgG and IgM) represented in SARS-CoV-2 antibody tests  can increase the sensitivity of COVID-19 tests when compared with tests to detect anti-SARS-CoV-2 IgG and/or IgM .

Logical Biological offers serum and plasma samples with measured positive levels of SARS-CoV-2 IgA, IgM and IgG as well as SARS-CoV-2 positive swabs.

With the world’s attention focused on SARS-CoV-2 and the serious impact COVID-19 is having both on our health and on society as a whole, it is worth noting that humans have in fact co-existed with numerous coronaviruses (CoVs) for millions of years. It is little understood how these related viruses have such startlingly different effects on infected individuals but some researchers have found evidence that mild CoV infection offers some protection from SARS-CoV-2. Could it be that the common cold may actually be a useful ally in our struggle to combat COVID-19?

It is only in recent years, after the emergence of SARS-CoV, that coronaviruses have been considered a significant threat to human health; before this time it was thought coronaviruses caused only mild respiratory infections in humans. HCoV-229E, HCoV-NL63, HCoV-OC43 and HCoV-HKU1 are all endemic in the human population1,2,3,4, causing 15-30% of respiratory tract infections each year and are mostly experienced as a mild cold by those infected. Only rarely do they lead to lower respiratory tract infections in high-risk individuals. This is in marked contrast to SARS-CoV, MERS-CoV and of course the current headliner SARS-CoV-2.


Two individuals with possible endemic human Coronavirus infection


There is a clear distinction between the endemic, mild disease-causing Human CoVs and the three newly emerged, highly debilitating CoVs. With the latter all due to recent jumps from animal hosts it is clear that zoonotic diseases can be highly debilitating to the human immune system. However, with some individuals being exposed to the novel zoonotic CoVs and only eliciting mild symptoms, is there any chance that the endemic, older strains may be serving up some protection that explains this variability in disease progression?

Tantalisingly, this has been suggested by a recent study published in Science by Jose Mateus and colleagues5. Using samples from unexposed individuals the team were able to identify memory CD4+ T cells that cross-reacted with the four common cold coronaviruses and to SARS-CoV-2, suggesting that previous infection with a milder coronavirus may produce CD4+T cells that can also protect against COVID-19. In accordance with this finding it was also recently found that children that had developed a serious form of COVID-19, called multisystem inflammatory syndrome (MIS-C) carried no antibodies to two of the common endemic coronaviruses, unlike children who had suffered only mild COVID-19 symptoms6. The authors speculated that this lack of protection may have played a role in the serious disease progression seen in these small number of cases.

Another interesting study analysed the CoV-specific antibody repertoires in children and adults and found these to be qualitatively different between these two groups. The anti-HCoV IgG specificities in children were more likely to target regions that are functionally important and structurally conserved in the viral spike and nucleocapsid with some appearing to be broadly cross-reactive across human CoVs7. This fascinating insight into differences in the immune response between adults and children could in part explain why COVID-19 disease is much milder in younger members of the population as well as hinting at the possibility of cross-reactivity of antibodies generated to previous mild CoV infection.

Although highly speculative at the moment, the cross-reactivity of antibodies generated to mild endemic CoVs may in part explain the huge variance in COVID-19 disease states. Perhaps in a COVID-19 future we will embrace catching a common cold each year, celebrating the antibodies it has gifted us to protect against its more dangerous relatives.


Antibodies that cross-react between coronavirus strains may be highly desirable in the population but for in vitro diagnostic SARS-CoV-2 antibody tests it is essential that such tests do not detect antibodies individuals have raised against the other endemic CoVs. The FDA publishes a list of potentially cross-reacting markers that manufacturers of SARS-CoV-2 antibody tests wishing to gain Emergency Use Authorisation should ensure are not recognised by their test. These include antibodies to the 4 circulating human CoVs as well as antibodies raised against various other infectious diseases.

Patient/donor serum and plasma specimens collected before the COVID-19 pandemic and containing measured levels of these potential cross-reactors are available at Logical Biological.

The current US FDA list (as of 23rd September 2020) is:

anti-Influenza A IgG & IgM
anti-Influenza B IgG & IgM
anti-HCV (IgG and IgM)
anti-Hepatitis B Virus (HBV) IgG & IgM
anti-Haemophilus influenzae IgG & IgM
anti-229E Alpha Coronavirus
anti-NL63 Alpha Coronavirus
anti-OC43 Beta Coronavirus
anti-HKU1 Beta Coronavirus 
ANA (Anti-Nuclear Antibodies)
anti-Respiratory Syncytial Virus (RSV) IgG & IgM